HEADER HYDROLASE 22-MAR-16 5IWH TITLE STRUCTURE OF P. VULGARIS HIGB TOXIN DELTA H92 COMPND MOL_ID: 1; COMPND 2 MOLECULE: ENDORIBONUCLEASE HIGB; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: HOST INHIBITION OF GROWTH PROTEIN B,KILLER PROTEIN,TOXIN COMPND 5 HIGB,MRNA INTERFERASE HIGB; COMPND 6 EC: 3.1.-.-; COMPND 7 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: PROTEUS VULGARIS; SOURCE 3 ORGANISM_TAXID: 585; SOURCE 4 VARIANT: DELTA H92; SOURCE 5 GENE: HIGB; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI BW25113; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 679895 KEYWDS BACTERIAL TOXINS, BIOFILMS, CELL METABOLISM, ENERGY METABOLISM, KEYWDS 2 MICROBIAL PATHOGENESIS, STRESS RESPONSE, STRINGENT RESPONSE, KEYWDS 3 TRANSLATION CONTROL, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR M.A.SCHURECK,A.A.REPACK,S.J.MILES,J.MARQUEZ,C.M.DUNHAM REVDAT 3 27-SEP-23 5IWH 1 JRNL REMARK REVDAT 2 05-OCT-16 5IWH 1 JRNL REVDAT 1 20-JUL-16 5IWH 0 JRNL AUTH M.A.SCHURECK,A.REPACK,S.J.MILES,J.MARQUEZ,C.M.DUNHAM JRNL TITL MECHANISM OF ENDONUCLEASE CLEAVAGE BY THE HIGB TOXIN. JRNL REF NUCLEIC ACIDS RES. V. 44 7944 2016 JRNL REFN ESSN 1362-4962 JRNL PMID 27378776 JRNL DOI 10.1093/NAR/GKW598 REMARK 2 REMARK 2 RESOLUTION. 1.10 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.8.3_1479 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) : 1.10 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 14.97 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 94.7 REMARK 3 NUMBER OF REFLECTIONS : 32734 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.140 REMARK 3 R VALUE (WORKING SET) : 0.138 REMARK 3 FREE R VALUE : 0.169 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.630 REMARK 3 FREE R VALUE TEST SET COUNT : 1843 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 14.9753 - 2.5850 0.74 1923 120 0.1804 0.1942 REMARK 3 2 2.5850 - 2.0534 0.93 2360 134 0.1453 0.1584 REMARK 3 3 2.0534 - 1.7944 0.96 2390 149 0.1322 0.1867 REMARK 3 4 1.7944 - 1.6305 0.96 2415 142 0.1234 0.1661 REMARK 3 5 1.6305 - 1.5138 0.97 2428 146 0.1136 0.1570 REMARK 3 6 1.5138 - 1.4246 0.97 2435 146 0.1156 0.1760 REMARK 3 7 1.4246 - 1.3533 0.97 2414 146 0.1132 0.1570 REMARK 3 8 1.3533 - 1.2944 0.97 2425 150 0.1191 0.1431 REMARK 3 9 1.2944 - 1.2446 0.97 2421 140 0.1181 0.1424 REMARK 3 10 1.2446 - 1.2017 0.97 2420 146 0.1231 0.1577 REMARK 3 11 1.2017 - 1.1641 0.97 2440 149 0.1211 0.1508 REMARK 3 12 1.1641 - 1.1309 0.97 2435 148 0.1316 0.1532 REMARK 3 13 1.1309 - 1.1011 0.96 2385 127 0.1433 0.1621 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) : 0.080 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 14.590 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 : 0.011 924 REMARK 3 ANGLE : 1.481 1261 REMARK 3 CHIRALITY : 0.069 129 REMARK 3 PLANARITY : 0.008 165 REMARK 3 DIHEDRAL : 13.681 363 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 5IWH COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 24-MAR-16. REMARK 100 THE DEPOSITION ID IS D_1000219527. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 07-JUL-12 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 22-ID REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.0 REMARK 200 MONOCHROMATOR : CRYOGENICALLY-COOLED SI-220 REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARMOSAIC 300 MM CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 32761 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.100 REMARK 200 RESOLUTION RANGE LOW (A) : 15.