HEADER IMMUNE SYSTEM 06-JUL-09 2KLK TITLE SOLUTION STRUCTURE OF GB1 A34F MUTANT WITH RDC AND SAXS COMPND MOL_ID: 1; COMPND 2 MOLECULE: IMMUNOGLOBULIN G-BINDING PROTEIN G; COMPND 3 CHAIN: A, B; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: STAPHYLOCOCCUS AUREUS; SOURCE 3 ORGANISM_TAXID: 1280; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 6 EXPRESSION_SYSTEM_VECTOR: DE3 KEYWDS GB1 A34F VARIANT, RDC, SAXS, PROTEIN BINDING, IMMUNE SYSTEM EXPDTA SOLUTION SCATTERING; SOLUTION NMR NUMMDL 10 AUTHOR J.WANG,X.ZUO,P.YU,I.L.BYEON,J.JUNG,C.D.SCHWIETERS,A.M.GRONENBORN, AUTHOR 2 Y.WANG REVDAT 3 16-MAR-22 2KLK 1 REMARK REVDAT 2 07-APR-10 2KLK 1 REMARK REVDAT 1 06-OCT-09 2KLK 0 JRNL AUTH J.WANG,X.ZUO,P.YU,I.J.BYEON,J.JUNG,X.WANG,M.DYBA,S.SEIFERT, JRNL AUTH 2 C.D.SCHWIETERS,J.QIN,A.M.GRONENBORN,Y.X.WANG JRNL TITL DETERMINATION OF MULTICOMPONENT PROTEIN STRUCTURES IN JRNL TITL 2 SOLUTION USING GLOBAL ORIENTATION AND SHAPE RESTRAINTS. JRNL REF J.AM.CHEM.SOC. V. 131 10507 2009 JRNL REFN ISSN 0002-7863 JRNL PMID 19722627 JRNL DOI 10.1021/JA902528F REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : X-PLOR NIH 2.22 REMARK 3 AUTHORS : SCHWIETERS, KUSZEWSKI, TJANDRA AND CLORE REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 2KLK COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 02-SEP-09. REMARK 100 THE DEPOSITION ID IS D_1000101271. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 298 REMARK 210 PH : 5.5 REMARK 210 IONIC STRENGTH : 0.10 REMARK 210 PRESSURE : AMBIENT REMARK 210 SAMPLE CONTENTS : 2.2 MM [U-100% 15N] ENTITY_1-1, REMARK 210 95% H2O/5% D2O; 0.3 MM ENTITY_1- REMARK 210 2, 95% H2O/5% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D 1H-15N HSQC 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 : NULL REMARK 210 METHOD USED : SIMULATED ANNEALING REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 100 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 10 REMARK 210 CONFORMERS, SELECTION CRITERIA : STRUCTURES WITH THE LOWEST REMARK 210 ENERGY 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 265 REMARK 265 EXPERIMENTAL DETAILS REMARK 265 REMARK 265 EXPERIMENT TYPE : SMALL ANGLE X-RAY SCATTERING REMARK 265 DATA ACQUISITION REMARK 265 RADIATION/NEUTRON SOURCE : APS ARGONNE REMARK 265 SYNCHROTRON (Y/N) : Y REMARK 265 BEAMLINE TYPE : 12-ID REMARK 265 BEAMLINE INSTRUMENT : NULL REMARK 265 DETECTOR TYPE : CCD CAMERA REMARK 265 DETECTOR MANUFACTURER DETAILS : HOME-MADE REMARK 265 TEMPERATURE (KELVIN) : 298 REMARK 265 PH : 5.5 REMARK 265 NUMBER OF TIME FRAMES USED : 20 REMARK 265 PROTEIN CONCENTRATION RANGE (MG/ML) : 1.0-3.6 REMARK 265 SAMPLE BUFFER : 20 MM NACL 20 MM MES REMARK 265 