Header list of 1d1d.pdb file
Complete list - c 21 2 Bytes
HEADER VIRAL PROTEIN 15-SEP-99 1D1D TITLE NMR SOLUTION STRUCTURE OF THE CAPSID PROTEIN FROM ROUS SARCOMA VIRUS COMPND MOL_ID: 1; COMPND 2 MOLECULE: PROTEIN (CAPSID PROTEIN); COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES; COMPND 5 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ROUS SARCOMA VIRUS; SOURCE 3 ORGANISM_TAXID: 11886; SOURCE 4 STRAIN: SCHMIDT RUPPIN A-2; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: HMS174(DE3) PLYSS; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PET-16B (NOVAGEN); SOURCE 10 OTHER_DETAILS: THE SOURCE OF THE CA_RSV GENE IS PLASMID PSRA-2 OF SOURCE 11 ATCC 45000, WHICH IS A PLASMID CLONE CONTAINING FULL LENGTH ROUS SOURCE 12 SARCOMA VIRUS, STRAIN SCHMIDT RUPPIN A-2, DERIVED FROM UNINTEGRATED SOURCE 13 DNA FROM AN ACUTE INFECTION OF QT-6 CELLS KEYWDS TWO INDEPENDENT DOMAINS HELICAL BUNDLES, VIRUS/VIRAL PROTEIN, VIRAL KEYWDS 2 PROTEIN EXPDTA SOLUTION NMR NUMMDL 20 AUTHOR R.CAMPOS-OLIVAS,J.L.NEWMAN,M.F.SUMMERS REVDAT 6 21-DEC-22 1D1D 1 SEQADV REVDAT 5 16-FEB-22 1D1D 1 REMARK REVDAT 4 24-FEB-09 1D1D 1 VERSN REVDAT 3 01-APR-03 1D1D 1 JRNL REVDAT 2 10-APR-00 1D1D 1 JRNL REVDAT 1 10-DEC-99 1D1D 0 JRNL AUTH R.CAMPOS-OLIVAS,J.L.NEWMAN,M.F.SUMMERS JRNL TITL SOLUTION STRUCTURE AND DYNAMICS OF THE ROUS SARCOMA VIRUS JRNL TITL 2 CAPSID PROTEIN AND COMPARISON WITH CAPSID PROTEINS OF OTHER JRNL TITL 3 RETROVIRUSES. JRNL REF J.MOL.BIOL. V. 296 633 2000 JRNL REFN ISSN 0022-2836 JRNL PMID 10669613 JRNL DOI 10.1006/JMBI.1999.3475 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : DYANA 1.5 REMARK 3 AUTHORS : P.GUNTHER, ETH-ZURICH REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: 20 CONFORMERS COMPATIBLE WITH THE NMR REMARK 3 CONSTRAINTS WERE CALCULATED USING DYANA 1.5 AND THE STANDARD REMARK 3 TORSION ANGLE SIMULATED ANHEALING PROTOCOL. PRELIMINARY REMARK 3 CALCULATIONS WERE CARRIED OUT INDEPENDENTLY FOR EACH OF THE TWO REMARK 3 N- AND C- TERMINAL DOMAINS OF THE PROTEIN. INITIALLY ONLY NOE REMARK 3 DISTANCE CONSTRAINTS WERE IMPOSED. THE INITIAL STRUCTURES WERE REMARK 3 THEN USED TO ASSES THE ACCURACY OF THE TORSION ANGLE CONSTRAINTS REMARK 3 GENERATED BY ANALYSIS OF HA, CA, CB, CO AND N CHEMICAL SHIFTS REMARK 3 WITH THE PROGRAM TALOS. FINALLY, UPPER AND LOWER LIMIT DISTANCE REMARK 3 CONSTRAINTS WERE IMPOSED FOR UNAMBIGUOUS INTRAHELICAL H-BONDS. REMARK 4 REMARK 4 1D1D COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 20-SEP-99. REMARK 100 THE DEPOSITION ID IS D_1000009702. