Header list of 1r84.pdb file
Complete list - r 2 2 Bytes
HEADER MEMBRANE PROTEIN 23-OCT-03 1R84 TITLE NMR STRUCTURE OF THE 13-CIS-15-SYN RETINAL IN DARK_ADAPTED TITLE 2 BACTERIORHODOPSIN COMPND MOL_ID: 1; COMPND 2 MOLECULE: BACTERIORHODOPSIN; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: RESIDUES 1-232; COMPND 5 SYNONYM: BR SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HALOBACTERIUM SALINARUM; SOURCE 3 ORGANISM_TAXID: 2242; SOURCE 4 STRAIN: R1 KEYWDS PROTON PUMP, MEMBRANE PROTEIN, RETINAL PROTEIN, PHOTORECEPTOR, KEYWDS 2 HALOARCHEA, PROTON TRANSPORT EXPDTA SOLUTION NMR NUMMDL 12 AUTHOR H.PATZELT,B.SIMON,A.TER LAAK,B.KESSLER,R.KUHNE,P.SCHMIEDER, AUTHOR 2 D.OESTERHAELT,H.OSCHKINAT REVDAT 3 02-MAR-22 1R84 1 REMARK LINK REVDAT 2 24-FEB-09 1R84 1 VERSN REVDAT 1 11-NOV-03 1R84 0 JRNL AUTH H.PATZELT,B.SIMON,A.TER LAAK,B.KESSLER,R.KUHNE,P.SCHMIEDER, JRNL AUTH 2 D.OESTERHAELT,H.OSCHKINAT JRNL TITL THE STRUCTURES OF THE ACTIVE CENTER IN DARK-ADAPTED JRNL TITL 2 BACTERIORHODOPSIN BY SOLUTION-STATE NMR SPECTROSCOPY JRNL REF PROC.NATL.ACAD.SCI.USA V. 99 9765 2002 JRNL REFN ISSN 0027-8424 JRNL PMID 12119389 JRNL DOI 10.1073/PNAS.132253899 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : XWINNMR 2.6, AMBER 4.1 REMARK 3 AUTHORS : BRUKER AG (XWINNMR), KOLLMAN, P. (AMBER) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: THE STRUCTURE WAS ALSO REFINED WITH REMARK 3 SHIFTS (AUTHOR; CASE, D) REMARK 4 REMARK 4 1R84 COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 28-OCT-03. REMARK 100 THE DEPOSITION ID IS D_1000020554. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 308; 313; 318 REMARK 210 PH : 6.5; 6.5; 6.5 REMARK 210 IONIC STRENGTH : 1; 1; 1 REMARK 210 PRESSURE : 1 ATM; 1 ATM; 1 ATM REMARK 210 SAMPLE CONTENTS : RESIDUE SPECIFICALLY LABELED REMARK 210 PURPLE MEMBRANE (12-20MG REMARK 210 BACTERIORHODOPSIN) SUSPENDED IN REMARK 210 1% DEUTERATED DODECAL MALTOSIDE, REMARK 210 10MM POTASSIUM PHOSPHATE BUFFER REMARK 210 IN D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D NOESY REMARK 210 SPECTROMETER FIELD STRENGTH : 800 MHZ; 750 MHZ REMARK 210 SPECTROMETER MODEL : DRX; DMX REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : NULL REMARK 210 METHOD USED : SIMULATED ANNEALING REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 100 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 12 REMARK 210 CONFORMERS, SELECTION CRITERIA : RMSD BETWEEN OBSERVED AND REMARK 