DATA REDUCTION SOFTWARE : MARDETECTOR,HOME REMARK 265 -WRITTEN PROGRAM REMARK 265 GUINIER MEAN RADIUS OF GYRATION (NM) : 1.46 REMARK 265 SIGMA MEAN RADIUS OF GYRATION : 0.03 REMARK 265 R(XS-1) MEAN CROSS SECTIONAL RADII (NM) : NULL REMARK 265 R(XS-1) SIGMA MEAN CROSS SECTIONAL RADII : NULL REMARK 265 R(XS-2) MEAN CROSS SECTIONAL RADII (NM) : NULL REMARK 265 R(XS-2) SIGMA MEAN CROSS SECTIONAL RADII : NULL REMARK 265 P(R) PROTEIN LENGTH (NM) : 0.5 REMARK 265 REMARK 265 DATA ANALYSIS AND MODEL FITTING: REMARK 265 METHOD USED TO DETERMINE THE STRUCTURE: NULL REMARK 265 SOFTWARE USED : GNOM REMARK 265 SOFTWARE AUTHORS : NULL REMARK 265 STARTING MODEL : NULL REMARK 265 REMARK 265 CONFORMERS, NUMBER CALCULATED : 100 REMARK 265 CONFORMERS, NUMBER SUBMITTED : 10 REMARK 265 CONFORMERS, SELECTION CRITERIA : STRUCTURES WITH THE LOWEST REMARK 265 ENERGY REMARK 265 REMARK 265 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : 1 REMARK 265 REMARK 265 OTHER DETAILS: NULL 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: DIMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B 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: 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 TYR B 33 HD22 ASN B 37 1.51 REMARK 500 H GLU A 42 O THR A 55 1.53 REMARK 500 OD1 ASP A 46 H THR A 49 1.53 REMARK 500 OD1 ASP B 46 H THR B 49 1.55 REMARK 500 H GLU B 42 O THR B 55 1.56 REMARK 500 O ASP A 36 N GLY A 38 1.95 REMARK 500 O ALA B 23 OE1 GLU B 27 1.95 REMARK 500 O ALA A 23 OE1 GLU A 27 2.00 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND ANGLES 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,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) 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 ATM2 ATM3 REMARK 500 1 ASP A 36 CB - CG - OD1 ANGL. DEV. = -14.6 DEGREES REMARK 500 2 ASP A 36 CB - CG - OD1 ANGL. DEV. = -15.2 DEGREES REMARK 500 3 ASP A 36 CB - CG - OD1 ANGL. DEV. = -12.3 DEGREES REMARK 500 4 ASP A 36 CB - CG - OD1 ANGL. DEV. = -15.1 DEGREES REMARK 500 5 PHE A 34 CB - CG - CD1 ANGL. DEV. = -5.1 DEGREES REMARK 500 5 ASP A 36 CB - CG - OD1 ANGL. DEV. = -14.7 DEGREES REMARK 500 6 ASP A 36 CB - CG - OD1 ANGL. DEV. = -13.5 DEGREES REMARK 500 7 ASP A 36 CB - CG - OD1 ANGL. DEV. = -16.2 DEGREES REMARK 500 7 ASP B 36 CB - CG - OD2 ANGL. DEV. = -5.7 DEGREES REMARK 500 7 ASN B 37 CB - CG - OD1 ANGL. DEV. = -13.9 DEGREES REMARK 500 8 ASP A 36 CB - CG - OD1 ANGL. DEV. = -13.8 DEGREES REMARK 500 9 ASP A 36 CB - CG - OD1 ANGL. DEV. = -17.1 DEGREES REMARK 500 9 ASP A 36 CB - CG - OD2 ANGL. DEV. = -5.6 DEGREES REMARK 500 9 ASN A 37 CB - CG - OD1 ANGL. DEV. = -12.6 DEGREES REMARK 500 9 GLN B 32 CG - CD - OE1 ANGL. DEV. = -12.2 