10 20 30 40 50 60 70 80 1BDD - Header ----|----|----|----|----|----|----|----|----|----|----|----|----|----|----|----| Asymmetric UnitHEADER IMMUNOGLOBULIN-BINDING PROTEIN 28-JUN-96 1BDD
TITLE STAPHYLOCOCCUS AUREUS PROTEIN A, IMMUNOGLOBULIN-BINDING B TITLE 2 DOMAIN, NMR, MINIMIZED AVERAGE STRUCTURE
COMPND MOL_ID: 1; COMPND 2 MOLECULE: STAPHYLOCOCCUS AUREUS PROTEIN A; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: B DOMAIN; COMPND 5 ENGINEERED: YES
SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: STAPHYLOCOCCUS AUREUS; SOURCE 3 ORGANISM_TAXID: 1280; SOURCE 4 GENE: SYNTHETIC GENE; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 7 EXPRESSION_SYSTEM_PLASMID: PPRAFW1
KEYWDS IMMUNOGLOBULIN-BINDING PROTEIN, REPEAT, TRANSMEMBRANE, CELL KEYWDS 2 WALL, SIGNAL, IMMUNOGLOBULIN BINDING DOMAIN
EXPDTA SOLUTION NMR
AUTHOR H.GOUDA,H.TORIGOE,A.SAITO,M.SATO,Y.ARATA,I.SHIMADA
REVDAT 2 24-FEB-09 1BDD 1 VERSN REVDAT 1 11-JAN-97 1BDD 0
JRNL AUTH H.GOUDA,H.TORIGOE,A.SAITO,M.SATO,Y.ARATA,I.SHIMADA JRNL TITL THREE-DIMENSIONAL SOLUTION STRUCTURE OF THE B JRNL TITL 2 DOMAIN OF STAPHYLOCOCCAL PROTEIN A: COMPARISONS OF JRNL TITL 3 THE SOLUTION AND CRYSTAL STRUCTURES. JRNL REF BIOCHEMISTRY V. 31 9665 1992 JRNL REFN ISSN 0006-2960 JRNL PMID 1390743 JRNL DOI 10.1021/BI00155A020
REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH H.TORIGOE,I.SHIMADA,M.WAELCHLI,A.SAITO,M.SATO, REMARK 1 AUTH 2 Y.ARATA REMARK 1 TITL 15N NUCLEAR MAGNETIC RESONANCE STUDIES OF THE B REMARK 1 TITL 2 DOMAIN OF STAPHYLOCOCCAL PROTEIN A: SEQUENCE REMARK 1 TITL 3 SPECIFIC ASSIGNMENTS OF THE IMIDE 15N RESONANCES REMARK 1 TITL 4 OF THE PROLINE RESIDUES AND THE INTERACTION WITH REMARK 1 TITL 5 HUMAN IMMUNOGLOBULIN G REMARK 1 REF FEBS LETT. V. 269 174 1990 REMARK 1 REFN ISSN 0014-5793 REMARK 1 REFERENCE 2 REMARK 1 AUTH H.TORIGOE,I.SHIMADA,A.SAITO,M.SATO,Y.ARATA REMARK 1 TITL SEQUENTIAL 1H NMR ASSIGNMENTS AND SECONDARY REMARK 1 TITL 2 STRUCTURE OF THE B DOMAIN OF STAPHYLOCOCCAL REMARK 1 TITL 3 PROTEIN A: STRUCTURAL CHANGES BETWEEN THE FREE B REMARK 1 TITL 4 DOMAIN IN SOLUTION AND THE FC-BOUND B DOMAIN IN REMARK 1 TITL 5 CRYSTAL REMARK 1 REF BIOCHEMISTRY V. 29 8787 1990 REMARK 1 REFN ISSN 0006-2960 REMARK 1 REFERENCE 3 REMARK 1 AUTH A.SAITO,S.HONDA,T.NISHI,M.KOIKE,K.OKAZAKI,S.ITOH, REMARK 1 AUTH 2 M.SATO REMARK 1 TITL HIGH LEVEL EXPRESSION OF A SYNTHETIC GENE CODING REMARK 1 TITL 2 FOR IGG-BINDING DOMAIN B OF STAPHYLOCOCCAL PROTEIN REMARK 1 TITL 3 A REMARK 1 REF PROTEIN ENG. V. 2 481 1989 REMARK 1 REFN ISSN 0269-2139
REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE.
REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : X-PLOR REMARK 3 AUTHORS : BRUNGER REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL
REMARK 4 REMARK 4 1BDD COMPLIES WITH FORMAT V. 3.15, 01-DEC-08
REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY BNL.
REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 303 REMARK 210 PH : 5.0 REMARK 210 IONIC STRENGTH : NULL REMARK 210 PRESSURE : NULL REMARK 210 SAMPLE CONTENTS : NULL REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : DQF-COSY, HOHAHA, NOESY, PE- REMARK 210 COSY; 1H-15N HSQC, DOUBLE- REMARK 210 DEPT, 2D-HMQC-HOHAHA, 2D-HMQC- REMARK 210 NOESY, HMQC-J REMARK 210 SPECTROMETER FIELD STRENGTH : 500 MHZ REMARK 210 SPECTROMETER MODEL : JNM-GSX REMARK 210 SPECTROMETER MANUFACTURER : JEOL REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : EMBOSS, X-PLOR REMARK 210 METHOD USED : HYBRID DISTANCE GEOMETRY- REMARK 210 DYNAMICAL SIMULATED ANNEALING REMARK 210 METHOD REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 55 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 1 REMARK 210 CONFORMERS, SELECTION CRITERIA : AT FIRST, THE DEPOSITORS REMARK 210 CARRIED OUT THE DISTANCE REMARK 210 GEOMETRY CALCULATION BY REMARK 210 STARTING FROM 55 INITIAL REMARK 210 STRUCTURES. THIS CALCULATION REMARK 210 RESULTED IN 41 SOLUTIONS, REMARK 210 WHICH HAD CORRECT POLYPEPTIDE REMARK 210 FOLDS EXCLUDING 14 MIRROR- REMARK 210 IMAGE SUBSTRUCTURES. NEXT, THE REMARK 210 DYNAMICAL SIMULATED ANNEALING REMARK 210 CALCULATIONS WERE PERFORMED BY REMARK 210 USING THESE 41 SUBSTRUCTURES. REMARK 210 THE DISTANCE AND TORSION ANGLE REMARK 210 VIOLATIONS OF THE 41 SOLUTIONS REMARK 210 OBTAINED BY THE DYNAMICAL REMARK 210 SIMULATED ANNEALING REMARK 210 CALCULATIONS WERE SMALLER THAN REMARK 210 0.6 ANGSTROMS AND 27 DEGREES, REMARK 210 RESPECTIVELY. THE DEPOSITORS REMARK 210 SELECTED 10 SOLUTIONS THAT HAD REMARK 210 THE DISTANCE AND TORSION ANGLE REMARK 210 VIOLATIONS OF SMALLER THAN 0.5 REMARK 210 ANGSTROMS AND 10 DEGREES, REMARK 210 RESPECTIVELY. 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 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND LENGTHS 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,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3) 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 RES CSSEQI ATM2 DEVIATION REMARK 500 HIS A 19 CG HIS A 19 ND1 -0.124 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 ALA A 2 -95.43 45.88 REMARK 500 LYS A 5 53.48 -168.03 REMARK 500 ASN A 7 -38.46 -154.84 REMARK 500 LYS A 8 -26.20 -39.57 REMARK 500 GLU A 9 -25.61 163.64 REMARK 500 GLN A 11 -73.10 -61.86 REMARK 500 PHE A 14 -70.69 -40.15 REMARK 500 ILE A 17 -26.45 -39.82 REMARK 500 LEU A 18 33.07 -80.27 REMARK 500 HIS A 19 -21.59 -145.90 REMARK 500 LEU A 20 94.12 -37.66 REMARK 500 PRO A 39 42.07 -69.68 REMARK 500 ASP A 54 -36.08 -39.84 REMARK 500 LYS A 59 45.80 -83.08 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 28 0.19 SIDE_CHAIN REMARK 500 PHE A 31 0.08 SIDE_CHAIN REMARK 500 REMARK 500 REMARK: NULL
REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1BDC RELATED DB: PDB
DBREF 1BDD A 2 60 UNP P38507 SPA2_STAAU 212 270
SEQRES 1 A 60 THR ALA ASP ASN LYS PHE ASN LYS GLU GLN GLN ASN ALA SEQRES 2 A 60 PHE TYR GLU ILE LEU HIS LEU PRO ASN LEU ASN GLU GLU SEQRES 3 A 60 GLN ARG ASN GLY PHE ILE GLN SER LEU LYS ASP ASP PRO SEQRES 4 A 60 SER GLN SER ALA ASN LEU LEU ALA GLU ALA LYS LYS LEU SEQRES 5 A 60 ASN ASP ALA GLN ALA PRO LYS ALA
HELIX 1 1 GLN A 10 HIS A 19 1 10 HELIX 2 2 GLU A 25 ASP A 37 1 13 HELIX 3 3 SER A 42 ALA A 55 1 14
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