Header list of 1vrv.pdb file
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HEADER TRANSFERASE 17-JUN-05 1VRV TITLE STRUCTURE OF PHOSPHORYLATED IIB (C384(SEP)) DOMAIN OF THE MANNITOL- TITLE 2 SPECIFIC PERMEASE ENZYME II COMPND MOL_ID: 1; COMPND 2 MOLECULE: MANNITOL-SPECIFIC PTS SYSTEM ENZYME IIABC COMPONENTS; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: IIB DOMAIN; COMPND 5 SYNONYM: IIBMTL PHOSPHOTRANSFERASE ENZYME II, B COMPONENT, EIIB-MTL; COMPND 6 ENGINEERED: YES; COMPND 7 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ESCHERICHIA COLI; SOURCE 3 ORGANISM_TAXID: 83334; SOURCE 4 STRAIN: O157:H7; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS PHOSPHOTRANSFERASE, TRANSFERASE, KINASE, SUGAR TRANSPORT EXPDTA SOLUTION NMR AUTHOR J.Y.SUH,C.TANG,M.CAI,G.M.CLORE REVDAT 4 20-OCT-21 1VRV 1 REMARK SEQADV LINK REVDAT 3 13-JUL-11 1VRV 1 VERSN REVDAT 2 24-FEB-09 1VRV 1 VERSN REVDAT 1 22-NOV-05 1VRV 0 JRNL AUTH J.Y.SUH,C.TANG,M.CAI,G.M.CLORE JRNL TITL VISUALIZATION OF THE PHOSPHORYLATED ACTIVE SITE LOOP OF THE JRNL TITL 2 CYTOPLASMIC B DOMAIN OF THE MANNITOL TRANSPORTER JRNL TITL 3 II(MANNITOL) OF THE ESCHERICHIA COLI PHOSPHOTRANSFERASE JRNL TITL 4 SYSTEM BY NMR SPECTROSCOPY AND RESIDUAL DIPOLAR COUPLINGS. JRNL REF J.MOL.BIOL. V. 353 1129 2005 JRNL REFN ISSN 0022-2836 JRNL PMID 16219324 JRNL DOI 10.1016/J.JMB.2005.09.033 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : X-PLOR NIH (HTTP://NMR.CIT.NIH.GOV/XPLOR_NIH) REMARK 3 AUTHORS : SCHWIETERS, KUSZEWSKI, TJANDRA, CLORE REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: REMARK 3 THE TARGET FUNCTION COMPRISES TERMS FOR THE NOE-DERIVED REMARK 3 INTERPROTON DISTANCE RESTRAINTS, TORSION ANGLE RESTRAINTS, AND REMARK 3 RESIDUAL DIPOLAR COUPLINGS (N-H, N-C' AND HN-C') IN THREE REMARK 3 ALIGNMENT MEDIA; A QUARTIC VAN DE WAALS REPULSION TERM, AND A REMARK 3 TORSION ANGLE DATABASE POTENTIAL OF MEAN FORCE. REMARK 3 REMARK 3 REMARK 3 REMARK 3 IN THIS ENTRY THE LAST COLUMN FOR REMARK 3 FOR THE ACTIVE SITE LOOP (RESIDUES 383-393) REMARK 3 REPRESENTS THE AVERAGE RMS REMARK 3 DIFFERENCE BETWEEN THE INDIVIDUAL 150 SIMULATED ANNEALING REMARK 3 STRUCTURES AND THE MEAN COORDINATE POSITIONS. REMARK 3 NOTE ONLY THE COORDINATES OF THE ACTIVE SITE LOOP REMARK 3 (RESIDUES 383-393) HAVE BEEN REFINED; THE REMAINDER REMARK 3 OF THE PROTEIN COORDINATES ARE HELD FIXED AT THEIR REMARK 3 POSITIONS IN UNPHOSPHORYLATED IIBMTL (PDB ACCESSION REMARK 3 CODE 1VKR). THE LAST COLUMN FOR RESIDUES OUTSIDE THE REMARK 3 ACTIVE SITE REPRESENTS THE AVERAGE RMS DIFFERENCE REMARK 3 BETWEEN THE INDIVIDUAL 100 SIMULATED ANNEALING STRUCTURES REMARK 3 AND THE MEAN COORDINATE POSITIONS FOR THE STRUCTURE OF REMARK 3 THE PREVIOUSLY DETERMINED UNPHOSPHORYLATED STATE (PDB REMARK 3 ACCESSION CODE 1VKR). REMARK 3 REMARK 3 EXPERIMENTAL RESTRAINTS INVOLVING THE PHOSPHORYLATED REMARK 3 ACTIVE SITE RESIDUES 383-394: REMARK 3 83 NOE-DERIVED INTERPROTON DISTANCE RESTRAINTS (8 REMARK 3 INTRARESIDUE, 17 SEQUENTIAL, 20 MEDIUM RANGE AND 38 REMARK 3 LONG-RANGE INTERRESIDUE) REMARK 3 21 TORSION ANGLES (10 PHI, 9 PSI AND TWO CHI1) REMARK 3 11 N-H, 11 N-C' AND 11 HN-C' RDCS IN PHAGE PF1 REMARK 3 11 N-H, 6 N-C' AND 6 HN-C' RDCS IN NEUTRAL ANISOTROPIC REMARK 3 GEL REMARK 3 10 N-H RDCS IN A POSITIVELY CHARGED ANISOTROPIC GEL REMARK 3 12 RESTRAINTS FOR 6 BACKBONE H-BONDS INVOLVING ONE REMARK 3 ACTIVE SITE RESIDUE REMARK 3 2 RESTRAINTS FOR A PHOSPHORYL-NH(SER391) H-BOND REMARK 3 DEMONSTRATED BY OBSERVATION OF A 3JNP COUPLING. REMARK 3 THE TOTAL NUMBER OF RDCS MEASURED FOR THE WHOLE PROTEIN REMARK 3 WAS: 192 IN PHAGE PF1, 