HEADER SUGAR BINDING PROTEIN 17-MAY-12 4AUJ TITLE FIMH LECTIN DOMAIN CO-CRYSTAL WITH A ALPHA-D-MANNOSIDE O-LINKED TO TITLE 2 PARA HYDROXYPROPARGYL PHENYL COMPND MOL_ID: 1; COMPND 2 MOLECULE: FIMH; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: LECTIN DOMAIN, RESIDUES 10-167; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ESCHERICHIA COLI; SOURCE 3 ORGANISM_TAXID: 364106; SOURCE 4 STRAIN: UTI89; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 8 EXPRESSION_SYSTEM_VARIANT: C43; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PET24A KEYWDS SUGAR BINDING PROTEIN, FIMBRIAE, VARIABLE IMMUNOGLOBULIN FOLD, KEYWDS 2 URINARY TRACT INFECTION EXPDTA X-RAY DIFFRACTION AUTHOR J.BOUCKAERT,M.TOUAIBIA,G.ROOS,T.C.SHIAO,Q.WANG,A.PAPADOPOULOS,R.ROY REVDAT 7 23-OCT-24 4AUJ 1 REMARK REVDAT 6 08-MAY-24 4AUJ 1 REMARK REVDAT 5 20-DEC-23 4AUJ 1 HETSYN REVDAT 4 29-JUL-20 4AUJ 1 COMPND REMARK HETNAM SITE REVDAT 3 18-JUN-14 4AUJ 1 JRNL REVDAT 2 25-DEC-13 4AUJ 1 JRNL REVDAT 1 29-MAY-13 4AUJ 0 JRNL AUTH G.ROOS,A.WELLENS,M.TOUAIBIA,N.YAMAKAWA,P.GEERLINGS,R.ROY, JRNL AUTH 2 L.WYNS,J.BOUCHAERT JRNL TITL VALIDATION OF REACTIVITY DESCRIPTORS TO ASSESS THE AROMATIC JRNL TITL 2 STACKING WITHIN THE TYROSINE GATE OF FIMH. JRNL REF ACS MED.CHEM.LETT. V. 4 1085 2013 JRNL REFN ISSN 1948-5875 JRNL PMID 24900609 JRNL DOI 10.1021/ML400269V REMARK 2 REMARK 2 RESOLUTION. 1.53 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE) 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) : 1.53 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 31.78 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.400 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 3 NUMBER OF REFLECTIONS : 21115 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.162 REMARK 3 R VALUE (WORKING SET) : 0.160 REMARK 3 FREE R VALUE : 0.185 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 1082 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 31.7871 - 3.0534 1.00 2674 135 0.1592 0.1716 REMARK 3 2 3.0534 - 2.4238 1.00 2549 132 0.1587 0.1805 REMARK 3 3 2.4238 - 2.1175 1.00 2501 126 0.1484 0.1674 REMARK 3 4 2.1175 - 1.9239 1.00 2502 119 0.1487 0.1810 REMARK 3 5 1.9239 - 1.7860 1.00 2462 154 0.1574 0.2018 REMARK 3 6 1.7860 - 1.6807 1.00 2460 139 0.1644 0.2233 REMARK 3 7 1.6807 - 1.5966 1.00 2453 129 0.1823 0.1977 REMARK 3 8 1.5966 - 1.5271 0.99 2432 148 0.2110 0.2361 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.00 REMARK 3 SHRINKAGE RADIUS : 0.73 REMARK 3 K_SOL : 0.37 REMARK 3 B_SOL : 54.47 REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.160 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 15.010 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 12.05 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 12.20 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.48520 REMARK 3 B22 (A**2) : -0.22160 REMARK 3 B33 (A**2) : -0.26360 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 : 0.007 1312 REMARK 3 ANGLE : 1.245 1822 REMARK 3 CHIRALITY : 0.075 216 REMARK 3 PLANARITY : 0.005 238 REMARK 3 DIHEDRAL : 18.351 477 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 4AUJ COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 17-MAY-12. REMARK 100 THE DEPOSITION ID IS D_1290052550. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : NULL 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 : SOLEIL REMARK 200 BEAMLINE : PROXIMA 1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.980 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARMOSAIC 225 MM CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XSCALE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 21157 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.530 REMARK 200 RESOLUTION RANGE LOW (A) : 48.170 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 200 DATA REDUNDANCY : 8.100 REMARK 200 R MERGE (I) : 0.06000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 22.9000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.53 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.60 REMARK 200 COMPLETENESS FOR SHELL (%) : 98.8 REMARK 200 DATA REDUNDANCY IN SHELL : 7.60 REMARK 200 R MERGE FOR SHELL (I) : 0.35000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 4.300 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: PDB ENTRY 1UWF REMARK 200 REMARK 200 REMARK: NONE REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 37.68 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.97 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 70% 2 METHYL 2,4 PENTANE DIOL 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 16.46000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 48.17000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 21.14500 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 48.17000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 16.46000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 21.14500 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 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 ALA A 6 CB REMARK 470 SER A 113 CB OG REMARK 470 SER A 114 OG 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 2024 O HOH A 2068 1.96 REMARK 500 OD1 ASN A 33 OG1 THR A 110 2.15 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND LENGTHS REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 RES CSSEQI ATM2 DEVIATION REMARK 500 SER A 80 C SER A 81 N -0.155 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND ANGLES REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 GLY A 79 O - C - N ANGL. DEV. = -12.9 DEGREES REMARK 500 SER A 80 CA - C - N ANGL. DEV. = -13.7 DEGREES 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 TYR A 48 55.82 -149.80 REMARK 500 ASN A 138 -159.18 -144.96 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4ATT RELATED DB: PDB REMARK 900 FIMH LECTIN DOMAIN CO-CRYSTAL WITH A ALPHA-D- MANNOSIDE O-LINKED TO REMARK 900 A PROPYNYL PARA METHOXY PHENYL DBREF 4AUJ A 1 158 UNP A2IC68 A2IC68_ECOLX 10 167 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 HNW A 201 22 HETNAM HNW 4-(3-HYDROXYPROP-1-YN-1-YL)PHENYL ALPHA-D- HETNAM 2 HNW MANNOPYRANOSIDE HETSYN HNW D-MANNOSE ALPHA1O P-HYDROXYPROPYNYL-PHENYL; 4-(3- HETSYN 2 HNW HYDROXYPROP-1-YN-1-YL)PHENYL ALPHA-D-MANNOSIDE; 4-(3- HETSYN 3 HNW HYDROXYPROP-1-YN-1-YL)PHENYL D-MANNOSIDE; 4-(3- HETSYN 4 HNW HYDROXYPROP-1-YN-1-YL)PHENYL MANNOSIDE FORMUL 2 HNW C15 H18 O7 FORMUL 3 HOH *187(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 2.05 CISPEP 1 PHE A 84 PRO A 85 0 2.59 CRYST1 32.920 42.290 96.340 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 0.030377 0.000000 0.000000 0.00000 SCALE2 0.000000 0.023646 0.000000 0.00000 SCALE3 0.000000 0.000000 0.010380 0.00000