210 CALULATED CHEMICAL SHIFTS REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : 1 REMARK 210 REMARK 210 REMARK: NULL REMARK 215 REMARK 215 NMR STUDY REMARK 215 THE COORDINATES IN THIS ENTRY WERE GENERATED FROM SOLUTION REMARK 215 NMR DATA. PROTEIN DATA BANK CONVENTIONS REQUIRE THAT REMARK 215 CRYST1 AND SCALE RECORDS BE INCLUDED, BUT THE VALUES ON REMARK 215 THESE RECORDS ARE MEANINGLESS. REMARK 300 REMARK 300 BIOMOLECULE: 1 REMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN REMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON REMARK 300 BURIED SURFACE AREA. REMARK 350 REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS REMARK 350 GIVEN BELOW. BOTH NON-CRYSTALLOGRAPHIC AND REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN. REMARK 350 REMARK 350 BIOMOLECULE: 1 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: A REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (RES=RESIDUE NAME; REMARK 470 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 470 MODELS 1-12 REMARK 470 RES CSSEQI ATOMS REMARK 470 GLU A 232 CG CD OE1 OE2 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 OE2 GLU A 204 H1 HOH A 233 1.58 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND ANGLES REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 1 ARG A 82 NE - CZ - NH1 ANGL. DEV. = 4.0 DEGREES REMARK 500 1 ARG A 225 NE - CZ - NH1 ANGL. DEV. = 3.4 DEGREES REMARK 500 1 PHE A 230 CB - CA - C ANGL. DEV. = 12.7 DEGREES REMARK 500 2 ARG A 225 NE - CZ - NH1 ANGL. DEV. = 3.3 DEGREES REMARK 500 2 PHE A 230 CB - CA - C ANGL. DEV. = 12.7 DEGREES REMARK 500 3 ARG A 225 NE - CZ - NH1 ANGL. DEV. = 3.3 DEGREES REMARK 500 3 PHE A 230 CB - CA - C ANGL. DEV. = 12.6 DEGREES REMARK 500 4 ARG A 225 NE - CZ - NH1 ANGL. DEV. = 3.3 DEGREES REMARK 500 4 PHE A 230 CB - CA - C ANGL. DEV. = 12.6 DEGREES REMARK 500 5 ARG A 82 NE - CZ - NH1 ANGL. DEV. = 3.3 DEGREES REMARK 500 5 ARG A 225 NE - CZ - NH1 ANGL. DEV. = 3.3 DEGREES REMARK 500 5 PHE A 230 CB - CA - C ANGL. DEV. = 12.6 DEGREES REMARK 500 6 ARG A 225 NE - CZ - NH1 ANGL. DEV. = 3.4 DEGREES REMARK 500 6 PHE A 230 CB - CA - C ANGL. DEV. = 12.7 DEGREES REMARK 500 7 ARG A 225 NE - CZ - NH1 ANGL. DEV. = 3.3 DEGREES REMARK 500 7 PHE A 230 CB - CA - C ANGL. DEV. = 12.7 DEGREES REMARK 500 8 ARG A 225 NE - CZ - NH1 ANGL. DEV. = 3.3 DEGREES REMARK 500 8 PHE A 230 CB - CA - C ANGL. DEV. = 12.7 DEGREES REMARK 500 9 ARG A 225 NE - CZ - NH1 ANGL. DEV. = 