HEADER CELL ADHESION 27-OCT-16 5H3X TITLE THE STRUCTURE OF THE N-TERMINAL OF THE FIBRONECTIN/FIBRINOGEN-BINDING TITLE 2 PROTEIN FROM STREPTOCOCCUS SUIS (FBPS) COMPND MOL_ID: 1; COMPND 2 MOLECULE: FIBRONECTIN/FIBRINOGEN BINDING PROTEIN; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: UNP RESIDUES 2-268; COMPND 5 ENGINEERED: YES; COMPND 6 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: STREPTOCOCCUS SUIS; SOURCE 3 ORGANISM_TAXID: 1307; SOURCE 4 GENE: FBPS; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 6 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: BL21(DE3) KEYWDS FIBRONECTIN-BINDING PROPERTY, CELL ADHESION EXPDTA X-RAY DIFFRACTION AUTHOR A.MOKIMUSYOKI,J.QI,G.F.GAO REVDAT 3 20-MAR-24 5H3X 1 REMARK REVDAT 2 14-DEC-16 5H3X 1 JRNL REVDAT 1 16-NOV-16 5H3X 0 JRNL AUTH A.M.MUSYOKI,Z.SHI,C.XUAN,G.LU,J.QI,F.GAO,B.ZHENG,Q.ZHANG, JRNL AUTH 2 Y.LI,J.HAYWOOD,C.LIU,J.YAN,Y.SHI,G.F.GAO JRNL TITL STRUCTURAL AND FUNCTIONAL ANALYSIS OF AN ANCHORLESS JRNL TITL 2 FIBRONECTIN-BINDING PROTEIN FBPS FROM GRAM-POSITIVE JRNL TITL 3 BACTERIUM STREPTOCOCCUS SUIS JRNL REF PROC. NATL. ACAD. SCI. V. 113 13869 2016 JRNL REF 2 U.S.A. JRNL REFN ESSN 1091-6490 JRNL PMID 27834729 JRNL DOI 10.1073/PNAS.1608406113 REMARK 2 REMARK 2 RESOLUTION. 2.10 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.5_2 REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VINCENT CHEN,IAN REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE-KUNSTLEVE, REMARK 3 : LI-WEI HUNG,ROBERT IMMORMINO,TOM IOERGER, REMARK 3 : AIRLIE MCCOY,ERIK MCKEE,NIGEL MORIARTY, REMARK 3 : REETAL PAI,RANDY READ,JANE RICHARDSON, REMARK 3 : DAVID RICHARDSON,TOD ROMO,JIM SACCHETTINI, REMARK 3 : NICHOLAS SAUTER,JACOB SMITH,LAURENT REMARK 3 : STORONI,TOM TERWILLIGER,PETER ZWART REMARK 3 REMARK 3 REFINEMENT TARGET : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.10 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 33.60 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 0.120 REMARK 3 COMPLETENESS FOR RANGE (%) : 91.6 REMARK 3 NUMBER OF REFLECTIONS : 15547 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.218 REMARK 3 R VALUE (WORKING SET) : 0.216 REMARK 3 FREE R VALUE : 0.246 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.090 REMARK 3 FREE R VALUE TEST SET COUNT : 791 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (IN BINS). REMARK 3 BIN RESOLUTION RANGE COMPL. NWORK NFREE RWORK RFREE REMARK 3 1 33.6018 - 3.8089 0.97 2800 129 0.1853 0.1941 REMARK 3 2 3.8089 - 3.0239 0.97 2625 141 0.2097 0.2481 REMARK 3 3 3.0239 - 2.6418 0.94 2507 129 0.2459 0.2570 REMARK 3 4 2.6418 - 2.4004 0.91 2391 135 0.2431 0.3084 REMARK 3 5 2.4004 - 2.2283 0.89 2333 138 0.2485 0.2900 REMARK 3 6 2.2283 - 2.0970 0.80 2100 119 0.2594 0.2878 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : NULL REMARK 3 SOLVENT RADIUS : 1.11 REMARK 3 SHRINKAGE RADIUS : 0.90 REMARK 3 K_SOL : 0.34 REMARK 3 B_SOL : 33.84 REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.220 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 23.300 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 4.34980 REMARK 3 B22 (A**2) : 4.34980 REMARK 3 B33 (A**2) : -8.69950 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 TWINNING INFORMATION. REMARK 3 FRACTION: NULL REMARK 3 OPERATOR: NULL REMARK 3 REMARK 3 DEVIATIONS FROM IDEAL VALUES. REMARK 3 RMSD COUNT REMARK 3 BOND : 0.013 2204 REMARK 3 ANGLE : 1.215 2980 REMARK 3 CHIRALITY : 0.112 331 REMARK 3 PLANARITY : 0.008 393 REMARK 3 DIHEDRAL : 21.829 824 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 1 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: