HEADER CELL ADHESION 20-FEB-20 6Y4F TITLE X-RAY STRUCTURE OF THE ZN-DEPENDENT RECEPTOR-BINDING DOMAIN OF PROTEUS TITLE 2 MIRABILIS MR/P FIMBRIAL ADHESIN MRPH COMPND MOL_ID: 1; COMPND 2 MOLECULE: FIMBRIAL ADHESIN; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES; COMPND 5 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: PROTEUS MIRABILIS (STRAIN HI4320); SOURCE 3 ORGANISM_TAXID: 529507; SOURCE 4 GENE: MRPH, PMI0270; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 511693 KEYWDS METAL BINDING PROTEIN, ADHESIN, CELL ADHESION EXPDTA X-RAY DIFFRACTION AUTHOR S.D.KNIGHT,W.UBHAYASEKERA,W.JIANG REVDAT 2 24-JAN-24 6Y4F 1 REMARK REVDAT 1 19-AUG-20 6Y4F 0 JRNL AUTH W.JIANG,W.UBHAYASEKERA,M.C.BREED,A.N.NORSWORTHY,N.SERR, JRNL AUTH 2 H.L.T.MOBLEY,M.M.PEARSON,S.D.KNIGHT JRNL TITL MRPH, A NEW CLASS OF METAL-BINDING ADHESIN, REQUIRES ZINC TO JRNL TITL 2 MEDIATE BIOFILM FORMATION. JRNL REF PLOS PATHOG. V. 16 08707 2020 JRNL REFN ESSN 1553-7374 JRNL PMID 32780778 JRNL DOI 10.1371/JOURNAL.PPAT.1008707 REMARK 2 REMARK 2 RESOLUTION. 1.75 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.18RC1_3777 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 : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.75 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 19.05 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.330 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.1 REMARK 3 NUMBER OF REFLECTIONS : 12225 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.154 REMARK 3 R VALUE (WORKING SET) : 0.153 REMARK 3 FREE R VALUE : 0.183 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.160 REMARK 3 FREE R VALUE TEST SET COUNT : 631 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 19.0500 - 2.9900 1.00 2467 124 0.1356 0.1548 REMARK 3 2 2.9900 - 2.3700 1.00 2344 127 0.1425 0.1831 REMARK 3 3 2.3700 - 2.0700 1.00 2293 141 0.1447 0.1717 REMARK 3 4 2.0700 - 1.8900 1.00 2303 110 0.1648 0.2023 REMARK 3 5 1.8800 - 1.7500 0.96 2187 129 0.2514 0.2684 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : NULL 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) : 0.146 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 18.083 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 11.18 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 13.75 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 : 0.003 1106 REMARK 3 ANGLE : 0.704 1517 REMARK 3 CHIRALITY : 0.050 166 REMARK 3 PLANARITY : 0.004 202 REMARK 3 DIHEDRAL : 12.603 416 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 4 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 25 THROUGH 84 ) REMARK 3 ORIGIN FOR THE GROUP (A): -9.1201 -1.6717 15.7911 REMARK 3 T TENSOR REMARK 3 T11: 0.0830 T22: 0.0760 REMARK 3 T33: 0.0860 T12: -0.0036 REMARK 3 T13: -0.0076 T23: -0.0065 REMARK 3 L TENSOR REMARK 3 L11: 0.4977 L22: 0.8956 REMARK 3 L33: 0.5921 L12: 0.1597 REMARK 3 L13: -0.2549 L23: -0.3727 REMARK 3 S TENSOR REMARK 3 S11: -0.0428 S12: 0.0387 S13: -0.0456 REMARK 3 S21: -0.0647 S22: 0.0347 S23: 0.0314 REMARK 3 S31: 0.0561 S32: -0.0297 S33: 0.0143 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 85 THROUGH 106 ) REMARK 3 ORIGIN FOR THE GROUP (A): 0.7008 1.6332 6.8104 REMARK 3 T TENSOR REMARK 3 T11: 0.0688 T22: 0.0974 REMARK 3 T33: 0.0833 T12: -0.0077 