3.3 DEGREES REMARK 500 9 PHE A 230 CB - CA - C ANGL. DEV. = 12.7 DEGREES REMARK 500 10 ARG A 225 NE - CZ - NH1 ANGL. DEV. = 3.3 DEGREES REMARK 500 10 PHE A 230 CB - CA - C ANGL. DEV. = 12.6 DEGREES REMARK 500 11 ARG A 82 NE - CZ - NH1 ANGL. DEV. = 3.2 DEGREES REMARK 500 11 ARG A 225 NE - CZ - NH1 ANGL. DEV. = 3.3 DEGREES REMARK 500 11 PHE A 230 CB - CA - C ANGL. DEV. = 12.7 DEGREES REMARK 500 12 ARG A 225 NE - CZ - NH1 ANGL. DEV. = 3.3 DEGREES REMARK 500 12 PHE A 230 CB - CA - C ANGL. DEV. = 12.6 DEGREES REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: TORSION ANGLES REMARK 500 REMARK 500 TORSION ANGLES OUTSIDE THE EXPECTED RAMACHANDRAN REGIONS: REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT:(10X,I3,1X,A3,1X,A1,I4,A1,4X,F7.2,3X,F7.2) REMARK 500 REMARK 500 EXPECTED VALUES: GJ KLEYWEGT AND TA JONES (1996). PHI/PSI- REMARK 500 CHOLOGY: RAMACHANDRAN REVISITED. STRUCTURE 4, 1395 - 1400 REMARK 500 REMARK 500 M RES CSSEQI PSI PHI REMARK 500 1 ALA A 2 91.88 23.29 REMARK 500 1 GLN A 3 65.05 28.67 REMARK 500 1 ARG A 7 -51.35 -158.54 REMARK 500 1 GLU A 9 4.32 -67.14 REMARK 500 1 VAL A 29 40.96 -76.38 REMARK 500 1 LYS A 30 -44.91 -140.84 REMARK 500 1 VAL A 34 88.81 33.01 REMARK 500 1 PHE A 153 -70.26 -77.04 REMARK 500 1 MET A 163 -92.62 -91.94 REMARK 500 1 LYS A 216 -68.76 -130.14 REMARK 500 1 ILE A 229 102.31 40.10 REMARK 500 1 PHE A 230 -55.42 71.81 REMARK 500 2 ALA A 2 91.87 23.43 REMARK 500 2 GLN A 3 65.04 28.63 REMARK 500 2 ARG A 7 -51.27 -158.59 REMARK 500 2 GLU A 9 4.34 -67.28 REMARK 500 2 VAL A 29 41.04 -76.43 REMARK 500 2 LYS A 30 -44.80 -140.90 REMARK 500 2 VAL A 34 88.75 33.07 REMARK 500 2 PHE A 153 -70.40 -76.92 REMARK 500 2 MET A 163 -92.63 -91.95 REMARK 500 2 LYS A 216 -74.16 -128.11 REMARK 500 2 ILE A 229 102.31 40.06 REMARK 500 2 PHE A 230 -55.40 71.82 REMARK 500 3 ALA A 2 91.91 23.34 REMARK 500 3 GLN A 3 65.04 28.59 REMARK 500 3 ARG A 7 -51.30 -158.54 REMARK 500 3 GLU A 9 4.34 -67.25 REMARK 500 3 VAL A 29 40.94 -76.37 REMARK 500 3 LYS A 30 -44.86 -140.87 REMARK 500 3 VAL A 34 88.81 32.96 REMARK 500 3 ASP A 85 -70.76 -52.56 REMARK 500 3 PHE A 153 -70.34 -76.97 REMARK 500 3 MET A 163 -92.61 -91.89 REMARK 500 3 LYS A 216 -71.74 -100.14 REMARK 500 3 ILE A 229 102.30 40.10 REMARK 500 3 PHE A 230 -55.37 71.77 REMARK 500 4 ALA A 2 91.80 23.42 REMARK 500 4 GLN A 3 65.07 28.66 REMARK 500 4 ARG A 7 -51.36 -158.57 REMARK 500 4 GLU A 9 4.32 -67.15 REMARK 500 4 VAL A 29 40.96 -76.38 REMARK 500 4 LYS A 30 -44.84 -140.88 REMARK 500 4 VAL A 34 88.83 32.98 REMARK 500 4 ASP A 85 -70.56 -53.76 REMARK 500 4 PHE A 153 -70.32 -76.98 REMARK 500 4 MET A 163 -92.63 -91.93 REMARK 500 4 LYS A 216 -72.16 -85.75 REMARK 500 4 ILE A 229 102.26 40.16 REMARK 500 4 PHE A 230 -55.43 71.85 REMARK 500 REMARK 500 THIS ENTRY HAS 150 RAMACHANDRAN OUTLIERS. REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: PLANAR GROUPS REMARK 500 REMARK 500 PLANAR GROUPS IN THE FOLLOWING RESIDUES HAVE A TOTAL REMARK 500 RMS DISTANCE OF ALL ATOMS FROM THE BEST-FIT PLANE REMARK 500 BY MORE THAN AN EXPECTED VALUE OF 6*RMSD, WITH AN REMARK 500 RMSD 0.02 ANGSTROMS, OR AT LEAST ONE ATOM HAS REMARK 500 AN RMSD GREATER THAN THIS VALUE REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI RMS TYPE REMARK 500 1 ARG A 7 0.10 SIDE CHAIN REMARK 500 1 TYR A 43 0.12 SIDE CHAIN REMARK 500 1 ASP A 96 0.09 SIDE CHAIN REMARK 500 1 ASP A 115 0.09 SIDE CHAIN REMARK 500 2 ARG A 7 0.10 SIDE CHAIN REMARK 500 2 TYR A 43 0.12 SIDE CHAIN REMARK 500 2 ASP A 96 0.09 SIDE CHAIN REMARK 500 3 ARG A 7 0.10 SIDE CHAIN REMARK 500 3 TYR A 43 0.12 SIDE CHAIN REMARK 500 3 ASP A 96 0.09 SIDE CHAIN REMARK 500 4 ARG A 7 0.10 SIDE CHAIN REMARK 500 4 TYR A 43 0.12 SIDE CHAIN REMARK 500 4 TYR A 83 0.07 SIDE CHAIN REMARK 500 4 ASP A 96 0.09 SIDE CHAIN REMARK 500 4 ASP A 115 0.07 SIDE CHAIN REMARK 500 5 ARG A 7 0.10 SIDE CHAIN REMARK 500 5 TYR A 43 0.12 SIDE CHAIN REMARK 500 5 TYR A 83 0.07 SIDE CHAIN REMARK 500 5 ASP A 96 0.09 SIDE CHAIN REMARK 500 6 ARG A 7 0.10 SIDE CHAIN REMARK 500 6 TYR A 43 0.12 SIDE CHAIN REMARK 500 6 ASP A 96 0.09 SIDE CHAIN REMARK 500 7 ARG A 7 0.10 SIDE CHAIN REMARK 500 7 TYR A 43 0.12 SIDE CHAIN REMARK 500 7 ASP A 96 0.09 SIDE CHAIN REMARK 500 8 ARG A 7 0.10 SIDE CHAIN REMARK 500 8 TYR A 43 0.12 SIDE CHAIN REMARK 500 8 TYR A 83 0.07 SIDE CHAIN REMARK 500 8 ASP A 96 0.09 SIDE CHAIN REMARK 500 9 ARG A 7 0.10 SIDE CHAIN REMARK 500 9 TYR A 43 0.12 SIDE CHAIN REMARK 500 9 ASP A 96 0.09 SIDE CHAIN REMARK 500 9 ASP A 115 0.09 SIDE CHAIN REMARK 500 10 ARG A 7 0.10 SIDE CHAIN REMARK 500 10 TYR A 43 0.12 SIDE CHAIN REMARK 500 10 ASP A 96 0.09 SIDE CHAIN REMARK 500 10 ASP A 115 0.09 SIDE CHAIN REMARK 500 11 ARG A 7 0.10 SIDE CHAIN REMARK 500 11 TYR A 43 0.12 SIDE CHAIN REMARK 500 11 ASP A 96 0.09 SIDE CHAIN REMARK 500 12 ARG A 7 0.10 SIDE CHAIN REMARK 500 12 TYR A 43 0.12 SIDE CHAIN REMARK 500 12 ASP A 96 0.09 