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 303.00 REMARK 210 PH : 6.00 REMARK 210 IONIC STRENGTH : 10 MM PHOSPHATE REMARK 210 PRESSURE : 1 ATM REMARK 210 SAMPLE CONTENTS : ~1 MM CA_RSV, 10 MM PHOSPHATE REMARK 210 (PH 6.0), 0.2 MM N3NA, 0.1 MM REMARK 210 EDTA, 0.1 MM PMSF, 1 MG/L REMARK 210 PEPSTATIN A, 5 MM BETA- REMARK 210 MERCAPTOETHANOL; ~1 MM CA_RSV, REMARK 210 10 MM PHOSPHATE (PH 6.0), 0.2 MM REMARK 210 N3NA, 0.1 MM EDTA, 0.1 MM PMSF, REMARK 210 1 MG/L PEPSTATIN A, 5 MM BETA- REMARK 210 MERCAPTOETHANOL REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 4D_13C-SEPARATED_NOESY; REMARK 210 4D_13C/15N-SEPARATED_ NOESY; 4D_ REMARK 210 15N-SEPARATED_ NOESY; 3D_15N- REMARK 210 SEPARATED_NOESY REMARK 210 SPECTROMETER FIELD STRENGTH : 800 MHZ REMARK 210 SPECTROMETER MODEL : DRX REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : XWINNMR 2.5, NMRPIPE 1999, REMARK 210 NMRVIEW 3.0, TALOS 1999.019.15.47 REMARK 210 METHOD USED : TORSION ANGLE DYNAMICS SIMULATED REMARK 210 ANNEALING REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 20 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 20 REMARK 210 CONFORMERS, SELECTION CRITERIA : TARGET FUNCTION REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : 7 REMARK 210 REMARK 210 REMARK: THE 1H, 13C, AND 15N CHEMICAL SHIFT ASSIGNMENTS HAVE BEEN REMARK 210 DEPOSITED ATTHE BIOMOLECULAR RESONANCE DATABANK (BMRB ENTRY 4384) REMARK 210 . 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 465 REMARK 465 MISSING RESIDUES REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE REMARK 465 EXPERIMENT. (RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 465 SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 MODELS 1-20 REMARK 465 RES C SSSEQI REMARK 465 GLY A -22 REMARK 465 HIS A -21 REMARK 465 HIS A -20 REMARK 465 HIS A -19 REMARK 465 HIS A -18 REMARK 465 HIS A -17 REMARK 465 HIS A -16 REMARK 465 HIS A -15 REMARK 465 HIS A -14 REMARK 465 HIS A -13 REMARK 465 HIS A -12 REMARK 465 SER A -11 REMARK 465 SER A -10 REMARK 465 GLY A -9 REMARK 465 HIS A -8 REMARK 465 ILE A -7 REMARK 465 GLU A -6 REMARK 465 GLY A -5 REMARK 465 ARG A -4 REMARK 465 HIS A -3 REMARK 465 ASN A -2 REMARK 465 MET A -1 REMARK 465 PRO A 1 REMARK 465 VAL A 2 REMARK 465 VAL A 3 REMARK 465 ILE A 4 REMARK 465 LYS A 5 REMARK 465 THR A 6 REMARK 465 GLU A 7 REMARK 465 GLY A 8 REMARK 465 PRO A 9 REMARK 465 ALA A 10 REMARK 465 LEU A 231 REMARK 465 THR A 232 REMARK 465 ASP A 233 REMARK 465 GLN A 234 REMARK 465 GLY A 235 REMARK 465 ILE A 236 REMARK 465 ALA A 237 REMARK 