HEADER DNA BINDING PROTEIN 13-MAY-21 7MTT TITLE CRYSTAL STRUCTURE OF COLIBACTIN SELF-RESISTANCE PROTEIN CLBS IN TITLE 2 COMPLEX WITH TWO MOLECULES OF CHES COMPND MOL_ID: 1; COMPND 2 MOLECULE: COLIBACTIN SELF-PROTECTION PROTEIN CLBS; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ESCHERICHIA COLI; SOURCE 3 ORGANISM_TAXID: 562; SOURCE 4 GENE: CLBS, APU18_08100, AWF59_018730, AZZ83_004503, CT146_21495, SOURCE 5 CUB99_02165, D3C88_24730, DNR41_00045, DNX30_29170, DS966_21615, SOURCE 6 DU333_02935, DW236_02620, ELT23_23590, ELT33_24270, EPS70_02685, SOURCE 7 EPS94_00180, EWK56_23755, FPI65_12320, FQU83_11985, GFU47_04510, SOURCE 8 GP945_05010, GP946_20500, HHG54_004716, HHJ44_00090, HJL93_000008, SOURCE 9 HJM41_001166, HJO44_004707, HJS53_002303, HMCMSJML146_00176, SOURCE 10 HNX34_25610, HV055_09710, HV098_09980, HV348_09415, NCTC9075_02752, SOURCE 11 NCTC9434_01964; SOURCE 12 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 13 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS HYDROLASE, DNA REPAIR, DNA BINDING PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR P.TRIPATHI,S.D.BRUNER REVDAT 3 18-OCT-23 7MTT 1 REMARK REVDAT 2 09-JUN-21 7MTT 1 JRNL REVDAT 1 26-MAY-21 7MTT 0 JRNL AUTH P.TRIPATHI,S.D.BRUNER JRNL TITL STRUCTURAL BASIS FOR THE INTERACTIONS OF THE COLIBACTIN JRNL TITL 2 RESISTANCE GENE PRODUCT CLBS WITH DNA. JRNL REF BIOCHEMISTRY V. 60 1619 2021 JRNL REFN ISSN 0006-2960 JRNL PMID 33945270 JRNL DOI 10.1021/ACS.BIOCHEM.1C00201 REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH P.TRIPATHI,S.D.BRUNER REMARK 1 TITL CLBS IS A CYCLOPROPANE HYDROLASE THAT CONFERS COLIBACTIN REMARK 1 TITL 2 RESISTANCE REMARK 1 REF JOURNAL OF AMERICAN CHEMICAL 2017 REMARK 1 REF 2 SOCIETY REMARK 1 REFN ESSN 1520-5126 REMARK 1 PMID 29112397 REMARK 1 DOI 10.1021/JACS.7B09971 REMARK 2 REMARK 2 RESOLUTION. 1.85 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.18.2-3874 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 : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.85 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 44.62 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.4 REMARK 3 NUMBER OF REFLECTIONS : 16871 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.192 REMARK 3 R VALUE (WORKING SET) : 0.190 REMARK 3 FREE R VALUE : 0.231 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.200 REMARK 3 FREE R VALUE TEST SET COUNT : 934 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 1.8970 - 1.8500 0.97 1198 66 0.2650 0.3320 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : MASK REMARK 3 SOLVENT RADIUS : 1.20 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 K_SOL : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.096 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : NULL REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 36.13 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 1.10000 REMARK 3 B22 (A**2) : -3.00000 REMARK 3 B33 (A**2) : 1.91000 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 : NULL NULL REMARK 3 ANGLE : NULL NULL REMARK 3 CHIRALITY : NULL NULL REMARK 3 PLANARITY : NULL NULL REMARK 3 DIHEDRAL : NULL NULL 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: HYDROGENS HAVE BEEN ADDED IN THE RIDING REMARK 3 POSITIONS U VALUES : REFINED INDIVIDUALLY REMARK 4 REMARK 4 7MTT COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 14-MAY-21. REMARK 100 THE DEPOSITION ID IS D_1000256868. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 05-DEC-19 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 : APS REMARK 200 BEAMLINE : 21-ID-G REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.033 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARMOSAIC 300 MM CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : AIMLESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 17844 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.850 REMARK 200 RESOLUTION RANGE LOW (A) : 44.620 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.6 REMARK 200 DATA REDUNDANCY : 6.400 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 19.4000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.85 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.92 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: PHASER REMARK 200 STARTING MODEL: 6ANR REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 52.13 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.57 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M CHES, PH 9.5, AND 20% (W/V) PEG REMARK 280 8000, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 277K 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 25.27250 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 33.24850 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 30.08650 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 33.24850 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 25.27250 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 30.08650 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 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 MET A 1 REMARK 465 LEU A 171 REMARK 465 GLU A 172 REMARK 465 HIS A 173 REMARK 465 HIS A 174 REMARK 465 HIS A 175 REMARK 465 HIS A 176 REMARK 465 HIS A 177 REMARK 465 HIS A 178 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 TRP A 136 -51.61 -129.98 REMARK 500 ASN A 138 -123.05 46.51 REMARK 500 THR A 150 -85.27 -129.50 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 NHE A 201 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue NHE A 202 DBREF 7MTT A 1 170 UNP Q0P7K8 Q0P7K8_ECOLX 1 170 SEQADV 7MTT LEU A 171 UNP Q0P7K8 EXPRESSION TAG SEQADV 7MTT GLU A 172 UNP Q0P7K8 EXPRESSION TAG SEQADV 7MTT HIS A 173 UNP Q0P7K8 EXPRESSION TAG SEQADV 7MTT HIS A 174 UNP Q0P7K8 EXPRESSION TAG SEQADV 7MTT HIS A 175 UNP Q0P7K8 EXPRESSION TAG SEQADV 7MTT HIS A 176 UNP Q0P7K8 EXPRESSION TAG SEQADV 7MTT HIS A 177 UNP Q0P7K8 EXPRESSION TAG SEQADV 7MTT HIS A 178 UNP Q0P7K8 EXPRESSION TAG SEQRES 1 A 178 MET ALA VAL PRO SER SER LYS GLU GLU LEU ILE LYS ALA SEQRES 2 A 178 ILE ASN SER ASN PHE SER LEU LEU ASN LYS LYS LEU GLU SEQRES 3 A 178 SER ILE THR PRO GLN LEU ALA PHE GLU PRO LEU LEU GLU SEQRES 4 A 178 GLY HIS ALA LYS GLY THR THR ILE SER VAL ALA ASN LEU SEQRES 5 A 178 VAL SER TYR LEU ILE GLY TRP GLY GLU LEU VAL LEU HIS SEQRES 6 A 178 TRP HIS ASP GLN GLU ALA LYS GLY LYS THR ILE ILE PHE SEQRES 7 A 178 PRO GLU GLU GLY PHE LYS TRP ASN GLU LEU GLY ARG LEU SEQRES 8 A 178 ALA GLN LYS PHE TYR ARG ASP TYR GLU ASP ILE THR GLU SEQRES 9 A 178 TYR GLU VAL LEU LEU ALA ARG LEU LYS GLU ASN LYS GLN SEQRES 10 A 178 GLN LEU VAL ALA LEU ILE GLU ARG PHE SER ASN ASP GLU SEQRES 11 A 178 LEU TYR GLY LYS PRO TRP TYR ASN LYS TRP THR ARG GLY SEQRES 12 A 178 ARG MET ILE GLN PHE ASN THR ALA SER PRO TYR LYS ASN SEQRES 13 A 178 ALA SER GLY ARG LEU ASN LYS LEU GLN LYS CYS LEU ALA SEQRES 14 A 178 GLU LEU GLU HIS HIS HIS HIS HIS HIS HET NHE A 201 13 HET NHE A 202 13 HETNAM NHE 2-[N-CYCLOHEXYLAMINO]ETHANE SULFONIC ACID HETSYN NHE N-CYCLOHEXYLTAURINE; CHES FORMUL 2 NHE 2(C8 H17 N O3 S) FORMUL 4 HOH *50(H2 O) HELIX 1 AA1 SER A 6 SER A 27 1 22 HELIX 2 AA2 ILE A 28 ALA A 33 5 6 HELIX 3 AA3 SER A 48 LYS A 72 1 25 HELIX 4 AA4 LYS A 84 ASN A 86 5 3 HELIX 5 AA5 GLU A 87 TYR A 99 1 13 HELIX 6 AA6 GLU A 104 ARG A 125 1 22 HELIX 7 AA7 SER A 127 GLY A 133 1 7 HELIX 8 AA8 THR A 141 ASN A 149 1 9 HELIX 9 AA9 THR A 150 LEU A 168 1 19 SHEET 1 AA1 2 LEU A 38 GLU A 39 0 SHEET 2 AA1 2 THR A 46 ILE A 47 -1 O ILE A 47 N LEU A 38 CISPEP 1 PHE A 78 PRO A 79 0 -4.56 SITE 1 AC1 8 GLU A 35 TYR A 55 PHE A 148 ASN A 149 SITE 2 AC1 8 PRO A 153 ASN A 156 HOH A 306 HOH A 313 SITE 1 AC2 3 THR A 29 TRP A 85 PHE A 148 CRYST1 50.545 60.173 66.497 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 0.019784 0.000000 0.000000 0.00000 SCALE2 0.000000 0.016619 0.000000 0.00000 SCALE3 0.000000 0.000000 0.015038 0.00000