ALL REMARK 3 ORIGIN FOR THE GROUP (A): -3.9158 12.7473 10.2025 REMARK 3 T TENSOR REMARK 3 T11: 0.2114 T22: 0.1524 REMARK 3 T33: 0.1714 T12: -0.0107 REMARK 3 T13: -0.0336 T23: -0.0072 REMARK 3 L TENSOR REMARK 3 L11: 1.1289 L22: 0.6414 REMARK 3 L33: 0.8324 L12: -0.4623 REMARK 3 L13: 0.1281 L23: 0.0469 REMARK 3 S TENSOR REMARK 3 S11: -0.0742 S12: -0.0494 S13: 0.0041 REMARK 3 S21: 0.0054 S22: 0.0637 S23: -0.0192 REMARK 3 S31: -0.0794 S32: 0.0391 S33: -0.0000 REMARK 3 REMARK 3 NCS DETAILS REMARK 3 NUMBER OF NCS GROUPS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 5H3X COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 28-OCT-16. REMARK 100 THE DEPOSITION ID IS D_1300001970. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 03-MAR-10 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : BSRF REMARK 200 BEAMLINE : 1W2B REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.0 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MAR CCD 165 MM REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 16622 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.100 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 97.6 REMARK 200 DATA REDUNDANCY : 12.90 REMARK 200 R MERGE (I) : 0.08400 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 29.9800 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.10 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.18 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.51200 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: SAD REMARK 200 SOFTWARE USED: PHASER REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 45.11 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.24 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1M NA CITRATE (PH 5.6), 20%(W/V) PEG REMARK 280 4,000, 0.2M NACL, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 291K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 41 21 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z+1/2 REMARK 290 3555 -Y+1/2,X+1/2,Z+1/4 REMARK 290 4555 Y+1/2,-X+1/2,Z+3/4 REMARK 290 5555 -X+1/2,Y+1/2,-Z+1/4 REMARK 290 6555 X+1/2,-Y+1/2,-Z+3/4 REMARK 290 7555 Y,X,-Z REMARK 290 8555 -Y,-X,-Z+1/2 REMARK 290 REMARK 290 WHERE NNN -> OPERATOR NUMBER REMARK 290 MMM -> TRANSLATION VECTOR REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY REMARK 290 RELATED MOLECULES. REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 2 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 55.09150 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 35.27750 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 35.27750 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 27.54575 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 35.27750 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 35.27750 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 82.63725 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 35.27750 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 35.27750 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 27.54575 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 35.27750 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 35.27750 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 82.63725 REMARK 290 SMTRY1 7 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 7 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 55.09150 REMARK 290 REMARK 290 REMARK: 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: 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 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT 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 GLU A 136 O HOH A 301 1.81 REMARK 500 CD ARG A 164 OE1 GLU A 167 1.98 REMARK 500 O HOH A 313 O HOH A 409 1.98 REMARK 500 OD1 ASN A 38 O HOH A 302 1.99 REMARK 500 OD2 ASP A 95 O HOH A 303 2.02 REMARK 500 CB GLU A 136 O HOH A 301 2.07 REMARK 500 O HOH A 304 O HOH A 400 2.11 REMARK 500 O HIS A 145 O HOH A 304 2.16 REMARK 500 N HIS A 145 O HOH A 304 2.16 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 ASP A 95 -139.48 49.85 REMARK 500 MET A 123 54.92 -146.53 REMARK 500 SER A 135 -76.81 -58.04 REMARK 500 GLN A 137 66.35 -45.32 REMARK 500 SER A 149 -7.62 -147.04 REMARK 500 GLN A 150 89.12 49.42 REMARK 500 ASN A 151 -27.72 157.31 REMARK 500 PRO A 165 151.85 -42.69 REMARK 500 ASN A 212 -9.74 -56.25 REMARK 500 ASP A 217 51.03 38.74 REMARK 500 THR A 235 -165.31 -115.73 REMARK 500 SER A 238 -141.65 -166.12 REMARK 500 ASN A 250 43.07 -92.15 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 5H3W RELATED DB: PDB DBREF 5H3X A 2 268 UNP Q8RP86 Q8RP86_STRSU 2 268 SEQADV 5H3X ASN A 28 UNP Q8RP86 HIS 28 ENGINEERED MUTATION SEQRES 1 A 267 SER PHE ASP GLY PHE PHE LEU HIS HIS MET THR ALA GLU SEQRES 2 A 267 LEU ARG ALA ASN LEU GLU GLY GLY ARG ILE GLN LYS ILE SEQRES 3 A 267 ASN GLN PRO PHE GLU GLN GLU ILE VAL LEU ASN ILE ARG SEQRES 4 A 267 SER ASN ARG GLN SER HIS LYS LEU LEU LEU SER ALA HIS SEQRES 5 A 267 SER VAL PHE GLY ARG VAL GLN LEU THR GLN SER ASP PHE SEQRES 6 A 267 THR ASN PRO LYS VAL PRO ASN THR PHE THR MET ILE LEU SEQRES 7 A 267 ARG LYS TYR LEU GLN GLY ALA ILE ILE GLU GLU ILE ARG SEQRES 8 A 267 GLN LEU ASP ASN ASP ARG ILE LEU GLU PHE SER VAL SER SEQRES 9 A 267 ASN LYS ASP GLU ILE GLY ASP HIS ILE GLN ALA THR LEU SEQRES 10 A 267 ILE VAL GLU ILE MET GLY LYS HIS SER ASN ILE ILE LEU SEQRES 11 A 267 VAL ASP LYS SER GLU GLN LYS ILE ILE GLU ALA ILE LYS SEQRES 12 A 267 HIS VAL GLY PHE SER GLN ASN SER TYR ARG THR ILE LEU SEQRES 13 A 267 PRO GLY SER THR TYR ILE ARG PRO PRO GLU THR HIS SER SEQRES 14 A 267 LEU ASN PRO TYR THR VAL SER ASP GLU LYS LEU PHE GLU SEQRES 15 A 267 ILE LEU SER THR GLN GLU LEU SER PRO LYS ASN LEU GLN SEQRES 16 A 267 GLN VAL PHE GLN GLY LEU GLY ARG ASP THR ALA SER GLU SEQRES 17 A 267 LEU ALA ASN HIS LEU GLN ILE ASP ARG LEU LYS ASN PHE SEQRES 18 A 267 ARG ALA PHE PHE ASP GLN ALA THR GLN PRO SER LEU THR SEQRES 19 A 267 ASP LYS SER TYR ALA ALA LEU PRO PHE ALA ASN SER PRO SEQRES 20 A 267 GLU ASN GLN PRO HIS PHE GLU SER LEU SER SER LEU LEU SEQRES 21 A 267 ASP PHE TYR TYR GLN ASP LYS FORMUL 2 HOH *129(H2 O) HELIX 1 AA1 ASP A 4 GLU A 20 1 17 HELIX 2 AA2 ASN A 73 GLN A 84 1 12 HELIX 3 AA3 MET A 123 SER A 127 5 5 HELIX 4 AA4 SER A 177 GLN A 188 1 12 HELIX 5 AA5 SER A 191 PHE A 199 1 9 HELIX 6 AA6 GLY A 203 ASN A 212 1 10 HELIX 7 AA7 ASP A 217 ASP A 227 1 11 HELIX 8 AA8 SER A 256 TYR A 265 1 10 SHEET 1 AA1 4 ARG A 23 PHE A 31 0 SHEET 2 AA1 4 GLU A 34 SER A 41 -1 O VAL A 36 N ASN A 28 SHEET 3 AA1 4 GLN A 44 SER A 51 -1 O HIS A 46 N ILE A 39 SHEET 4 AA1 4 ARG A 58 LEU A 61 -1 O GLN A 60 N LEU A 49 SHEET 1 AA2 5 ILE A 87 GLN A 93 0 SHEET 2 AA2 5 ILE A 99 LYS A 107 -1 O SER A 103 N GLU A 90 SHEET 3 AA2 5 HIS A 113 GLU A 121 -1 O ILE A 114 N ASN A 106 SHEET 4 AA2 5 ASN A 128 ASP A 133 -1 O ILE A 130 N ILE A 119 SHEET 5 AA2 5 LYS A 138 ALA A 142 -1 O ILE A 140 N LEU A 131 SHEET 1 AA3 2 SER A 233 LEU A 234 0 SHEET 2 AA3 2 TYR A 239 ALA A 240 -1 O ALA A 240 N SER A 233 CRYST1 70.555 70.555 110.183 90.00 90.00 90.00 P 41 21 2 8 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 0.014173 0.000000 0.000000 0.00000 SCALE2 0.000000 0.014173 0.000000 0.00000 SCALE3 0.000000 0.000000 0.009076 0.00000