Header list of 1j5d.pdb file
Complete list - 27 20 Bytes
HEADER ELECTRON TRANSPORT 02-APR-02 1J5D
TITLE SOLUTION STRUCTURE OF OXIDIZED PARAMAGNETIC CU(II) PLASTOCYANIN FROM
TITLE 2 SYNECHOCYSTIS PCC6803-MINIMIZED AVERAGE STRUCTURE
COMPND MOL_ID: 1;
COMPND 2 MOLECULE: PLASTOCYANIN;
COMPND 3 CHAIN: A;
COMPND 4 ENGINEERED: YES;
COMPND 5 MUTATION: YES
SOURCE MOL_ID: 1;
SOURCE 2 ORGANISM_SCIENTIFIC: SYNECHOCYSTIS SP. PCC 6803;
SOURCE 3 ORGANISM_TAXID: 1148;
SOURCE 4 STRAIN: PCC6803;
SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI;
SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562;
SOURCE 7 EXPRESSION_SYSTEM_STRAIN: BLR(DE3);
SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID;
SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PET3D
KEYWDS COPPER PROTEIN BETA BARREL ELECTRON TRANSFER, ELECTRON TRANSPORT
EXPDTA SOLUTION NMR
AUTHOR I.BERTINI,S.CIURLI,A.DIKIY,C.O.FERNANDEZ,C.LUCHINAT,N.SAFAROV,
AUTHOR 2 S.SHUMILIN,A.J.VILA
REVDAT 3 27-OCT-21 1J5D 1 REMARK SEQADV LINK
REVDAT 2 24-FEB-09 1J5D 1 VERSN
REVDAT 1 10-APR-02 1J5D 0
SPRSDE 10-APR-02 1J5D 1I0Y
JRNL AUTH I.BERTINI,S.CIURLI,A.DIKIY,C.O.FERNANDEZ,C.LUCHINAT,
JRNL AUTH 2 N.SAFAROV,S.SHUMILIN,A.J.VILA
JRNL TITL THE FIRST SOLUTION STRUCTURE OF A PARAMAGNETIC COPPER(II)
JRNL TITL 2 PROTEIN: THE CASE OF OXIDIZED PLASTOCYANIN FROM THE
JRNL TITL 3 CYANOBACTERIUM SYNECHOCYSTIS PCC6803.
JRNL REF J.AM.CHEM.SOC. V. 123 2405 2001
JRNL REFN ISSN 0002-7863
JRNL PMID 11456890
JRNL DOI 10.1021/JA0033685
REMARK 2
REMARK 2 RESOLUTION. NOT APPLICABLE.
REMARK 3
REMARK 3 REFINEMENT.
REMARK 3 PROGRAM : XWINNMR 2.0, DYANA 1.5, AMBER 5.0
REMARK 3 AUTHORS : BRUKER (XWINNMR), GUENTERT (DYANA), KOLLMAN
REMARK 3 (AMBER)
REMARK 3
REMARK 3 OTHER REFINEMENT REMARKS: THE PROTEIN CONTAINS PARAMAGNETIC
REMARK 3 COPPER(II), WHOSE ELECTRONIC RELAXATION TIMES ARE QUITE
REMARK 3 UNFAVORABLE FOR NMR SOLUTION STUDIES. THE STRUCTURE HAS BEEN
REMARK 3 SOLVED ON THE BASIS OF 1041 MEANINGFUL NOESY CROSS PEAKS, 18 1D
REMARK 3 NOES, 26 T1 VALUES, 96 DIHEDRAL ANGLE CONSTRAINTS AND 18 H-
REMARK 3 BONDS. THE DETECTION OF BROAD HYPERFINE SHIFTED SIGNALS AND
REMARK 3 THEIR FULL ASSIGNMENT ALLOWED THE IDENTIFICATION OF THE
REMARK 3 COPPER(II) LIGANDS AND THE DETERMINATION OF THE CU-S-C-H
REMARK 3 DIHEDRAL ANGLE FOR THE COORDINATED CYSTEINE. THE GLOBAL ROOT
