HEADER IMMUNE SYSTEM 06-JUL-12 4FZ4 TITLE CRYSTAL STRUCTURE OF HP0197-18KD COMPND MOL_ID: 1; COMPND 2 MOLECULE: UNCHARACTERIZED PROTEIN CONSERVED IN BACTERIA; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: UNP RESIDUES 51-199; COMPND 5 SYNONYM: 0197-18KD; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: STREPTOCOCCUS SUIS; SOURCE 3 ORGANISM_TAXID: 391296; SOURCE 4 STRAIN: 98HAH33; SOURCE 5 GENE: SSU98_0197; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS SURFACE ANTIGEN, IMMUNE SYSTEM EXPDTA X-RAY DIFFRACTION AUTHOR Z.YUAN,X.YAN REVDAT 4 20-MAR-24 4FZ4 1 REMARK SEQADV REVDAT 3 04-OCT-17 4FZ4 1 REMARK REVDAT 2 04-SEP-13 4FZ4 1 JRNL REVDAT 1 05-DEC-12 4FZ4 0 JRNL AUTH Z.Z.YUAN,X.J.YAN,A.D.ZHANG,B.CHEN,Y.Q.SHEN,M.L.JIN JRNL TITL MOLECULAR MECHANISM BY WHICH SURFACE ANTIGEN HP0197 MEDIATES JRNL TITL 2 HOST CELL ATTACHMENT IN THE PATHOGENIC BACTERIA JRNL TITL 3 STREPTOCOCCUS SUIS JRNL REF J.BIOL.CHEM. V. 288 956 2013 JRNL REFN ISSN 0021-9258 JRNL PMID 23184929 JRNL DOI 10.1074/JBC.M112.388686 REMARK 2 REMARK 2 RESOLUTION. 2.44 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS 1.2 REMARK 3 AUTHORS : BRUNGER,ADAMS,CLORE,DELANO,GROS,GROSSE- REMARK 3 : KUNSTLEVE,JIANG,KUSZEWSKI,NILGES,PANNU, REMARK 3 : READ,RICE,SIMONSON,WARREN REMARK 3 REMARK 3 REFINEMENT TARGET : ENGH & HUBER REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.44 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 18.82 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : 850665.530 REMARK 3 DATA CUTOFF LOW (ABS(F)) : 0.0000 REMARK 3 COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 NUMBER OF REFLECTIONS : 6551 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING SET) : 0.222 REMARK 3 FREE R VALUE : 0.263 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 336 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : 0.014 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 6 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 2.44 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.59 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 96.40 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 993 REMARK 3 BIN R VALUE (WORKING SET) : 0.2730 REMARK 3 BIN FREE R VALUE : 0.3180 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 5.30 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 56 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.043 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1267 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 6 REMARK 3 SOLVENT ATOMS : 31 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 47.10 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.85000 REMARK 3 B22 (A**2) : 4.73000 REMARK 3 B33 (A**2) : -3.88000 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 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.31 REMARK 3 ESD FROM SIGMAA (A) : 0.25 REMARK 3 LOW RESOLUTION CUTOFF (A) : 5.00 REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : 0.39 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.28 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.006 REMARK 3 BOND ANGLES (DEGREES) : 1.100 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 17.90 REMARK 3 IMPROPER ANGLES (DEGREES) : 0.670 REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : RESTRAINED REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : 5.720 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE (A**2) : 8.080 ; 2.000 REMARK 3 SIDE-CHAIN BOND (A**2) : 8.460 ; 2.000 REMARK 3 SIDE-CHAIN ANGLE (A**2) : 11.740; 2.500 REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : FLAT MODEL REMARK 3 KSOL : 0.35 REMARK 3 BSOL : 58.45 REMARK 3 REMARK 3 NCS MODEL : NULL REMARK 3 REMARK 3 NCS RESTRAINTS. RMS SIGMA/WEIGHT REMARK 3 GROUP 1 POSITIONAL (A) : NULL ; NULL REMARK 3 GROUP 1 B-FACTOR (A**2) : NULL ; NULL REMARK 3 REMARK 3 PARAMETER FILE 1 : PROTEIN_REP.PARAM REMARK 3 PARAMETER FILE 2 : WATER_REP.PARAM REMARK 3 PARAMETER FILE 3 : ION.PARAM REMARK 3 PARAMETER FILE 4 : NO3.PARAM REMARK 3 PARAMETER FILE 5 : NULL REMARK 3 TOPOLOGY FILE 1 : PROTEIN.TOP REMARK 3 TOPOLOGY FILE 2 : WATER.TOP REMARK 3 TOPOLOGY FILE 3 : ION.TOP REMARK 3 TOPOLOGY FILE 4 : NO3.TOP REMARK 3 TOPOLOGY FILE 5 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: BULK SOLVENT MODEL USED REMARK 4 REMARK 4 4FZ4 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 18-JUL-12. REMARK 100 THE DEPOSITION ID IS D_1000073533. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 20-NOV-08 REMARK 200 TEMPERATURE (KELVIN) : 298 REMARK 200 PH : 7.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SSRF REMARK 200 BEAMLINE : BL17U REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9795 REMARK 200 MONOCHROMATOR : GRAPHITE REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : MAR555 FLAT PANEL REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 6551 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.440 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 2.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 85.2 REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : NULL REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.40 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.49 REMARK 200 COMPLETENESS FOR SHELL (%) : 97.8 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL 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: PHENIX REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 46.65 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.31 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 30% PEG 3350, 0.4M NANO3 , PH 7.5, REMARK 280 EVAPORATION, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z REMARK 290 3555 -X+1/2,Y+1/2,-Z REMARK 290 4555 X+1/2,-Y+1/2,-Z 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 0.00000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 24.61750 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 43.80050 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 24.61750 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 43.80050 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA 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 375 REMARK 375 SPECIAL POSITION REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL REMARK 375 POSITIONS. REMARK 375 REMARK 375 ATOM RES CSSEQI REMARK 375 HOH A 423 LIES ON A SPECIAL POSITION. 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 111 -33.62 -36.72 REMARK 500 ASP A 149 115.50 -30.03 REMARK 500 ARG A 182 -92.20 -111.46 REMARK 500 REMARK 500 REMARK: NULL REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CL A 301 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CL A 302 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NO3 A 303 DBREF 4FZ4 A 51 199 UNP A4VZ16 A4VZ16_STRS2 51 199 SEQADV 4FZ4 VAL A 62 UNP A4VZ16 LEU 62 CONFLICT SEQADV 4FZ4 ILE A 200 UNP A4VZ16 EXPRESSION TAG SEQADV 4FZ4 LEU A 201 UNP A4VZ16 EXPRESSION TAG SEQADV 4FZ4 GLU A 202 UNP A4VZ16 EXPRESSION TAG SEQADV 4FZ4 HIS A 203 UNP A4VZ16 EXPRESSION TAG SEQADV 4FZ4 HIS A 204 UNP A4VZ16 EXPRESSION TAG SEQRES 1 A 154 GLU ALA MET ALA LYS VAL GLU GLU VAL GLN LYS VAL VAL SEQRES 2 A 154 LYS GLU LEU GLU LYS GLU LEU GLY GLU LEU ASP LYS VAL SEQRES 3 A 154 PRO SER TYR GLY ASP ALA GLN ASP TYR SER TYR GLN LYS SEQRES 4 A 154 ALA LEU TRP GLU GLU PHE LEU ARG ILE GLY LYS ASP ASN SEQRES 5 A 154 MET ASP TYR ALA SER LYS MET LYS ALA ASP ASP LYS PHE SEQRES 6 A 154 PHE HIS LYS VAL LYS GLY ASP LEU ASN ASP PHE LYS TYR SEQRES 7 A 154 GLN ILE LYS VAL GLU ASN TYR ILE ARG GLN VAL ALA GLU SEQRES 8 A 154 LEU ARG LYS LYS TYR PRO GLY ASP ASN THR ILE GLU GLU SEQRES 9 A 154 GLU TYR ASN ALA HIS LEU LYS GLN ASP GLU GLY LYS SER SEQRES 10 A 154 ILE ALA SER GLN GLU GLY ALA THR LEU ARG ASP TYR VAL SEQRES 11 A 154 ASP ARG GLU ALA SER GLU ALA MET GLY ARG ILE LYS GLN SEQRES 12 A 154 ARG VAL ALA GLU LEU GLU ILE LEU GLU HIS HIS HET CL A 301 1 HET CL A 302 1 HET NO3 A 303 4 HETNAM CL CHLORIDE ION HETNAM NO3 NITRATE ION FORMUL 2 CL 2(CL 1-) FORMUL 4 NO3 N O3 1- FORMUL 5 HOH *31(H2 O) HELIX 1 1 ALA A 52 ASP A 74 1 23 HELIX 2 2 ALA A 82 ASP A 84 5 3 HELIX 3 3 TYR A 85 ALA A 106 1 22 HELIX 4 4 PHE A 115 TYR A 146 1 32 HELIX 5 5 ASP A 149 LEU A 160 1 12 HELIX 6 6 GLU A 172 ARG A 182 1 11 HELIX 7 7 ARG A 182 HIS A 203 1 22 SITE 1 AC1 3 GLN A 162 LYS A 166 TYR A 179 SITE 1 AC2 3 GLU A 183 GLU A 186 ARG A 190 SITE 1 AC3 5 PHE A 95 GLY A 99 ASP A 122 PHE A 126 SITE 2 AC3 5 GLN A 129 CRYST1 49.235 87.601 38.540 90.00 90.00 90.00 P 21 21 2 4 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 0.020311 0.000000 0.000000 0.00000 SCALE2 0.000000 0.011415 0.000000 0.00000 SCALE3 0.000000 0.000000 0.025947 0.00000