HEADER SUGAR BINDING PROTEIN 02-DEC-15 5F3F TITLE CRYSTAL STRUCTURE OF PARA-BIPHENYL-2-METHYL-3'-METHYL AMIDE MANNOSIDE TITLE 2 BOUND TO FIMH LECTIN DOMAIN COMPND MOL_ID: 1; COMPND 2 MOLECULE: PROTEIN FIMH; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: LECTIN DOMAIN (UNP RESIDUES 22-179); COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ESCHERICHIA COLI J96; SOURCE 3 ORGANISM_TAXID: 1206108; SOURCE 4 STRAIN: J96; SOURCE 5 GENE: FIMH; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: C600; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PMMB91 KEYWDS MANNOSIDE, FIMH, ADHESIN, CARBOHYDRATE BINDING PROTEIN, SUGAR BINDING KEYWDS 2 PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR R.D.KLEIN,S.J.HULTGREN REVDAT 3 03-JAN-24 5F3F 1 JRNL REVDAT 2 27-SEP-23 5F3F 1 REMARK REVDAT 1 07-DEC-16 5F3F 0 JRNL AUTH L.MYDOCK-MCGRANE,Z.CUSUMANO,Z.HAN,J.BINKLEY,M.KOSTAKIOTI, JRNL AUTH 2 T.HANNAN,J.S.PINKNER,R.KLEIN,V.KALAS,J.CROWLEY,N.P.RATH, JRNL AUTH 3 S.J.HULTGREN,J.W.JANETKA JRNL TITL ANTIVIRULENCE C-MANNOSIDES AS ANTIBIOTIC-SPARING, ORAL JRNL TITL 2 THERAPEUTICS FOR URINARY TRACT INFECTIONS. JRNL REF J.MED.CHEM. V. 59 9390 2016 JRNL REFN ISSN 0022-2623 JRNL PMID 27689912 JRNL DOI 10.1021/ACS.JMEDCHEM.6B00948 REMARK 2 REMARK 2 RESOLUTION. 1.76 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.8.4_1496 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 : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.76 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 24.49 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.360 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.7 REMARK 3 NUMBER OF REFLECTIONS : 17014 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.137 REMARK 3 R VALUE (WORKING SET) : 0.135 REMARK 3 FREE R VALUE : 0.172 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.060 REMARK 3 FREE R VALUE TEST SET COUNT : 861 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 24.4874 - 3.1962 1.00 2860 129 0.1408 0.1546 REMARK 3 2 3.1962 - 2.5378 1.00 2687 168 0.1356 0.1659 REMARK 3 3 2.5378 - 2.2172 1.00 2692 134 0.1304 0.1816 REMARK 3 4 2.2172 - 2.0146 1.00 2666 149 0.1226 0.1837 REMARK 3 5 2.0146 - 1.8703 1.00 2651 140 0.1310 0.1746 REMARK 3 6 1.8703 - 1.7600 0.98 2597 141 0.1470 0.2214 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.11 REMARK 3 SHRINKAGE RADIUS : 0.90 REMARK 3 K_SOL : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.160 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 14.760 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) : NULL REMARK 3 B22 (A**2) : NULL REMARK 3 B33 (A**2) : NULL REMARK 3 B12 (A**2) : NULL REMARK 3 B13 (A**2) : NULL REMARK 3 B23 (A**2) : NULL 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 1305 REMARK 3 ANGLE : 1.410 1801 REMARK 3 CHIRALITY : 0.056 211 REMARK 3 PLANARITY : 0.007 229 REMARK 3 DIHEDRAL : 13.705 450 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 5F3F COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 03-DEC-15. REMARK 100 THE DEPOSITION ID IS D_1000215857. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 05-JUN-12 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 5.8 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : ROTATING ANODE REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : RIGAKU MICROMAX-007 REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.54179 REMARK 200 MONOCHROMATOR : MIRRORS REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : MAR SCANNER 345 MM PLATE REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM REMARK 200 DATA SCALING SOFTWARE : AIMLESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 17060 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.760 REMARK 200 RESOLUTION RANGE LOW (A) : 24.490 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.7 REMARK 200 DATA REDUNDANCY : 6.600 REMARK 200 R MERGE (I) : 0.04800 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 24.7000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.76 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.86 REMARK 200 COMPLETENESS FOR SHELL (%) : 98.1 REMARK 200 DATA REDUNDANCY IN SHELL : 5.50 REMARK 200 R MERGE FOR SHELL (I) : 0.15200 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 9.900 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER REMARK 200 STARTING MODEL: 4AUU REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 52.28 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.58 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.2 M AMSO4, 20% PEG 3350, PH 5.8, REMARK 280 VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 291K 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 24.48500 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 30.44500 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 27.83000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 30.44500 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 24.48500 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 27.83000 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 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 491 O HOH A 500 2.19 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 352 O HOH A 447 2554 2.11 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 ILE A 13 134.04 -39.40 REMARK 500 TYR A 48 57.34 -152.64 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 5US A 201 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 5F2F RELATED DB: PDB DBREF 5F3F 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 5US A 201 108 HETNAM 5US 3-[4-[(2~{R},3~{S},4~{S},5~{S},6~{R})-6- HETNAM 2 5US (HYDROXYMETHYL)-3,4,5-TRIS(OXIDANYL)OXAN-2-YL]OXY-3- HETNAM 3 5US METHYL-PHENYL]-~{N}-METHYL-BENZAMIDE FORMUL 2 5US C21 H25 N O7 FORMUL 3 HOH *237(H2 O) HELIX 1 AA1 TYR A 64 ASN A 70 1 7 SHEET 1 AA1 4 ALA A 10 ILE A 11 0 SHEET 2 AA1 4 ALA A 2 THR A 5 -1 N CYS A 3 O ILE A 11 SHEET 3 AA1 4 ILE A 42 HIS A 45 -1 O PHE A 43 N LYS A 4 SHEET 4 AA1 4 LYS A 101 PRO A 102 -1 O LYS A 101 N CYS A 44 SHEET 1 AA2 5 GLY A 16 VAL A 22 0 SHEET 2 AA2 5 PHE A 142 ALA A 150 1 O TYR A 149 N VAL A 20 SHEET 3 AA2 5 LEU A 125 ASN A 135 -1 N ALA A 127 O ILE A 148 SHEET 4 AA2 5 ASP A 54 ALA A 63 -1 N ARG A 60 O ILE A 130 SHEET 5 AA2 5 VAL A 93 TYR A 95 -1 O VAL A 93 N VAL A 56 SHEET 1 AA3 4 LEU A 34 ASP A 37 0 SHEET 2 AA3 4 VAL A 105 PRO A 111 -1 O LEU A 109 N LEU A 34 SHEET 3 AA3 4 PHE A 71 TYR A 77 -1 N SER A 72 O THR A 110 SHEET 4 AA3 4 SER A 80 PHE A 84 -1 O SER A 80 N TYR A 77 SHEET 1 AA4 2 GLY A 117 ILE A 120 0 SHEET 2 AA4 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 2.02 CISPEP 1 PHE A 84 PRO A 85 0 -2.17 SITE 1 AC1 16 PHE A 1 ILE A 13 VAL A 30 GLY A 31 SITE 2 AC1 16 ASN A 46 ASP A 47 TYR A 48 ILE A 52 SITE 3 AC1 16 ASP A 54 ARG A 98 SER A 113 GLN A 133 SITE 4 AC1 16 ASN A 135 ASN A 138 ASP A 140 HOH A 327 CRYST1 48.970 55.660 60.890 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 0.020421 0.000000 0.000000 0.00000 SCALE2 0.000000 0.017966 0.000000 0.00000 SCALE3 0.000000 0.000000 0.016423 0.00000