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE RET A 999 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1R2N RELATED DB: PDB REMARK 900 RELATED ID: 1BRR RELATED DB: PDB REMARK 900 RELATED ID: 1C3W RELATED DB: PDB DBREF 1R84 A 1 232 UNP P02945 BACR_HALN1 14 245 SEQRES 1 A 232 GLN ALA GLN ILE THR GLY ARG PRO GLU TRP ILE TRP LEU SEQRES 2 A 232 ALA LEU GLY THR ALA LEU MET GLY LEU GLY THR LEU TYR SEQRES 3 A 232 PHE LEU VAL LYS GLY MET GLY VAL SER ASP PRO ASP ALA SEQRES 4 A 232 LYS LYS PHE TYR ALA ILE THR THR LEU VAL PRO ALA ILE SEQRES 5 A 232 ALA PHE THR MET TYR LEU SER MET LEU LEU GLY TYR GLY SEQRES 6 A 232 LEU THR MET VAL PRO PHE GLY GLY GLU GLN ASN PRO ILE SEQRES 7 A 232 TYR TRP ALA ARG TYR ALA ASP TRP LEU PHE THR THR PRO SEQRES 8 A 232 LEU LEU LEU LEU ASP LEU ALA LEU LEU VAL ASP ALA ASP SEQRES 9 A 232 GLN GLY THR ILE LEU ALA LEU VAL GLY ALA ASP GLY ILE SEQRES 10 A 232 MET ILE GLY THR GLY LEU VAL GLY ALA LEU THR LYS VAL SEQRES 11 A 232 TYR SER TYR ARG PHE VAL TRP TRP ALA ILE SER THR ALA SEQRES 12 A 232 ALA MET LEU TYR ILE LEU TYR VAL LEU PHE PHE GLY PHE SEQRES 13 A 232 THR SER LYS ALA GLU SER MET ARG PRO GLU VAL ALA SER SEQRES 14 A 232 THR PHE LYS VAL LEU ARG ASN VAL THR VAL VAL LEU TRP SEQRES 15 A 232 SER ALA TYR PRO VAL VAL TRP LEU ILE GLY SER GLU GLY SEQRES 16 A 232 ALA GLY ILE VAL PRO LEU ASN ILE GLU THR LEU LEU PHE SEQRES 17 A 232 MET VAL LEU ASP VAL SER ALA LYS VAL GLY PHE GLY LEU SEQRES 18 A 232 ILE LEU LEU ARG SER ARG ALA ILE PHE GLY GLU HET RET A 999 48 HETNAM RET RETINAL FORMUL 2 RET C20 H28 O FORMUL 3 HOH *4(H2 O) HELIX 1 1 GLU A 9 VAL A 29 1 21 HELIX 2 2 ASP A 36 LEU A 62 1 27 HELIX 3 3 TRP A 80 ASP A 102 1 23 HELIX 4 4 ASP A 104 THR A 128 1 25 HELIX 5 5 VAL A 130 GLY A 155 1 26 HELIX 6 6 GLY A 155 GLU A 161 1 7 HELIX 7 7 ARG A 164 GLY A 192 1 29 HELIX 8 8 PRO A 200 ALA A 215 1 16 HELIX 9 9 LYS A 216 LEU A 224 1 9 SHEET 1 A 2 THR A 67 PHE A 71 0 SHEET 2 A 2 GLU A 74 ILE A 78 -1 O ILE A 78 N THR A 67 LINK NZ LYS A 216 C15 RET A 999 1555 1555 1.35 SITE 1 AC1 7 TRP A 86 MET A 118 TRP A 182 TYR A 185 SITE 2 AC1 7 TRP A 189 ASP A 212 LYS A 216 CRYST1 1.000 1.000 1.000 90.00 90.00 90.00 P 1 1 ORIGX1 1.000000 0.000000 0.000000 0.00000 ORIGX2 0.000000 1.000000 0.000000 0.00000 ORIGX3 0.000000 0.000000 1.000000 0.00000 SCALE1 1.000000 0.000000 0.000000 0.00000 SCALE2 0.000000 1.000000 0.000000 0.00000 SCALE3 0.000000 0.000000 1.000000 0.00000 MODEL 1
Complete list - r 2 2 Bytes