REMARK 3 MEAN SQUARE DEVIATION FROM THE MEAN STRUCTURE FOR THE SOLUTION
REMARK 3 STRUCTURE FAMILY IS 0.72 AND 1.16 FOR BACKBONE AND HEAVY ATOMS,
REMARK 3 RESPECTIVELY. THE MEAN STRUCTURE FROM THE DYANA FAMILY WAS
REMARK 3 CALCULATED USING MOLMOL AND SUBJECTED TO RESTRAINED ENERGY
REMARK 3 MINIMIZATION (REM) USING THE SANDER MODULE OF THE AMBER 5.0
REMARK 3 PROGRAM PACKAGE. THE FORCE FIELD PARAMETERS FOR ALL RESIDUES,
REMARK 3 EXCLUDED THOSE FOR THE COPPER-COORDINATED LIGANDS, WERE THE
REMARK 3 STANDARD AMBER "ALL-ATOMS" PARAMETERS. THE CALCULATIONS WERE
REMARK 3 PERFORMED IN VACUO WITH THE DISTANCE-DEPENDENT DIELECTRIC
REMARK 3 CONSTANT OPTION. THE NON-BONDED INTERACTIONS WERE EVALUATED WITH
REMARK 3 A CUT-OFF OF 10 A. THE MIXED LINEAR-HARMONIC FLAT-BOTTOMED
REMARK 3 POTENTIAL IMPLEMENTED IN SANDER WAS APPLIED TO ALL STRUCTURAL
REMARK 3 CONSTRAINTS. THIS POTENTIAL INVOLVES A NULL FORCE CONSTANT FOR
REMARK 3 STRUCTURAL CONSTRAINTS WITHIN THE ALLOWED LIMITS, A NON-ZERO
REMARK 3 HARMONIC FORCE CONSTANT IN A SMALL INTERVAL OUTSIDE THE ALLOWED
REMARK 3 LIMITS, AND A LINEARLY DEPENDENT POTENTIAL BEYOND THAT LIMIT.
REMARK 3 NOE-DERIVED DISTANCE CONSTRAINTS WERE RESTRICTED BELOW THE UPPER
REMARK 3 DISTANCE LIMIT (RI), USING A FORCE CONSTANT OF 32 KCAL MOL-1 A-2
REMARK 3 FOR THE INTERVAL RI+0.5 A. DISTANCE CONSTRAINTS INVOLVING THE
REMARK 3 SAME H-BONDS USED FOR DYANA CALCULATIONS WERE INCLUDED IN THE
REMARK 3 REM CALCULATION, RESTRICTING THE NH...O AND N...O DISTANCES TO
REMARK 3 THE SAME UPPER (RI) VALUES USED IN DYANA, WITH A FORCE CONSTANT
REMARK 3 OF 32 KCAL MOL-1 A-2 FOR THE RANGE RI + 0.5 A. THE CU-H
REMARK 3 DISTANCES DERIVED FROM THE ANALYSIS OF THE NON-SELECTIVE
REMARK 3 LONGITUDINAL RELAXATION RATES WERE ALSO RESTRAINED TO THE SAME
REMARK 3 UPPER (RI) LIMITS USED IN DYANA, WITH A FORCE CONSTANT OF 32
REMARK 3 KCAL MOL-1 A-2 FOR RI + 0.5 A. THE CU-NHIS AND CU-SCYS DISTANCES
REMARK 3 WERE CONSTRAINED AT 2.1+/-0.1 A AND 2.2+/-0.1 A, RESPECTIVELY,
REMARK 3 USING A LINEAR-HARMONIC FLAT-BOTTOMED POTENTIAL WITH FORCE
REMARK 3 CONSTANTS OF 50 KCAL MOL-1 A-2 IN THE 0.3-A DISTANCE RANGES
REMARK 3 BELOW AND ABOVE THESE LIMITS. THE CU-SMET DISTANCE WAS
REMARK 3 ANALOGOUSLY CONSTRAINED WITHIN THE 2.75+/-0.05 A RANGE, USING A
REMARK 3 FORCE CONSTANT OF 40 KCAL MOL-1 A-2. THE CU-N(HIS)-CG, CU-N(HIS)-
