10 20 30 40 50 60 70 80 2OED - Header ----|----|----|----|----|----|----|----|----|----|----|----|----|----|----|----| Asymmetric UnitHEADER IMMUNE SYSTEM 29-DEC-06 2OED
TITLE GB3 SOLUTION STRUCTURE OBTAINED BY REFINEMENT OF X-RAY TITLE 2 STRUCTURE WITH DIPOLAR COUPLINGS
COMPND MOL_ID: 1; COMPND 2 MOLECULE: IMMUNOGLOBULIN G-BINDING PROTEIN G; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: THIRD IGG-BINDING DOMAIN; COMPND 5 SYNONYM: IGG-BINDING PROTEIN G; COMPND 6 ENGINEERED: YES
SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: STREPTOCOCCUS SP. 'GROUP G'; SOURCE 3 ORGANISM_TAXID: 1320; SOURCE 4 GENE: SPG; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: HMS174; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PET-11A
KEYWDS IMMUNE SYSTEM, RESIDUAL DIPOLAR COUPLINGS
EXPDTA SOLUTION NMR
AUTHOR T.S.ULMER,B.E.RAMIREZ,F.DELAGLIO,A.BAX,A.GRISHAEV
REVDAT 2 24-FEB-09 2OED 1 VERSN REVDAT 1 30-JAN-07 2OED 0
JRNL AUTH T.S.ULMER,B.E.RAMIREZ,F.DELAGLIO,A.BAX JRNL TITL EVALUATION OF BACKBONE PROTON POSITIONS AND JRNL TITL 2 DYNAMICS IN A SMALL PROTEIN BY LIQUID CRYSTAL NMR JRNL TITL 3 SPECTROSCOPY JRNL REF J.AM.CHEM.SOC. V. 125 9179 2003 JRNL REFN ISSN 0002-7863 JRNL PMID 15369375 JRNL DOI 10.1021/JA0350684
REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH J.P.DERRICK,D.B.WIGGLEY REMARK 1 TITL THE THIRD IGG-BINDING DOMAIN FROM STREPTOCOCCAL REMARK 1 TITL 2 PROTEIN G. AN ANALYSIS BY X-RAY CRYSTALLOGRAPHY OF REMARK 1 TITL 3 THE STRUCTURE ALONE AND IN A COMPLEX WITH FAB REMARK 1 REF J.MOL.BIOL. V. 243 906 1994 REMARK 1 REFN ISSN 0022-2836
REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE.
REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : DYNAMO 2.1 REMARK 3 AUTHORS : DELAGLIO REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: GB3 SOLUTION STRUCTURE IS OBTAINED REMARK 3 BY REFINEMENT OF THE X-RAY STRUCTURE OF GB3 (1IGD) WITH REMARK 3 C(ALPHA)-C', C'-N, C(ALPHA)-H(ALPHA) AND N-H DIPOLAR COUPLINGS REMARK 3 MEASURED IN FIVE ALIGNING MEDIA (BICELLE, PEG, PF1 PHAGE, REMARK 3 NEGATIVELY AND POSITIVELY CHARGED POLYACRYLAMIDE GELS). REMARK 3 DIPOLAR COUPLINGS ORIGINATING ON RESIDUES 10-11, 24-26, 39-41 REMARK 3 AND THE N- AND C-TERMINAL RESIDUES WERE EXCLUDED, RESULTING IN REMARK 3 NEAR-IDENTITY WITH THE X-RAY STRUCTURE FOR THESE RESIDUES. REMARK 3 THIS DEPOSITION CORRESPONDS TO THE REFINED-II STRUCTURE OF THE REMARK 3 PRIMARY CITATION THAT WAS REFINED AGAINST ALL 4 TYPES OF REMARK 3 DIPOLAR COUPLINGS IN 5 MEDIA. THE RELATED DEPOSITIONS 1P7E AND REMARK 3 1P7F CORRESPOND TO THE REFINED-III AND REFINED-IV STRUCTURES, REMARK 3 RESPECTIVELY. THE DEPOSITED STRUCTURE WAS CALCULATED WITH REMARK 3 DYNAMO 2.1 FOLLOWING A SHORT LOW-TEMPERATURE MOLECULAR REMARK 3 DYNAMICS SIMULATED ANNEALING RUN STARTING FROM THE REGULARIZED REMARK 3 COORDINATES OF THE X-RAY STRUCTURE 1IGD USING ATOMIC REMARK 3 COORDINATE