465 ALA A 238 REMARK 465 ALA A 239 REMARK 465 MET A 240 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 O MET A 57 H LEU A 61 1.43 REMARK 500 O HIS A 51 HG1 THR A 54 1.53 REMARK 500 O PRO A 16 H THR A 20 1.55 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 SER A 45 -32.11 -37.20 REMARK 500 1 ARG A 89 22.49 -153.48 REMARK 500 1 GLN A 95 -43.32 -165.03 REMARK 500 1 ARG A 100 132.09 64.09 REMARK 500 1 ARG A 125 157.92 -43.99 REMARK 500 1 ALA A 147 71.55 -176.86 REMARK 500 1 SER A 183 -37.14 -179.73 REMARK 500 1 ALA A 186 -57.54 175.45 REMARK 500 1 LYS A 196 -84.64 -126.79 REMARK 500 1 SER A 197 -150.10 34.44 REMARK 500 1 THR A 213 47.55 -158.03 REMARK 500 1 LYS A 227 -150.29 41.90 REMARK 500 2 ILE A 35 -31.21 168.43 REMARK 500 2 SER A 45 -35.30 -35.34 REMARK 500 2 ARG A 89 14.35 -141.44 REMARK 500 2 GLN A 95 50.99 -159.58 REMARK 500 2 GLU A 99 70.06 69.53 REMARK 500 2 ALA A 110 171.09 -58.39 REMARK 500 2 ARG A 125 159.09 -39.19 REMARK 500 2 LEU A 146 100.45 -49.19 REMARK 500 2 SER A 183 -30.89 163.90 REMARK 500 2 ALA A 186 -57.76 175.08 REMARK 500 2 LYS A 196 71.04 -163.91 REMARK 500 2 GLN A 198 154.46 -38.34 REMARK 500 2 THR A 213 43.17 -159.87 REMARK 500 2 ALA A 229 87.57 -168.49 REMARK 500 3 SER A 45 -31.20 -37.72 REMARK 500 3 GLN A 95 48.15 -173.42 REMARK 500 3 GLU A 99 -73.29 -74.11 REMARK 500 3 ARG A 100 147.40 60.72 REMARK 500 3 ARG A 125 158.33 -39.50 REMARK 500 3 LEU A 146 158.22 -45.06 REMARK 500 3 ALA A 147 -84.07 -176.67 REMARK 500 3 SER A 183 -38.75 179.49 REMARK 500 3 ALA A 186 -56.45 172.67 REMARK 500 3 LYS A 196 73.57 -171.94 REMARK 500 3 GLN A 198 159.21 -39.59 REMARK 500 3 THR A 213 45.16 -160.75 REMARK 500 3 PRO A 215 49.45 -75.01 REMARK 500 4 SER A 45 -39.02 -35.22 REMARK 500 4 ARG A 89 26.23 -152.37 REMARK 500 4 GLU A 99 -73.23 -136.98 REMARK 500 4 ARG A 100 148.45 61.24 REMARK 500 4 ARG A 125 158.01 -40.55 REMARK 500 4 ASP A 179 70.77 -100.07 REMARK 500 4 SER A 183 -30.06 164.73 REMARK 500 4 ALA A 186 -56.47 171.76 REMARK 500 4 LYS A 196 -89.09 -145.52 REMARK 500 4 SER A 197 -158.46 38.77 REMARK 500 4 THR A 213 51.11 -161.27 REMARK 500 REMARK 500 THIS ENTRY HAS 247 RAMACHANDRAN OUTLIERS. REMARK 500 REMARK 500 REMARK: NULL DBREF 1D1D A 1 240 UNP O92954 O92954_RSVSB 240 479 SEQADV 1D1D GLY A -22 UNP O92954 EXPRESSION TAG SEQADV 1D1D HIS A -21 UNP O92954 EXPRESSION TAG SEQADV 1D1D HIS A -20 UNP O92954 EXPRESSION TAG SEQADV 1D1D HIS A -19 UNP O92954 EXPRESSION TAG SEQADV 1D1D HIS A -18 UNP O92954 EXPRESSION TAG SEQADV 1D1D HIS A -17 UNP O92954 EXPRESSION TAG