DEGREES REMARK 500 10 ASP A 36 CB - CG - OD1 ANGL. DEV. = -12.9 DEGREES REMARK 500 10 GLN B 32 CG - CD - OE1 ANGL. DEV. = -12.4 DEGREES REMARK 500 10 ASP B 36 CB - CG - OD2 ANGL. DEV. = -6.0 DEGREES 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 ASP A 22 -170.12 -172.02 REMARK 500 1 PHE A 34 48.15 -89.66 REMARK 500 1 ASP A 36 -47.24 -160.99 REMARK 500 1 ASN A 37 56.53 -17.91 REMARK 500 1 ASP A 40 38.68 34.17 REMARK 500 1 LYS A 50 85.41 32.08 REMARK 500 1 ASP B 22 -169.34 -172.55 REMARK 500 1 PHE B 34 44.82 -87.95 REMARK 500 1 ASP B 36 -119.90 -145.70 REMARK 500 1 ASP B 40 39.42 33.46 REMARK 500 1 LYS B 50 84.46 33.22 REMARK 500 2 PHE A 34 41.06 -89.81 REMARK 500 2 ASP A 36 -10.93 -173.05 REMARK 500 2 ASN A 37 48.03 -50.40 REMARK 500 2 ASP A 40 38.66 26.86 REMARK 500 2 LYS A 50 79.40 44.48 REMARK 500 2 PHE B 34 38.55 -89.43 REMARK 500 2 ASP B 36 -112.59 -152.44 REMARK 500 2 ASN B 37 25.84 45.42 REMARK 500 2 ASP B 40 38.59 26.58 REMARK 500 2 LYS B 50 78.78 45.71 REMARK 500 3 LYS A 10 -68.83 -123.68 REMARK 500 3 PHE A 34 47.31 -87.72 REMARK 500 3 ASP A 36 -20.64 -147.86 REMARK 500 3 ASN A 37 48.97 -46.21 REMARK 500 3 ASP A 40 44.00 24.09 REMARK 500 3 LYS A 50 89.50 22.53 REMARK 500 3 LYS B 10 -68.92 -123.72 REMARK 500 3 PHE B 34 44.52 -87.96 REMARK 500 3 ASP B 36 -124.37 -128.47 REMARK 500 3 ASP B 40 43.48 24.05 REMARK 500 3 LYS B 50 92.92 23.64 REMARK 500 4 PHE A 34 44.92 -91.11 REMARK 500 4 ASP A 36 -19.04 -168.51 REMARK 500 4 ASN A 37 52.67 -50.14 REMARK 500 4 ASP A 40 38.95 25.37 REMARK 500 4 LYS A 50 80.37 42.08 REMARK 500 4 PHE B 34 42.41 -90.08 REMARK 500 4 ASP B 36 -116.48 -146.55 REMARK 500 4 ASP B 40 38.97 24.96 REMARK 500 4 LYS B 50 80.09 42.71 REMARK 500 5 PHE A 34 40.18 -86.11 REMARK 500 5 ASP A 36 -9.31 -164.59 REMARK 500 5 ASN A 37 43.41 -58.22 REMARK 500 5 ASP A 40 41.24 23.34 REMARK 500 5 ALA A 48 -13.80 -43.05 REMARK 500 5 PHE B 34 37.72 -86.20 REMARK 500 5 ASP B 36 -109.42 -138.77 REMARK 500 5 ASN B 37 25.49 37.03 REMARK 500 5 ASP B 40 41.15 23.08 REMARK 500 REMARK 500 THIS ENTRY HAS 104 RAMACHANDRAN OUTLIERS. 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 1 GLN A 32 0.08 SIDE CHAIN REMARK 500 1 ASP A 36 0.15 SIDE CHAIN REMARK 500 1 ASN A 37 0.09 SIDE CHAIN REMARK 500 1 GLN B 32 0.09 SIDE CHAIN REMARK 500 1 ASP B 36 0.08 SIDE CHAIN REMARK 500 1 ASN B 37 0.07 SIDE CHAIN REMARK 500 2 GLN A 32 0.08 SIDE CHAIN REMARK 500 2 ASP A 36 0.16 SIDE CHAIN REMARK 500 2 ASN A 37 0.08 SIDE CHAIN REMARK 500 2 GLN B 32 0.10 SIDE CHAIN REMARK 500 2 ASP B 36 0.08 SIDE CHAIN REMARK 500 3 ASP A 36 0.14 SIDE CHAIN REMARK 500 3 ASN A 37 0.08 SIDE CHAIN REMARK 500 3 GLN B 32 0.08 SIDE CHAIN REMARK 500 3 