RESTRAINTS TO THE OVERLAPPING 3-RESIDUE SEGMENTS OF REMARK 3 1IGD. THE FORCE CONSTANTS FOR THE HN-N-C-CA IMPROPERS WERE REMARK 3 SOFTENED 10-FOLD RELATIVE TO THEIR STANDARD SETTINGS. SEE THE REMARK 3 PRIMARY CITATION AND THE CORRESPONDING SUPPORTING INFORMATION REMARK 3 FILE FOR A DETAILED DESCRIPTION OF THE REFINEMENT PROCEDURE. REMARK 3 THE DEPOSITED RESTRAINTS FILE INCLUDES, IN ADDITION TO THE REMARK 3 DIPOLAR COUPLINGS AND BACKBONE H-BOND DISTANCE RESTRAINTS REMARK 3 (XPLOR/CNS FORMAT), AN XPLOR-NIH SCRIPT DESIGNED TO MIMIC THE REMARK 3 DEPOSITED STRUCTURE, AND THE FORCE FIELD PARAMETER FILES. A REMARK 3 SET OF OVERLAPPING 3-RESIDUE NCS RESTRAINT TERMS IS USED IN REMARK 3 THIS SCRIPT IN PLACE OF THE DYNAMO ATOMIC COORDINATE REMARK 3 RESTRAINTS.
REMARK 4 REMARK 4 2OED COMPLIES WITH FORMAT V. 3.15, 01-DEC-08
REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 12-JAN-07. REMARK 100 THE RCSB ID CODE IS RCSB041029.
REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 300 REMARK 210 PH : 6.5 REMARK 210 IONIC STRENGTH : 0.05 REMARK 210 PRESSURE : AMBIENT REMARK 210 SAMPLE CONTENTS : 25 MM NAH2PO4/NA2HPO4, 0.2 REMARK 210 MG/ML NAN3, 1.5 MM GB3 PROTEIN REMARK 210 AND ALIGNING MEDIA, 90% H2O, REMARK 210 10% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D IPAP [15N,1H]-HSQC, 3D REMARK 210 CT(H)CA(CO)NH, 13C-COUPLED 3D REMARK 210 HNCO, QUANTITATIVE J- REMARK 210 CORRELATION 3D TROSY-HNCO REMARK 210 SPECTROMETER FIELD STRENGTH : 600 MHZ, 800 MHZ REMARK 210 SPECTROMETER MODEL : DMX, DRX REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : DYNAMO 2.1 REMARK 210 METHOD USED : SIMULATED ANNEALING REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 1 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 1 REMARK 210 CONFORMERS, SELECTION CRITERIA : ALL CALCULATED STRUCTURES REMARK 210 SUBMITTED 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 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 ASN A 8 70.64 -112.77 REMARK 500 REMARK 500 REMARK: NULL
REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1P7F RELATED DB: PDB REMARK 900 RELATED ID: 1P7E RELATED DB: PDB REMARK 900 RELATED ID: 1IGD RELATED DB: PDB
DBREF 2OED A 3 56 UNP P19909 SPG2_STRSG 444 497
SEQADV 2OED MET A 1 UNP P19909 CLONING ARTIFACT SEQADV 2OED GLN A 2 UNP P19909 CLONING ARTIFACT
SEQRES 1 A 56 MET GLN TYR LYS LEU VAL ILE ASN GLY LYS THR LEU LYS SEQRES 2 A 56 GLY GLU THR THR THR LYS ALA VAL ASP ALA GLU THR ALA SEQRES 3 A 56 GLU LYS ALA PHE LYS GLN TYR ALA ASN ASP ASN GLY VAL SEQRES 4 A 56 ASP GLY VAL TRP THR TYR ASP ASP ALA THR LYS THR PHE SEQRES 5 A 56 THR VAL THR GLU
HELIX 1 1 ASP A 22 ASN A 37 1 16
SHEET 1 A 4 LYS A 13 LYS A 19 0 SHEET 2 A 4 GLN A 2 ASN A 8 -1 N TYR A 3 O THR A 18 SHEET 3 A 4 THR A 51 THR A 55 1 O VAL A 54 N ASN A 8 SHEET 4 A 4 VAL A 42 ASP A 46 -1 N ASP A 46 O THR A 51
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