HEADER CELL ADHESION 05-FEB-04 1UWF TITLE 1.7 A RESOLUTION STRUCTURE OF THE RECEPTOR BINDING DOMAIN OF THE FIMH TITLE 2 ADHESIN FROM UROPATHOGENIC E. COLI COMPND MOL_ID: 1; COMPND 2 MOLECULE: FIMH PROTEIN; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: N-TERMINAL LECTIN DOMAIN, RESIDUES 22-179; COMPND 5 SYNONYM: FIMH; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ESCHERICHIA COLI; SOURCE 3 ORGANISM_TAXID: 1206108; SOURCE 4 STRAIN: J96; SOURCE 5 ATCC: 47048; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: C600; SOURCE 9 EXPRESSION_SYSTEM_VARIANT: F-SUPE44 LACY1 THR-1 LEUB6 MCRB THI-1 SOURCE 10 FHUA21 HSDR LAMBDA; SOURCE 11 EXPRESSION_SYSTEM_PLASMID: PMMB91 KEYWDS BACTERIAL ADHESIN, CARBOHYDRATE RECOGNITION, ADHERENCE TO MAMMALIAN KEYWDS 2 CELLS, IG-VARIABLE FOLD, CELL ADHESION EXPDTA X-RAY DIFFRACTION AUTHOR J.BOUCKAERT,J.BERGLUND,E.D.GENST,L.COOLS,C.-S.HUNG,M.WUHRER, AUTHOR 2 A.ZAVIALOV,S.LANGERMANN,S.HULTGREN,L.WYNS,S.OSCARSON,S.D.KNIGHT,H.DE AUTHOR 3 GREVE REVDAT 5 13-DEC-23 1UWF 1 HETSYN REVDAT 4 29-JUL-20 1UWF 1 COMPND REMARK HETNAM SITE REVDAT 3 15-APR-15 1UWF 1 SOURCE JRNL REMARK VERSN REVDAT 3 2 1 FORMUL REVDAT 2 24-FEB-09 1UWF 1 VERSN REVDAT 1 16-FEB-05 1UWF 0 JRNL AUTH J.BOUCKAERT,J.BERGLUND,M.SCHEMBRI,E.DE GENST,L.COOLS, JRNL AUTH 2 M.WUHRER,C.HUNG,J.PINKNER,R.SLATTEGARD,A.ZAVIALOV, JRNL AUTH 3 D.CHOUDHURY,S.LANGERMANN,S.J.HULTGREN,L.WYNS,P.KLEMM, JRNL AUTH 4 S.OSCARSON,S.D.KNIGHT,H.DE GREVE JRNL TITL RECEPTOR BINDING STUDIES DISCLOSE A NOVEL CLASS OF JRNL TITL 2 HIGH-AFFINITY INHIBITORS OF THE ESCHERICHIA COLI FIMH JRNL TITL 3 ADHESIN. JRNL REF MOL.MICROBIOL. V. 55 441 2005 JRNL REFN ISSN 0950-382X JRNL PMID 15659162 JRNL DOI 10.1111/J.1365-2958.2004.04415.X REMARK 2 REMARK 2 RESOLUTION. 1.69 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS 1.1 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 : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.69 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 38.27 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : 1034321.060 REMARK 3 DATA CUTOFF LOW (ABS(F)) : NULL REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 98.7 REMARK 3 NUMBER OF REFLECTIONS : 18545 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) : 0.179 REMARK 3 FREE R VALUE : 0.218 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 8.400 REMARK 3 FREE R VALUE TEST SET COUNT : 1564 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : 0.006 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) : 1.69 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.80 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 96.90 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 2972 REMARK 3 BIN R VALUE (WORKING SET) : 0.2570 REMARK 3 BIN FREE R VALUE : 0.4540 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 0.40 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 11 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.137 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1196 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 22 REMARK 3 SOLVENT ATOMS : 307 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 24.30 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 16.80 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 