SEQADV 1D1D HIS A -16 UNP O92954 EXPRESSION TAG SEQADV 1D1D HIS A -15 UNP O92954 EXPRESSION TAG SEQADV 1D1D HIS A -14 UNP O92954 EXPRESSION TAG SEQADV 1D1D HIS A -13 UNP O92954 EXPRESSION TAG SEQADV 1D1D HIS A -12 UNP O92954 EXPRESSION TAG SEQADV 1D1D SER A -11 UNP O92954 EXPRESSION TAG SEQADV 1D1D SER A -10 UNP O92954 EXPRESSION TAG SEQADV 1D1D GLY A -9 UNP O92954 EXPRESSION TAG SEQADV 1D1D HIS A -8 UNP O92954 EXPRESSION TAG SEQADV 1D1D ILE A -7 UNP O92954 EXPRESSION TAG SEQADV 1D1D GLU A -6 UNP O92954 EXPRESSION TAG SEQADV 1D1D GLY A -5 UNP O92954 EXPRESSION TAG SEQADV 1D1D ARG A -4 UNP O92954 EXPRESSION TAG SEQADV 1D1D HIS A -3 UNP O92954 EXPRESSION TAG SEQADV 1D1D ASN A -2 UNP O92954 EXPRESSION TAG SEQRES 1 A 262 GLY HIS HIS HIS HIS HIS HIS HIS HIS HIS HIS SER SER SEQRES 2 A 262 GLY HIS ILE GLU GLY ARG HIS ASN MET PRO VAL VAL ILE SEQRES 3 A 262 LYS THR GLU GLY PRO ALA TRP THR PRO LEU GLU PRO LYS SEQRES 4 A 262 LEU ILE THR ARG LEU ALA ASP THR VAL ARG THR LYS GLY SEQRES 5 A 262 LEU ARG SER PRO ILE THR MET ALA GLU VAL GLU ALA LEU SEQRES 6 A 262 MET SER SER PRO LEU LEU PRO HIS ASP VAL THR ASN LEU SEQRES 7 A 262 MET ARG VAL ILE LEU GLY PRO ALA PRO TYR ALA LEU TRP SEQRES 8 A 262 MET ASP ALA TRP GLY VAL GLN LEU GLN THR VAL ILE ALA SEQRES 9 A 262 ALA ALA THR ARG ASP PRO ARG HIS PRO ALA ASN GLY GLN SEQRES 10 A 262 GLY ARG GLY GLU ARG THR ASN LEU ASP ARG LEU LYS GLY SEQRES 11 A 262 LEU ALA ASP GLY MET VAL GLY ASN PRO GLN GLY GLN ALA SEQRES 12 A 262 ALA LEU LEU ARG PRO GLY GLU LEU VAL ALA ILE THR ALA SEQRES 13 A 262 SER ALA LEU GLN ALA PHE ARG GLU VAL ALA ARG LEU ALA SEQRES 14 A 262 GLU PRO ALA GLY PRO TRP ALA ASP ILE THR GLN GLY PRO SEQRES 15 A 262 SER GLU SER PHE VAL ASP PHE ALA ASN ARG LEU ILE LYS SEQRES 16 A 262 ALA VAL GLU GLY SER ASP LEU PRO PRO SER ALA ARG ALA SEQRES 17 A 262 PRO VAL ILE ILE ASP CYS PHE ARG GLN LYS SER GLN PRO SEQRES 18 A 262 ASP ILE GLN GLN LEU ILE ARG ALA ALA PRO SER THR LEU SEQRES 19 A 262 THR THR PRO GLY GLU ILE ILE LYS TYR VAL LEU ASP ARG SEQRES 20 A 262 GLN LYS ILE ALA PRO LEU THR ASP GLN GLY ILE ALA ALA SEQRES 21 A 262 ALA MET HELIX 1 1 GLU A 15 GLY A 30 1 16 HELIX 2 2 PRO A 34 SER A 45 1 12 HELIX 3 3 LEU A 49 LEU A 61 1 13 HELIX 4 4 GLY A 62 ASP A 87 1 26 HELIX 5 5 ASN A 102 GLY A 108 1 7 HELIX 6 6 ASN A 116 LEU A 124 1 9 HELIX 7 7 GLY A 127 LEU A 146 1 20 HELIX 8 8 SER A 163 GLY A 177 1 15 HELIX 9 9 ALA A 186 ARG A 194 1 9 HELIX 10 10 GLN A 198 ALA A 207 1 10 HELIX 11 11 GLY A 216 LYS A 227 1 12 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 - c 21 2 Bytes