REMARK 3 CE, CU-S(CYS)-CB, CU-S(MET)-CG, AND CU-S(MET)-CE ANGLES WERE
REMARK 3 RESTRAINED AROUND 127+/-0, 127+/-0, 105+/-5, 130+/-10, 110+/-10,
REMARK 3 RESPECTIVELY, USING A LINEAR-HARMONIC FLAT-BOTTOMED POTENTIAL
REMARK 3 WITH FORCE CONSTANTS OF 50 KCAL MOL-1 DEG-2 IN THE 50 RANGES
REMARK 3 BELOW AND ABOVE THE GIVEN VALUES. ANALOGOUSLY, THE (HIS)N-CU-
REMARK 3 N(HIS), (HIS)N-CU-S(CYS), (HIS)N-CU-S(MET), AND (MET)S-CU-S(CYS)
REMARK 3 ANGLES WERE RESTRAINED IN THE 110+/-10, 125+/-15, 95+/-15, AND
REMARK 3 100+/-10 RANGE WITH A FORCE CONSTANT OF 20 KCAL MOL-1 DEG-2 IN
REMARK 3 THE 50 ANGLE RANGES BELOW AND ABOVE THESE LIMITS.
REMARK 4
REMARK 4 1J5D COMPLIES WITH FORMAT V. 3.30, 13-JUL-11
REMARK 100
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 02-APR-02.
REMARK 100 THE DEPOSITION ID IS D_1000001632.
REMARK 210
REMARK 210 EXPERIMENTAL DETAILS
REMARK 210 EXPERIMENT TYPE : NMR
REMARK 210 TEMPERATURE (KELVIN) : 295
REMARK 210 PH : 5.2
REMARK 210 IONIC STRENGTH : 50 MM PHOSPHATE
REMARK 210 PRESSURE : AMBIENT
REMARK 210 SAMPLE CONTENTS : 3 MM PLASTOCYANIN U-15N 50 MM
REMARK 210 PHOSPHATE BUFFER
REMARK 210
REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D NOESY; HNHA; PROTON T1 (HSQC)
REMARK 210 SPECTROMETER FIELD STRENGTH : 600 MHZ; 800 MHZ
REMARK 210 SPECTROMETER MODEL : AVANCE
REMARK 210 SPECTROMETER MANUFACTURER : BRUKER
REMARK 210
REMARK 210 STRUCTURE DETERMINATION.
REMARK 210 SOFTWARE USED : XWINNMR 2.0, XEASY 1.3.13
REMARK 210 METHOD USED : ENERGY MINIMIZATION
REMARK 210
REMARK 210 CONFORMERS, NUMBER CALCULATED : NULL
REMARK 210 CONFORMERS, NUMBER SUBMITTED : 1
REMARK 210 CONFORMERS, SELECTION CRITERIA : NULL
REMARK 210
REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : NULL
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 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 ALA A 25 102.41 -56.57
REMARK 500 ASN A 34 -74.16 -79.50
REMARK 500 GLU A 84 -68.26 -23.00
REMARK 500
REMARK 500 REMARK: NULL
REMARK 500
REMARK 500 GEOMETRY AND STEREOCHEMISTRY
REMARK 500 SUBTOPIC: NON-CIS, NON-TRANS
REMARK 500
REMARK 500 THE FOLLOWING PEPTIDE BONDS DEVIATE SIGNIFICANTLY FROM BOTH
REMARK 500 CIS AND TRANS CONFORMATION. CIS BONDS, IF ANY, ARE LISTED
REMARK 500 ON CISPEP RECORDS. TRANS IS DEFINED AS 180 +/- 30 AND
REMARK 500 CIS IS DEFINED AS 0 +/- 30 DEGREES.