5.49000 REMARK 3 B22 (A**2) : -1.44000 REMARK 3 B33 (A**2) : -4.05000 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) : 0.18 REMARK 3 ESD FROM SIGMAA (A) : 0.17 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) : 0.22 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.16 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.006 REMARK 3 BOND ANGLES (DEGREES) : 1.500 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 27.40 REMARK 3 IMPROPER ANGLES (DEGREES) : 0.780 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) : 0.970 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE (A**2) : 1.450 ; 2.000 REMARK 3 SIDE-CHAIN BOND (A**2) : 1.600 ; 2.000 REMARK 3 SIDE-CHAIN ANGLE (A**2) : 2.190 ; 2.500 REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : FLAT MODEL REMARK 3 KSOL : 0.37 REMARK 3 BSOL : 76.75 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 : GOL.PAR REMARK 3 PARAMETER FILE 3 : WATER_REP.PARAM REMARK 3 PARAMETER FILE 4 : DEG.PAR REMARK 3 PARAMETER FILE 5 : NULL REMARK 3 TOPOLOGY FILE 1 : PROTEIN.TOP REMARK 3 TOPOLOGY FILE 2 : GOL.TOP REMARK 3 TOPOLOGY FILE 3 : WATER.TOP REMARK 3 TOPOLOGY FILE 4 : DEG.TOP REMARK 3 TOPOLOGY FILE 5 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1UWF COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 05-FEB-04. REMARK 100 THE DEPOSITION ID IS D_1290014519. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 15-DEC-00 REMARK 200 TEMPERATURE (KELVIN) : 100.0 REMARK 200 PH : 7.50 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 19-BM REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.488 REMARK 200 MONOCHROMATOR : CARBON REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : NULL REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 18597 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.690 REMARK 200 RESOLUTION RANGE LOW (A) : 39.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.8 REMARK 200 DATA REDUNDANCY : 8.900 REMARK 200 R MERGE (I) : 0.05200 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 27.2500 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.69 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.73 REMARK 200 COMPLETENESS FOR SHELL (%) : 96.8 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.19600 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 8.200 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: AMORE REMARK 200 STARTING MODEL: PDB ENTRY 1QUN REMARK 200 REMARK 200 REMARK: DATA WERE COLLECTED AT THE APS, CHICAGO, USA REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 38.50 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.34 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 1.1 MM PROTEIN, 0.1 M HEPES PH 7.5, 10 REMARK 280 % PEG6000, 5% V/V MPD, PH 7.50 REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 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 19.95300 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 48.53500 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 20.81800 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 48.53500 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 19.95300 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 20.81800 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: PQS 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 400 REMARK 400 COMPOUND REMARK 400 RESIDUES 22-179 IN THE COMPND RECORD CORRESPOND TO RESIDUES REMARK 400 1-158 OF THE MATURE FIMH PROTEIN AND THUS TO THE LECTIN DOMAIN REMARK 400 OF THE ADHESIN. 