HEADER CELL ADHESION 26-FEB-24 9AT9 TITLE CRYSTAL STRUCTURE OF KLEBSIELLA PNEUMONIAE FIMH LECTIN DOMAIN BOUND TO TITLE 2 D-MANNOSE COMPND MOL_ID: 1; COMPND 2 MOLECULE: FIMH; COMPND 3 CHAIN: B; COMPND 4 SYNONYM: FIMBRIAL PROTEIN; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: KLEBSIELLA PNEUMONIAE; SOURCE 3 ORGANISM_TAXID: 573; SOURCE 4 STRAIN: TOP52 1721; SOURCE 5 GENE: FIMH, FIMH_1, FIMH_2; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS LECTIN DOMAIN, ADHESIN, COMPLEX, TYPE 1 PILUS, CELL ADHESION EXPDTA X-RAY DIFFRACTION AUTHOR E.LOPATTO,K.O.TAMADONFAR,S.J.HULTGREN REVDAT 3 16-OCT-24 9AT9 1 REMARK REVDAT 2 02-OCT-24 9AT9 1 JRNL REVDAT 1 25-SEP-24 9AT9 0 JRNL AUTH E.D.B.LOPATTO,J.S.PINKNER,D.A.SANICK,R.F.POTTER,L.X.LIU, JRNL AUTH 2 J.BAZAN VILLICANA,K.O.TAMADONFAR,Y.YE,M.I.ZIMMERMAN, JRNL AUTH 3 N.C.GUALBERTO,K.W.DODSON,J.W.JANETKA,D.A.HUNSTAD, JRNL AUTH 4 S.J.HULTGREN JRNL TITL CONFORMATIONAL ENSEMBLES IN KLEBSIELLA PNEUMONIAE FIMH JRNL TITL 2 IMPACT UROPATHOGENESIS. JRNL REF PROC.NATL.ACAD.SCI.USA V. 121 55121 2024 JRNL REFN ESSN 1091-6490 JRNL PMID 39288182 JRNL DOI 10.1073/PNAS.2409655121 REMARK 2 REMARK 2 RESOLUTION. 1.34 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX V1.20.1 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 : GEOSTD + MONOMER LIBRARY + CDL V1.2 REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.34 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 35.19 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.9 REMARK 3 NUMBER OF REFLECTIONS : 35161 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.216 REMARK 3 R VALUE (WORKING SET) : 0.215 REMARK 3 FREE R VALUE : 0.232 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.910 REMARK 3 FREE R VALUE TEST SET COUNT : 1728 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 35.1900 - 3.0700 1.00 3006 154 0.1833 0.1880 REMARK 3 2 3.0700 - 2.4300 1.00 2867 161 0.2104 0.2371 REMARK 3 3 2.4300 - 2.1300 1.00 2848 121 0.2009 0.2057 REMARK 3 4 2.1300 - 1.9300 1.00 2857 117 0.2034 0.1956 REMARK 3 5 1.9300 - 1.7900 1.00 2817 1135 0.2171 0.2525 REMARK 3 6 1.7900 - 1.6900 1.00 2791 165 0.2258 0.2591 REMARK 3 7 1.6900 - 1.6000 1.00 2786 165 0.2378 0.2693 REMARK 3 8 1.6000 - 1.5300 1.00 2755 151 0.2470 0.2544 REMARK 3 9 1.5300 - 1.4700 1.00 2801 139 0.2791 0.3323 REMARK 3 10 1.4700 - 1.4200 0.99 2712 153 0.3099 0.3236 REMARK 3 11 1.4200 - 1.3800 0.98 2733 125 0.3319 0.3386 REMARK 3 12 1.3800 - 1.3400 0.90 2460 160 0.3644 0.3755 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.10 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) : 0.185 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 25.590 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 14.77 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 27.08 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 1255 REMARK 3 ANGLE : 1.038 1730 REMARK 3 CHIRALITY : 0.083 209 REMARK 3 PLANARITY : 0.009 219 REMARK 3 DIHEDRAL : 6.185 186 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 1 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: ALL REMARK 3 ORIGIN FOR THE GROUP (A): -8.9137 5.2915 -13.8114 REMARK 3 T TENSOR REMARK 3 T11: 0.1424 T22: 0.1313 REMARK 3 T33: 0.1674 T12: 0.0201 REMARK 3 T13: -0.0047 T23: -0.0109 REMARK 3 L TENSOR REMARK 3 L11: 1.1185 L22: 0.6948 REMARK 3 L33: 3.8233 L12: -0.2875 REMARK 3 L13: 1.4778 L23: -0.1430 REMARK 3 S TENSOR REMARK 3 S11: 0.0913 S12: 0.1035 S13: -0.0573 REMARK 3 S21: -0.1373 S22: -0.0757 S23: 0.0436 REMARK 3 S31: 0.0445 S32: 0.0019 S33: -0.0195 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 9AT9 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 27-FEB-24. REMARK 100 THE DEPOSITION ID IS D_1000281811. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 27-MAR-22 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 : ALS REMARK 200 BEAMLINE : 4.2.2 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.072156 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CMOS REMARK 200 DETECTOR MANUFACTURER : RDI CMOS_8M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XDS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 35168 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.340 REMARK 200 RESOLUTION RANGE LOW (A) : 35.190 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.9 REMARK 200 DATA REDUNDANCY : 2.000 REMARK 200 R MERGE (I) : 0.03579 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 12.9200 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.34 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.39 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL 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: MOLECULAR REPLACEMENT 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 (%): 43.11 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.16 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PROTEIN MIXED WITH 10:1 MOLAR RATIO OF REMARK 280 D-MANNOSE TO PROTEIN. CRYSTALS GROWN IN 0.4 M MGCL2, 2.0 M NACL, REMARK 280 0.1 M TRIS PH 7, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE REMARK 280 292.15K 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 18.76950 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 50.52150 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 20.31300 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 50.52150 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 18.76950 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 20.31300 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: B 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 465 REMARK 465 MISSING RESIDUES REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE REMARK 465 EXPERIMENT. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 REMARK 465 M RES C SSSEQI REMARK 465 HIS B 164 REMARK 465 HIS B 165 REMARK 465 HIS B 166 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 LYS B 4 NZ REMARK 470 ASN B 29 CG OD1 ND2 REMARK 470 VAL B 30 CG1 CG2 REMARK 470 GLN B 32 CD OE1 NE2 REMARK 470 GLU B 50 CG CD OE1 OE2 REMARK 470 LYS B 76 CG CD CE NZ REMARK 470 ASP B 153 CG OD1 OD2 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 B 48 55.97 -150.88 REMARK 500 ASP B 96 31.41 -140.86 REMARK 500 REMARK 500 REMARK: NULL DBREF 9AT9 B 1 160 UNP B0LF88 B0LF88_KLEPN 24 183 SEQADV 9AT9 HIS B 161 UNP B0LF88 EXPRESSION TAG SEQADV 9AT9 HIS B 162 UNP B0LF88 EXPRESSION TAG SEQADV 9AT9 HIS B 163 UNP B0LF88 EXPRESSION TAG SEQADV 9AT9 HIS B 164 UNP B0LF88 EXPRESSION TAG SEQADV 9AT9 HIS B 165 UNP B0LF88 EXPRESSION TAG SEQADV 9AT9 HIS B 166 UNP B0LF88 EXPRESSION TAG SEQRES 1 B 166 PHE ALA CYS LYS THR ALA THR GLY ALA THR ILE PRO ILE SEQRES 2 B 166 GLY GLY GLY SER ALA ASN VAL TYR VAL ASN LEU THR PRO SEQRES 3 B 166 ALA VAL ASN VAL GLY GLN ASN LEU VAL VAL ASP LEU SER SEQRES 4 B 166 THR GLN ILE PHE CYS HIS ASN ASP TYR PRO GLU THR ILE SEQRES 5 B 166 THR ASP TYR VAL THR LEU GLN ARG GLY SER ALA TYR GLY SEQRES 6 B 166 GLY VAL LEU SER SER PHE SER GLY THR VAL LYS TYR ASN SEQRES 7 B 166 GLY THR SER TYR PRO PHE PRO THR THR THR GLU THR ALA SEQRES 8 B 166 ARG VAL ILE TYR ASP SER ARG THR ASP LYS PRO TRP PRO SEQRES 9 B 166 ALA VAL LEU TYR LEU THR PRO VAL SER THR ALA GLY GLY SEQRES 10 B 166 VAL ALA ILE THR ALA GLY SER LEU ILE ALA VAL LEU ILE SEQRES 11 B 166 LEU HIS GLN THR ASN ASN TYR ASN SER ASP SER PHE GLN SEQRES 12 B 166 PHE ILE TRP ASN ILE TYR ALA ASN ASN ASP VAL VAL VAL SEQRES 13 B 166 PRO THR GLY GLY HIS HIS HIS HIS HIS HIS HET MAN B 201 23 HETNAM MAN ALPHA-D-MANNOPYRANOSE HETSYN MAN ALPHA-D-MANNOSE; D-MANNOSE; MANNOSE FORMUL 2 MAN C6 H12 O6 FORMUL 3 HOH *85(H2 O) HELIX 1 AA1 TYR B 64 SER B 70 1 7 SHEET 1 AA1 4 THR B 10 ILE B 11 0 SHEET 2 AA1 4 ALA B 2 THR B 5 -1 N CYS B 3 O ILE B 11 SHEET 3 AA1 4 ILE B 42 HIS B 45 -1 O PHE B 43 N LYS B 4 SHEET 4 AA1 4 LYS B 101 PRO B 102 -1 O LYS B 101 N CYS B 44 SHEET 1 AA2 5 GLY B 16 VAL B 22 0 SHEET 2 AA2 5 PHE B 142 ALA B 150 1 O ASN B 147 N VAL B 20 SHEET 3 AA2 5 LEU B 125 ASN B 135 -1 N ALA B 127 O ILE B 148 SHEET 4 AA2 5 ASP B 54 ALA B 63 -1 N GLN B 59 O ILE B 130 SHEET 5 AA2 5 VAL B 93 TYR B 95 -1 O VAL B 93 N VAL B 56 SHEET 1 AA3 4 LEU B 34 ASP B 37 0 SHEET 2 AA3 4 ALA B 105 PRO B 111 -1 O LEU B 109 N LEU B 34 SHEET 3 AA3 4 PHE B 71 TYR B 77 -1 N LYS B 76 O VAL B 106 SHEET 4 AA3 4 THR B 80 PHE B 84 -1 O THR B 80 N TYR B 77 SHEET 1 AA4 2 GLY B 117 ILE B 120 0 SHEET 2 AA4 2 VAL B 154 VAL B 156 -1 O VAL B 156 N GLY B 117 SSBOND 1 CYS B 3 CYS B 44 1555 1555 2.13 CISPEP 1 PHE B 84 PRO B 85 0 -4.62 CRYST1 37.539 40.626 101.043 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 0.026639 0.000000 0.000000 0.00000 SCALE2 0.000000 0.024615 0.000000 0.00000 SCALE3 0.000000 0.000000 0.009897 0.00000