PDB Short entry for 3VOR HEADER CELL ADHESION 06-FEB-12 3VOR TITLE CRYSTAL STRUCTURE ANALYSIS OF THE COFA COMPND MOL_ID: 1; COMPND 2 MOLECULE: CFA/III PILIN; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: COFA, MAJOR PILIN SUBUNIT; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ESCHERICHIA COLI; SOURCE 3 ORGANISM_TAXID: 562; SOURCE 4 STRAIN: 260-1; SOURCE 5 GENE: COFA; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: ORIGAMIB(DE3); SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PET32B KEYWDS TYPE IV PILIN, COLONIZATION, CELL ADHESION EXPDTA X-RAY DIFFRACTION AUTHOR S.FUKAKUSA,K.KAWAHARA,S.NAKAMURA,T.IWASITA,S.BABA,M.NISHIMURA, AUTHOR 2 Y.KOBAYASHI,T.HONDA,T.IIDA,T.TANIGUCHI,T.OHKUBO REVDAT 2 31-JUL-13 3VOR 1 JRNL REVDAT 1 26-SEP-12 3VOR 0 JRNL AUTH S.FUKAKUSA,K.KAWAHARA,S.NAKAMURA,T.IWASHITA,S.BABA, JRNL AUTH 2 M.NISHIMURA,Y.KOBAYASHI,T.HONDA,T.IIDA,T.TANIGUCHI,T.OHKUBO JRNL TITL STRUCTURE OF THE CFA/III MAJOR PILIN SUBUNIT COFA FROM HUMAN JRNL TITL 2 ENTEROTOXIGENIC ESCHERICHIA COLI DETERMINED AT 0.90 A JRNL TITL 3 RESOLUTION BY SULFUR-SAD PHASING JRNL REF ACTA CRYSTALLOGR.,SECT.D V. 68 1418 2012 JRNL REFN ISSN 0907-4449 JRNL PMID 22993096 JRNL DOI 10.1107/S0907444912034464 REMARK 2 REMARK 2 RESOLUTION. 0.90 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE: 1.7.3_928) REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VICENT CHEN,IAN REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE- REMARK 3 : KUNSTLEVE,LI-WEI HUNG,ROBERT IMMORMINO, REMARK 3 : TOM IOERGER,AIRLIE MCCOY,ERIK MCKEE,NIGEL REMARK 3 : MORIARTY,REETAL PAI,RANDY READ,JANE REMARK 3 : RICHARDSON,DAVID RICHARDSON,TOD ROMO,JIM REMARK 3 : SACCHETTINI,NICHOLAS SAUTER,JACOB SMITH, REMARK 3 : LAURENT STORONI,TOM TERWILLIGER,PETER REMARK 3 : ZWART REMARK 3 REMARK 3 REFINEMENT TARGET : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 0.90 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 30.86 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.350 REMARK 3 COMPLETENESS FOR RANGE (%) : 96.4 REMARK 3 NUMBER OF REFLECTIONS : 91733 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.121 REMARK 3 R VALUE (WORKING SET) : 0.120 REMARK 3 FREE R VALUE : 0.130 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 4590 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 30.8832 - 2.7959 0.98 3041 161 0.1804 0.1768 REMARK 3 2 2.7959 - 2.2194 0.98 2994 158 0.1422 0.1540 REMARK 3 3 2.2194 - 1.9389 0.98 2967 156 0.1302 0.1519 REMARK 3 4 1.9389 - 1.7616 0.98 2944 155 0.1289 0.1325 REMARK 3 5 1.7616 - 1.6354 0.98 2960 156 0.1221 0.1401 REMARK 3 6 1.6354 - 1.5389 0.97 2941 155 0.1120 0.1171 REMARK 3 7 1.5389 - 1.4619 0.97 2942 155 0.1084 0.1376 REMARK 3 8 1.4619 - 1.3982 0.97 2957 155 0.1016 0.1204 REMARK 3 9 1.3982 - 1.3444 0.97 2924 154 0.1038 0.1255 REMARK 3 10 1.3444 - 1.2980 0.97 2911 153 0.0975 0.1009 REMARK 3 11 1.2980 - 1.2574 0.97 2916 154 0.0988 0.1096 REMARK 3 12 1.2574 - 1.2215 0.97 2917 154 0.0932 0.1022 REMARK 3 13 1.2215 - 1.1893 0.97 2933 154 0.0880 0.0974 REMARK 3 14 1.1893 - 1.1603 0.96 2876 151 0.0882 0.1166 REMARK 3 15 1.1603 - 1.1339 0.96 2898 153 0.0837 0.0968 REMARK 3 16 1.1339 - 1.1098 0.96 2894 152 0.0857 0.0815 REMARK 3 17 1.1098 - 1.0876 0.96 2874 151 0.0895 0.0902 REMARK 3 18 