REMARK 500 MODEL OMEGA
REMARK 500 ARG A 87 GLY A 88 145.17
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 ARG A 87 0.08 SIDE CHAIN
REMARK 500
REMARK 500 REMARK: NULL
REMARK 620
REMARK 620 METAL COORDINATION
REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER;
REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE):
REMARK 620
REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL
REMARK 620 CU A 99 CU
REMARK 620 N RES CSSEQI ATOM
REMARK 620 1 HIS A 39 ND1
REMARK 620 2 CYS A 83 SG 132.2
REMARK 620 3 HIS A 86 ND1 95.5 109.0
REMARK 620 4 MET A 91 SD 115.6 109.9 76.4
REMARK 620 N 1 2 3
REMARK 800
REMARK 800 SITE
REMARK 800 SITE_IDENTIFIER: AC1
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CU A 99
REMARK 900
REMARK 900 RELATED ENTRIES
REMARK 900 RELATED ID: 1J5C RELATED DB: PDB
REMARK 900 SOLUTION STRUCTURE OF OXIDIZED PARAMAGNETIC CU(II) PLASTOCYANIN
REMARK 900 FROM SYNECHOCYSTIS PCC6803
DBREF 1J5D A 1 98 UNP P21697 PLAS_SYNY3 29 126
SEQADV 1J5D ASP A 98 UNP P21697 GLU 126 ENGINEERED MUTATION
SEQRES 1 A 98 ALA ASN ALA THR VAL LYS MET GLY SER ASP SER GLY ALA
SEQRES 2 A 98 LEU VAL PHE GLU PRO SER THR VAL THR ILE LYS ALA GLY
SEQRES 3 A 98 GLU GLU VAL LYS TRP VAL ASN ASN LYS LEU SER PRO HIS
SEQRES 4 A 98 ASN ILE VAL PHE ALA ALA ASP GLY VAL ASP ALA ASP THR
SEQRES 5 A 98 ALA ALA LYS LEU SER HIS LYS GLY LEU ALA PHE ALA ALA
SEQRES 6 A 98 GLY GLU SER PHE THR SER THR PHE THR GLU PRO GLY THR
SEQRES 7 A 98 TYR THR TYR TYR CYS GLU PRO HIS ARG GLY ALA GLY MET
SEQRES 8 A 98 VAL GLY LYS VAL VAL VAL ASP
HET CU A 99 1
HETNAM CU COPPER (II) ION
FORMUL 2 CU CU 2+
HELIX 1 1 ASP A 49 SER A 57 1 9
SHEET 1 A 3 ALA A 3 LYS A 6 0
SHEET 2 A 3 GLU A 28 VAL A 32 1 O GLU A 28 N ALA A 3
SHEET 3 A 3 PHE A 69 THR A 72 -1 O PHE A 69 N TRP A 31
SHEET 1 B 5 THR A 20 ILE A 23 0
SHEET 2 B 5 GLY A 93 VAL A 97 1 O LYS A 94 N VAL A 21
SHEET 3 B 5 THR A 78 TYR A 82 -1 N TYR A 79 O VAL A 95
SHEET 4 B 5 HIS A 39 ALA A 44 -1 N VAL A 42 O TYR A 82
SHEET 5 B 5 HIS A 58 ALA A 62 -1 O HIS A 58 N ILE A 41
LINK ND1 HIS A 39 CU CU A 99 1555 1555 2.25
LINK SG CYS A 83 CU CU A 99 1555 1555 2.34
LINK ND1 HIS A 86 CU CU A 99 1555 1555 2.17
LINK SD MET A 91 CU CU A 99 1555 1555 2.66
CISPEP 1 GLU A 17 PRO A 18 0 -15.84
CISPEP 2 SER A 37 PRO A 38 0 -8.94
SITE 1 AC1 4 HIS A 39 CYS A 83 HIS A 86 MET A 91
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
Complete list - 27 20 Bytes