ASP B 36 0.08 SIDE CHAIN REMARK 500 4 GLN A 32 0.08 SIDE CHAIN REMARK 500 4 ASP A 36 0.15 SIDE CHAIN REMARK 500 4 ASN A 37 0.07 SIDE CHAIN REMARK 500 4 GLN B 32 0.10 SIDE CHAIN REMARK 500 4 ASP B 36 0.09 SIDE CHAIN REMARK 500 5 GLN A 32 0.07 SIDE CHAIN REMARK 500 5 ASN A 35 0.07 SIDE CHAIN REMARK 500 5 ASP A 36 0.15 SIDE CHAIN REMARK 500 5 ASN A 37 0.08 SIDE CHAIN REMARK 500 5 GLN B 32 0.09 SIDE CHAIN REMARK 500 5 ASP B 36 0.08 SIDE CHAIN REMARK 500 6 ASP A 36 0.15 SIDE CHAIN REMARK 500 6 ASN A 37 0.08 SIDE CHAIN REMARK 500 6 GLN B 32 0.09 SIDE CHAIN REMARK 500 6 ASP B 36 0.07 SIDE CHAIN REMARK 500 7 GLN A 32 0.08 SIDE CHAIN REMARK 500 7 ASP A 36 0.15 SIDE CHAIN REMARK 500 7 ASN A 37 0.09 SIDE CHAIN REMARK 500 7 GLN B 32 0.10 SIDE CHAIN REMARK 500 7 ASP B 36 0.09 SIDE CHAIN REMARK 500 7 ASN B 37 0.08 SIDE CHAIN REMARK 500 8 GLN A 32 0.07 SIDE CHAIN REMARK 500 8 ASP A 36 0.14 SIDE CHAIN REMARK 500 8 ASN A 37 0.08 SIDE CHAIN REMARK 500 8 GLN B 32 0.09 SIDE CHAIN REMARK 500 8 ASP B 36 0.09 SIDE CHAIN REMARK 500 9 GLN A 32 0.09 SIDE CHAIN REMARK 500 9 ASP A 36 0.16 SIDE CHAIN REMARK 500 9 ASN A 37 0.09 SIDE CHAIN REMARK 500 9 GLN B 32 0.11 SIDE CHAIN REMARK 500 9 ASP B 36 0.08 SIDE CHAIN REMARK 500 10 ASP A 36 0.14 SIDE CHAIN REMARK 500 10 ASN A 37 0.09 SIDE CHAIN REMARK 500 10 GLN B 32 0.11 SIDE CHAIN REMARK 500 10 ASN B 35 0.08 SIDE CHAIN REMARK 500 REMARK 500 THIS ENTRY HAS 51 PLANE DEVIATIONS. REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2RMM RELATED DB: PDB DBREF 2KLK A 1 56 PDB 2KLK 2KLK 1 56 DBREF 2KLK B 1 56 PDB 2KLK 2KLK 1 56 SEQRES 1 A 56 MET GLN TYR LYS LEU ILE LEU ASN GLY LYS THR LEU LYS SEQRES 2 A 56 GLY GLU THR THR THR GLU ALA VAL ASP ALA ALA THR ALA SEQRES 3 A 56 GLU LYS VAL PHE LYS GLN TYR PHE ASN ASP ASN GLY VAL SEQRES 4 A 56 ASP GLY GLU TRP THR TYR ASP ASP ALA THR LYS THR PHE SEQRES 5 A 56 THR VAL THR GLU SEQRES 1 B 56 MET GLN TYR LYS LEU ILE LEU ASN GLY LYS THR LEU LYS SEQRES 2 B 56 GLY GLU THR THR THR GLU ALA VAL ASP ALA ALA THR ALA SEQRES 3 B 56 GLU LYS VAL PHE LYS GLN TYR PHE ASN ASP ASN GLY VAL SEQRES 4 B 56 ASP GLY GLU TRP THR TYR ASP ASP ALA THR LYS THR PHE SEQRES 5 B 56 THR VAL THR GLU HELIX 1 1 ASP A 22 PHE A 34 1 13 HELIX 2 2 ASP B 22 PHE B 34 1 13 SHEET 1 A 4 GLY A 14 GLU A 19 0 SHEET 2 A 4 GLN A 2 ASN A 8 -1 N LEU A 5 O THR A 16 SHEET 3 A 4 THR A 51 THR A 55 1 O VAL A 54 N ILE A 6 SHEET 4 A 4 TYR A 45 ASP A 46 -1 N ASP A 46 O THR A 51 SHEET 1 B 4 GLY B 14 GLU B 19 0 SHEET 2 B 4 GLN B 2 ASN B 8 -1 N LEU B 5 O THR B 16 SHEET 3 B 4 THR B 51 THR B 55 1 O VAL B 54 N ILE B 6 SHEET 4 B 4 TYR B 45 ASP B 46 -1 N ASP B 46 O THR B 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 MODEL 1