1.0876 - 1.0671 0.96 2897 153 0.0930 0.1095 REMARK 3 19 1.0671 - 1.0480 0.96 2895 152 0.1000 0.1144 REMARK 3 20 1.0480 - 1.0303 0.96 2883 152 0.1017 0.1196 REMARK 3 21 1.0303 - 1.0136 0.96 2875 151 0.0997 0.1017 REMARK 3 22 1.0136 - 0.9980 0.96 2903 153 0.1066 0.1084 REMARK 3 23 0.9980 - 0.9834 0.95 2868 151 0.1073 0.1111 REMARK 3 24 0.9834 - 0.9695 0.96 2841 150 0.1148 0.1163 REMARK 3 25 0.9695 - 0.9564 0.95 2884 152 0.1197 0.1254 REMARK 3 26 0.9564 - 0.9440 0.95 2825 148 0.1209 0.1278 REMARK 3 27 0.9440 - 0.9322 0.95 2899 153 0.1283 0.1342 REMARK 3 28 0.9322 - 0.9209 0.95 2843 150 0.1324 0.1341 REMARK 3 29 0.9209 - 0.9102 0.95 2831 148 0.1394 0.1592 REMARK 3 30 0.9102 - 0.9000 0.95 2850 150 0.1458 0.1582 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : 0.47 REMARK 3 K_SOL : 0.56 REMARK 3 B_SOL : 36.90 REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.080 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 9.050 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 3.20 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 4.50 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -1.18940 REMARK 3 B22 (A**2) : 0.75230 REMARK 3 B33 (A**2) : 0.43710 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.00280 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 : 0.009 1611 REMARK 3 ANGLE : 1.541 2216 REMARK 3 CHIRALITY : 0.086 263 REMARK 3 PLANARITY : 0.009 299 REMARK 3 DIHEDRAL : 13.484 636 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL 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 3VOR COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 15-FEB-12. REMARK 100 THE RCSB ID CODE IS RCSB095311. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 26-OCT-11 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 3.8 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SPRING-8 REMARK 200 BEAMLINE : BL38B1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9 REMARK 200 MONOCHROMATOR : SI (111) DOUBLE CRYSTAL REMARK 200 MONOCHROMATOR REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XSCALE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 91809 REMARK 200 RESOLUTION RANGE HIGH (A) : 0.900 REMARK 200 RESOLUTION RANGE LOW (A) : 30.860 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 96.4 REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : 0.05000 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 18.6000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 0.90 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 0.95 REMARK 200 COMPLETENESS FOR SHELL (%) : 94.9 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.17000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 7.110 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: SAD REMARK 200 SOFTWARE USED: SHELXD REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 28.80 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.73 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 26% PEG 4000, PH 3.8, VAPOR DIFFUSION, REMARK 280 SITTING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 21 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,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 23.85500 REMARK 290 SMTRY3 2 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 