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 TYR A 48 54.76 -151.20 REMARK 500 REMARK 500 REMARK: NULL REMARK 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH A2046 DISTANCE = 6.38 ANGSTROMS REMARK 525 HOH A2086 DISTANCE = 5.85 ANGSTROMS REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1KIU RELATED DB: PDB REMARK 900 FIMH ADHESIN Q133N MUTANT-FIMC CHAPERONE COMPLEX WITHMETHYL-ALPHA-D- REMARK 900 MANNOSE REMARK 900 RELATED ID: 1KLF RELATED DB: PDB REMARK 900 FIMH ADHESIN-FIMC CHAPERONE COMPLEX WITH D- MANNOSE REMARK 900 RELATED ID: 1QUN RELATED DB: PDB REMARK 900 X-RAY STRUCTURE OF THE FIMC-FIMH CHAPERONE ADHESIN COMPLEX FROM REMARK 900 UROPATHOGENIC E.COLI DBREF 1UWF A 1 158 UNP P08191 FIMH_ECOLI 22 179 SEQRES 1 A 158 PHE ALA CYS LYS THR ALA ASN GLY THR ALA ILE PRO ILE SEQRES 2 A 158 GLY GLY GLY SER ALA ASN VAL TYR VAL ASN LEU ALA PRO SEQRES 3 A 158 VAL VAL ASN VAL GLY GLN ASN LEU VAL VAL ASP LEU SER SEQRES 4 A 158 THR GLN ILE PHE CYS HIS ASN ASP TYR PRO GLU THR ILE SEQRES 5 A 158 THR ASP TYR VAL THR LEU GLN ARG GLY SER ALA TYR GLY SEQRES 6 A 158 GLY VAL LEU SER ASN PHE SER GLY THR VAL LYS TYR SER SEQRES 7 A 158 GLY SER SER TYR PRO PHE PRO THR THR SER GLU THR PRO SEQRES 8 A 158 ARG VAL VAL TYR ASN SER ARG THR ASP LYS PRO TRP PRO SEQRES 9 A 158 VAL ALA LEU TYR LEU THR PRO VAL SER SER ALA GLY GLY SEQRES 10 A 158 VAL ALA ILE LYS ALA GLY SER LEU ILE ALA VAL LEU ILE SEQRES 11 A 158 LEU ARG GLN THR ASN ASN TYR ASN SER ASP ASP PHE GLN SEQRES 12 A 158 PHE VAL TRP ASN ILE TYR ALA ASN ASN ASP VAL VAL VAL SEQRES 13 A 158 PRO THR HET DEG A1159 16 HET GOL A1160 6 HETNAM DEG BUTYL ALPHA-D-MANNOPYRANOSIDE HETNAM GOL GLYCEROL HETSYN DEG BUTYL-A-D-MANNOSE; BUTYL ALPHA-D-MANNOSIDE; BUTYL D- HETSYN 2 DEG MANNOSIDE; BUTYL MANNOSIDE HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 2 DEG C10 H20 O6 FORMUL 3 GOL C3 H8 O3 FORMUL 4 HOH *307(H2 O) HELIX 1 1 TYR A 64 ASN A 70 1 7 SHEET 1 AA 4 ALA A 10 ILE A 11 0 SHEET 2 AA 4 ALA A 2 THR A 5 -1 O CYS A 3 N ILE A 11 SHEET 3 AA 4 ILE A 42 HIS A 45 -1 O PHE A 43 N LYS A 4 SHEET 4 AA 4 LYS A 101 PRO A 102 -1 O LYS A 101 N CYS A 44 SHEET 1 AB 5 GLY A 16 VAL A 22 0 SHEET 2 AB 5 PHE A 142 ALA A 150 1 O GLN A 143 N GLY A 16 SHEET 3 AB 5 LEU A 125 ASN A 135 -1 N ILE A 126 O ILE A 148 SHEET 4 AB 5 ASP A 54 ALA A 63 -1 O TYR A 55 N THR A 134 SHEET 5 AB 5 VAL A 93 TYR A 95 -1 O VAL A 93 N VAL A 56 SHEET 1 AC 4 LEU A 34 ASP A 37 0 SHEET 2 AC 4 VAL A 105 PRO A 111 -1 O LEU A 107 N VAL A 36 SHEET 3 AC 4 PHE A 71 TYR A 77 -1 O SER A 72 N THR A 110 SHEET 4 AC 4 SER A 80 PHE A 84 -1 O SER A 80 N TYR A 77 SHEET 1 AD 2 GLY A 117 ILE A 120 0 SHEET 2 AD 2 VAL A 154 VAL A 156 -1 O VAL A 154 N ALA A 119 SSBOND 1 CYS A 3 CYS A 44 1555 1555 2.04 CISPEP 1 PHE A 84 PRO A 85 0 0.01 CRYST1 39.906 41.636 97.070 90.00 90.00 90.00 P 21 21 21 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 0.025059 0.000000 0.000000 0.00000 SCALE2 0.000000 0.024018 0.000000 0.00000 SCALE3 0.000000 0.000000 0.010302 0.00000