REMARK 3 T13: 0.0171 T23: 0.0008 REMARK 3 L TENSOR REMARK 3 L11: 0.6304 L22: 0.7912 REMARK 3 L33: 1.4747 L12: -0.0648 REMARK 3 L13: 0.3754 L23: -0.1706 REMARK 3 S TENSOR REMARK 3 S11: 0.0249 S12: 0.0530 S13: -0.0634 REMARK 3 S21: -0.1198 S22: 0.0062 S23: -0.1397 REMARK 3 S31: 0.0196 S32: 0.1667 S33: -0.0178 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 107 THROUGH 118 ) REMARK 3 ORIGIN FOR THE GROUP (A): -4.7691 -6.4605 22.0838 REMARK 3 T TENSOR REMARK 3 T11: 0.0979 T22: 0.0683 REMARK 3 T33: 0.1001 T12: 0.0176 REMARK 3 T13: -0.0105 T23: 0.0037 REMARK 3 L TENSOR REMARK 3 L11: 1.3671 L22: 0.9882 REMARK 3 L33: 2.1271 L12: -0.5263 REMARK 3 L13: -1.0153 L23: 0.4777 REMARK 3 S TENSOR REMARK 3 S11: -0.0689 S12: -0.0068 S13: -0.0898 REMARK 3 S21: 0.0463 S22: -0.0101 S23: -0.0585 REMARK 3 S31: 0.1477 S32: 0.1256 S33: 0.0672 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 119 THROUGH 158 ) REMARK 3 ORIGIN FOR THE GROUP (A): -11.9396 -0.2638 17.2917 REMARK 3 T TENSOR REMARK 3 T11: 0.0626 T22: 0.0684 REMARK 3 T33: 0.0746 T12: 0.0070 REMARK 3 T13: -0.0054 T23: 0.0051 REMARK 3 L TENSOR REMARK 3 L11: 0.8996 L22: 0.7137 REMARK 3 L33: 0.9419 L12: 0.0201 REMARK 3 L13: -0.2115 L23: -0.3709 REMARK 3 S TENSOR REMARK 3 S11: -0.0107 S12: 0.0190 S13: 0.0111 REMARK 3 S21: -0.0605 S22: 0.0147 S23: 0.0662 REMARK 3 S31: 0.0370 S32: -0.0466 S33: -0.0184 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 6Y4F COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 20-FEB-20. REMARK 100 THE DEPOSITION ID IS D_1292106740. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 07-NOV-12 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ESRF REMARK 200 BEAMLINE : ID23-1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.972 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 12317 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.750 REMARK 200 RESOLUTION RANGE LOW (A) : 19.050 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.0 REMARK 200 DATA REDUNDANCY : 6.300 REMARK 200 R MERGE (I) : 0.10800 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 12.7000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.75 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.81 REMARK 200 COMPLETENESS FOR SHELL (%) : 93.8 REMARK 200 DATA REDUNDANCY IN SHELL : 6.40 REMARK 200 R MERGE FOR SHELL (I) : 0.56300 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.120 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: 6Y4E REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 32.80 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.83 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: MORPHEUS HT SCREEN (MOLECULAR REMARK 280 DIMENSIONS, UK) CONDITION D9 (0.02 M 1,6-HEXANEDIOL, 0.02 M 1- REMARK 280 BUTANOL, 0.02 M 1,2-PROPANEDIOL, 0.02 M 2-PROPANOL, 0.02 M 1,4- REMARK 280 BUTANEDIOL, 0.02 M 1,3-PROPANEDIOL, 0.1 M BICINE/TRIZMA BASE PH REMARK 280 8.5, 10% W/V PEG 20000 AND 20% V/V PEG MME 550), VAPOR DIFFUSION, REMARK 280 SITTING DROP, TEMPERATURE 293K 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 13.32750 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 39.98200 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 27.24500 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 39.98200 