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 HOH A 428 O HOH A 429 1.87 REMARK 500 O HOH A 367 O HOH A 429 1.90 REMARK 500 O HOH A 281 O HOH A 340 1.93 REMARK 500 O HOH A 341 O HOH A 347 1.94 REMARK 500 OE2 GLU A 118 O HOH A 436 1.95 REMARK 500 O HOH A 308 O HOH A 335 1.97 REMARK 500 OD1 ASP A 23 O HOH A 437 1.97 REMARK 500 O HOH A 411 O HOH A 423 2.03 REMARK 500 OD2 ASP A 23 O HOH A 348 2.06 REMARK 500 OD2 ASP A 66 O HOH A 422 2.09 REMARK 500 NE2 GLN A 56 O HOH A 423 2.12 REMARK 500 O HOH A 290 O HOH A 340 2.13 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15 REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375 REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS. REMARK 500 REMARK 500 DISTANCE CUTOFF: REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE REMARK 500 O HOH A 289 O HOH A 411 1556 1.36 REMARK 500 O HOH A 381 O HOH A 393 1455 1.77 REMARK 500 OD2 ASP A 23 O HOH A 425 2747 1.93 REMARK 500 O HOH A 346 O HOH A 399 2848 2.00 REMARK 500 O HOH A 313 O HOH A 376 2758 2.05 REMARK 500 O HOH A 288 O HOH A 354 1656 2.18 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 SER A 2 -161.84 -77.11 REMARK 500 REMARK 500 REMARK: NULL DBREF 3VOR A 3 182 UNP Q59393 Q59393_ECOLX 59 238 SEQADV 3VOR GLY A 1 UNP Q59393 EXPRESSION TAG SEQADV 3VOR SER A 2 UNP Q59393 EXPRESSION TAG SEQRES 1 A 182 GLY SER ASP SER ARG THR VAL SER GLU LEU VAL THR ASN SEQRES 2 A 182 THR ASN THR ILE ARG VAL ALA MET LYS ASP ALA TYR GLN SEQRES 3 A 182 ARG ASP GLY LYS TYR PRO ASP TYR GLN ALA PRO LEU SER SEQRES 4 A 182 LEU THR ALA ASP SER ILE LYS THR ASP SER THR GLY ILE SEQRES 5 A 182 ALA VAL ALA GLN LEU VAL GLN LEU GLY LYS LEU THR PRO SEQRES 6 A 182 ASP GLU ALA ARG ASN GLY ILE SER GLY ASP TYR ILE GLY SEQRES 7 A 182 ILE GLY GLY ALA ILE THR SER SER GLY SER THR ILE ASN SEQRES 8 A 182 LYS GLY PHE ALA MET GLU LEU ASN GLY LEU SER GLN GLU SEQRES 9 A 182 GLN CYS ARG SER ILE LEU GLY GLN VAL GLY ASP ASN TRP SEQRES 10 A 182 GLU TYR VAL ALA VAL GLY THR SER PRO SER GLY SER TYR SEQRES 11 A 182 ASP ALA LEU SER ALA GLY ALA VAL ASN MET LEU ALA ALA SEQRES 12 A 182 THR ASP ASN THR THR ILE LEU ARG SER LEU ALA ALA ASN SEQRES 13 A 182 GLY GLN VAL SER LEU THR ALA GLU LYS ILE LEU LYS THR SEQRES 14 A 182 CYS THR ALA THR VAL ASN SER ILE THR LEU ALA SER ARG FORMUL 2 HOH *237(H2 O) HELIX 1 1 SER A 4 GLN A 26 1 23 HELIX 2 2 ARG A 27 GLY A 29 5 3 HELIX 3 3 ASP A 43 THR A 47 5 5 HELIX 4 4 ILE A 52 LEU A 60 1 9 HELIX 5 5 THR A 64 GLU A 67 5 4 HELIX 6 6 SER A 102 GLY A 114 1 13 HELIX 7 7 ASP A 115 TRP A 117 5 3 HELIX 8 8 TYR A 130 ALA A 135 1 6 HELIX 9 9 THR A 162 LEU A 167 1 6 SHEET 1 A 2 ARG A 69 ASN A 70 0 SHEET 2 A 2 ASP A 75 TYR A 76 -1 O ASP A 75 N ASN A 70 SHEET 1 B 6 VAL A 138 ASN A 139 0 SHEET 2 B 6 GLY A 78 ILE A 83 1 N ILE A 83 O VAL A 138 SHEET 3 B 6 GLY A 93 LEU A 101 -1 O ALA A 95 N GLY A 80 SHEET 4 B 6 ASN A 175 SER A 181 -1 O ILE A 177 N LEU A 98 SHEET 5 B 6 TYR A 119 GLY A 123 -1 N ALA A 121 O THR A 178 SHEET 6 B 6 ILE A 149 ARG A 151 -1 O ARG A 151 N VAL A 120 SSBOND 1 CYS A 106 CYS A 170 1555 1555 2.06 CRYST1 33.820 47.710 42.450 90.00 107.52 90.00 P 1 21 1 2 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 0.029568 0.000000 0.009334 0.00000 SCALE2 0.000000 0.020960 0.000000 0.00000 SCALE3 0.000000 0.000000 0.024703 0.00000