139 IN NEUTRAL GEL, AND 55 IN REMARK 3 POSITIVE GEL. EXCLUDING A FEW OUTLIERS INVOLVING ONLY REMARK 3 RESIDUES 386-391 WITHIN THE ACTIVE SITE, THE REMAINING REMARK 3 RDCS FIT THE STRUCTURE OF THE UNPHOSPHORYLATED STATE REMARK 3 (COORDINATES 1VKR) EXTREMELY WELL INDICATING THAT THE REMARK 3 ONLY BACKBONE CONFORMATIONAL CHANGES THAT OCCUR UPON REMARK 3 PHOSPHORYLATION ARE LOCALIZED SPECIFICALLY TO THE REMARK 3 ACTIVE SITE (RESIDUES 383-393). THEREFORE ONLY THE REMARK 3 COORDINATES OF THE ACTIVE SITE WERE REFINED WITH THE REMARK 3 COORDINATES OF THE REMAINDER OF THE PROTEIN REMARK 3 FIXED TO THEIR POSITIONS IN 1VKR. REMARK 4 REMARK 4 1VRV COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 23-JUN-05. REMARK 100 THE DEPOSITION ID IS D_1000002097. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 303.00 REMARK 210 PH : 7.4 REMARK 210 IONIC STRENGTH : 0 EXCEPT FOR RDC MEASUREMENTS IN REMARK 210 PHAGE PF1 WHERE IT WAS 0.5M REMARK 210 PRESSURE : NULL REMARK 210 SAMPLE CONTENTS : NULL REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : (1) TRIPLE RESONANCE FOR REMARK 210 ASSIGNMENT OF PROTEIN; (2) REMARK 210 QUANTITATIVE J CORRELATION FOR REMARK 210 COUPLING CONSTANTS; (3) 3D REMARK 210 HETERONUCLEAR SEPARATED NOE REMARK 210 EXPTS; (4) IPAP AND COUPLED HSQC REMARK 210 EXPERIMENTS FOR DIPOLAR REMARK 210 COUPLINGS. REMARK 210 SPECTROMETER FIELD STRENGTH : 600 MHZ; 750 MHZ REMARK 210 SPECTROMETER MODEL : DMX600; DRX600; DMX650 REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : NULL REMARK 210 METHOD USED : TORSION ANGLE DYNAMICS REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 150 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 1 REMARK 210 CONFORMERS, SELECTION CRITERIA : REGULARIZED MEAN STRUCTURE 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 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 RES C SSSEQI REMARK 465 THR A 472 REMARK 465 GLU A 473 REMARK 465 ASN A 474 REMARK 465 GLU A 475 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 HD1 HIS A 430 H ASP A 432 1.16 REMARK 500 O1P SEP A 384 H SER A 391 1.52 REMARK 500 O2P SEP A 384 H MET A 388 1.54 REMARK 500 OG SEP A 384 H GLY A 387 1.60 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 ARG A 378 -3.04 -143.23 REMARK 500 ASP A 454 79.20 -62.04 REMARK 500 REMARK 500 REMARK: NULL DBREF 1VRV A 375 475 UNP P00550 PTM3C_ECOLI 375 475 SEQADV 1VRV SEP A 384 UNP P00550 CYS 384 ENGINEERED MUTATION SEQRES 1 A 101 SER HIS VAL ARG LYS ILE ILE VAL ALA SEP ASP ALA GLY SEQRES 2 A 101 MET GLY SER SER ALA MET GLY ALA GLY VAL LEU ARG LYS SEQRES 3 A 101 LYS ILE GLN ASP ALA GLY LEU SER GLN ILE SER VAL THR SEQRES 4 A 101 ASN SER ALA ILE ASN ASN LEU PRO PRO ASP VAL ASP LEU SEQRES 5 A 101 VAL ILE THR HIS ARG ASP LEU THR GLU ARG ALA MET ARG SEQRES 6 A 101 GLN VAL PRO GLN ALA GLN HIS ILE SER LEU THR ASN PHE SEQRES 7 A 101 LEU ASP SER GLY LEU TYR THR SER LEU THR GLU ARG LEU SEQRES 8 A 101 VAL ALA ALA GLN ARG HIS THR GLU ASN GLU MODRES 1VRV SEP A 384 SER PHOSPHOSERINE HET SEP A 384 14 HETNAM SEP PHOSPHOSERINE HETSYN SEP PHOSPHONOSERINE FORMUL 1 SEP C3 H8 N O6 P HELIX 1 1 GLY A 389 ALA A 405 1 17 HELIX 2 2 ARG A 431 VAL A 441 1 11 HELIX 3 3 ASP A 454 HIS A 471 1 18 SHEET 1 A 4 SER A 411 ALA A 416 0 SHEET 2 A 4 LYS A 379 SEP A 384 1 N VAL A 382 O SER A 415 SHEET 3 A 4 LEU A 426 HIS A 430 1 O ILE A 428 N ILE A 381 SHEET 4 A 4 GLN A 445 LEU A 449 1 O GLN A 445 N VAL A 427 LINK C ALA A 383 N SEP A 384 1555 1555 1.33 LINK C SEP A 384 N ASP A 385 1555 1555 1.33 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
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