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 13.32750 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 27.24500 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 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 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 VAL A 159 REMARK 465 HIS A 160 REMARK 465 HIS A 161 REMARK 465 HIS A 162 REMARK 465 HIS A 163 REMARK 465 HIS A 164 REMARK 465 HIS A 165 REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 201 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 72 NE2 REMARK 620 2 HIS A 74 ND1 129.4 REMARK 620 3 HIS A 117 ND1 109.2 100.2 REMARK 620 4 GLU A 202 OE2 110.0 100.9 104.6 REMARK 620 N 1 2 3 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ZN A 201 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GLU A 202 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 6Y4E RELATED DB: PDB DBREF 6Y4F A 25 159 UNP B4EUK6 B4EUK6_PROMH 25 159 SEQADV 6Y4F HIS A 160 UNP B4EUK6 EXPRESSION TAG SEQADV 6Y4F HIS A 161 UNP B4EUK6 EXPRESSION TAG SEQADV 6Y4F HIS A 162 UNP B4EUK6 EXPRESSION TAG SEQADV 6Y4F HIS A 163 UNP B4EUK6 EXPRESSION TAG SEQADV 6Y4F HIS A 164 UNP B4EUK6 EXPRESSION TAG SEQADV 6Y4F HIS A 165 UNP B4EUK6 EXPRESSION TAG SEQRES 1 A 141 SER ILE PHE SER TYR ILE THR GLU SER THR GLY THR PRO SEQRES 2 A 141 SER ASN ALA THR TYR THR TYR VAL ILE GLU ARG TRP ASP SEQRES 3 A 141 PRO GLU THR SER GLY ILE LEU ASN PRO CYS TYR GLY TRP SEQRES 4 A 141 PRO VAL CYS TYR VAL THR VAL ASN HIS LYS HIS THR VAL SEQRES 5 A 141 ASN GLY THR GLY GLY ASN PRO ALA PHE GLN ILE ALA ARG SEQRES 6 A 141 ILE GLU LYS LEU ARG THR LEU ALA GLU VAL ARG ASP VAL SEQRES 7 A 141 VAL LEU LYS ASN ARG SER PHE PRO ILE GLU GLY GLN THR SEQRES 8 A 141 THR HIS ARG GLY PRO SER LEU ASN SER ASN GLN GLU CYS SEQRES 9 A 141 VAL GLY LEU PHE TYR GLN PRO ASN SER SER GLY ILE SER SEQRES 10 A 141 PRO ARG GLY LYS LEU LEU PRO GLY SER LEU CYS GLY ILE SEQRES 11 A 141 ALA PRO PRO PRO VAL HIS HIS HIS HIS HIS HIS HET ZN A 201 1 HET GLU A 202 18 HETNAM ZN ZINC ION HETNAM GLU GLUTAMIC ACID FORMUL 2 ZN ZN 2+ FORMUL 3 GLU C5 H9 N O4 FORMUL 4 HOH *183(H2 O) HELIX 1 AA1 THR A 95 ARG A 107 1 13 HELIX 2 AA2 ASN A 123 GLU A 127 5 5 SHEET 1 AA1 4 ILE A 111 ARG A 118 0 SHEET 2 AA1 4 ASN A 39 TRP A 49 -1 N ILE A 46 O ILE A 111 SHEET 3 AA1 4 ILE A 26 GLY A 35 -1 N PHE A 27 O ARG A 48 SHEET 4 AA1 4 SER A 150 CYS A 152 1 O LEU A 151 N ILE A 26 SHEET 1 AA2 4 PHE A 85 ARG A 89 0 SHEET 2 AA2 4 TYR A 67 HIS A 72 -1 N VAL A 68 O ILE A 87 SHEET 3 AA2 4 VAL A 129 GLN A 134 -1 O GLN A 134 N TYR A 67 SHEET 4 AA2 4 LYS A 145 LEU A 146 -1 O LYS A 145 N TYR A 133 SSBOND 1 CYS A 60 CYS A 66 1555 1555 2.03 SSBOND 2 CYS A 128 CYS A 152 1555 1555 2.03 LINK NE2 HIS A 72 ZN ZN A 201 1555 1555 2.21 LINK ND1 HIS A 74 ZN ZN A 201 1555 1555 2.23 LINK ND1 HIS A 117 ZN ZN A 201 1555 1555 2.24 LINK ZN ZN A 201 OE2 GLU A 202 1555 1555 1.96 CISPEP 1 PHE A 109 PRO A 110 0 -0.51 SITE 1 AC1 4 HIS A 72 HIS A 74 HIS A 117 GLU A 202 SITE 1 AC2 12 THR A 53 HIS A 72 HIS A 74 GLY A 81 SITE 2 AC2 12 ASN A 82 HIS A 117 ARG A 118 ILE A 140 SITE 3 AC2 12 ZN A 201 HOH A 305 HOH A 346 HOH A 404 CRYST1 26.655 54.490 79.964 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 0.037516 0.000000 0.000000 0.00000 SCALE2 0.000000 0.018352 0.000000 0.00000 SCALE3 0.000000 0.000000 0.012506 0.00000