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 94.7 REMARK 200 DATA REDUNDANCY : 2.000 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 20.7000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.10 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.14 REMARK 200 COMPLETENESS FOR SHELL (%) : 96.7 REMARK 200 DATA REDUNDANCY IN SHELL : 2.00 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 9.300 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: 4PX8 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 22.32 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.58 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 30-40% W/V POLYETHYLENE GLYCOL REMARK 280 MONOMETHYLETHER 2,000 AND 0.15 M KBR, PH 7.5, VAPOR DIFFUSION, REMARK 280 SITTING DROP, TEMPERATURE 293.15K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 1 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,Y,-Z REMARK 290 3555 X+1/2,Y+1/2,Z 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 0.00000 REMARK 290 SMTRY2 2 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 3 1.000000 0.000000 0.000000 27.88800 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 16.58300 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 27.88800 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 16.58300 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 375 REMARK 375 SPECIAL POSITION REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL REMARK 375 POSITIONS. REMARK 375 REMARK 375 ATOM RES CSSEQI REMARK 375 HOH A 340 LIES ON A SPECIAL POSITION. 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 0 REMARK 465 LYS A 98 REMARK 465 LEU A 99 REMARK 465 ILE A 100 REMARK 465 SER A 101 REMARK 465 GLU A 102 REMARK 465 GLU A 103 REMARK 465 ASP A 104 REMARK 465 LEU A 105 REMARK 465 ASN A 106 REMARK 465 SER A 107 REMARK 465 ALA A 108 REMARK 465 VAL A 109 REMARK 465 ASP A 110 REMARK 465 HIS A 111 REMARK 465 HIS A 112 REMARK 465 HIS A 113 REMARK 465 HIS A 114 REMARK 465 HIS A 115 REMARK 465 HIS A 116 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 ALA A 70 -124.83 50.06 REMARK 500 REMARK 500 REMARK: NULL REMARK 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH A 417 DISTANCE = 7.02 ANGSTROMS REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue CL A 201 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue CL A 202 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4PX8 RELATED DB: PDB REMARK 900 RELATED ID: 4W4G RELATED DB: PDB REMARK 900 RELATED ID: 4YPB RELATED DB: PDB REMARK 900 RELATED ID: 4YZV RELATED DB: PDB REMARK 900 RELATED ID: 4MCT RELATED DB: PDB REMARK 900 RELATED ID: 4MCX RELATED DB: PDB REMARK 900 RELATED ID: 5IXL RELATED DB: PDB DBREF 5IWH A 2 91 UNP Q7A225 HIGB_PROVU 2 91 SEQADV 5IWH MET A 0 UNP Q7A225 INITIATING METHIONINE SEQADV 5IWH GLY A 1 UNP Q7A225 EXPRESSION TAG SEQADV 5IWH LYS A 92 UNP Q7A225 EXPRESSION TAG SEQADV 5IWH LEU A 93 UNP Q7A225 EXPRESSION TAG SEQADV 5IWH GLY A 94 UNP Q7A225 EXPRESSION TAG SEQADV 5IWH PRO A 95 UNP Q7A225 EXPRESSION TAG SEQADV 5IWH GLU A 96 UNP Q7A225 EXPRESSION TAG SEQADV 5IWH GLN A 97 UNP Q7A225 EXPRESSION TAG SEQADV 5IWH LYS A 98 UNP Q7A225 EXPRESSION TAG SEQADV 5IWH LEU A 99 UNP Q7A225 EXPRESSION TAG SEQADV 5IWH ILE A 100 UNP Q7A225 EXPRESSION TAG SEQADV 5IWH SER A 101 UNP Q7A225 EXPRESSION TAG SEQADV 5IWH GLU A 102 UNP Q7A225 EXPRESSION TAG SEQADV 5IWH GLU A 103 UNP Q7A225 EXPRESSION TAG SEQADV 5IWH ASP A 104 UNP Q7A225 EXPRESSION TAG SEQADV 5IWH LEU A 105 UNP Q7A225 EXPRESSION TAG SEQADV 5IWH ASN A 106 UNP Q7A225 EXPRESSION TAG SEQADV 5IWH SER A 107 UNP Q7A225 EXPRESSION TAG SEQADV 5IWH ALA A 108 UNP Q7A225 EXPRESSION TAG SEQADV 5IWH VAL A 109 UNP Q7A225 EXPRESSION TAG SEQADV 5IWH ASP A 110 UNP Q7A225 EXPRESSION TAG SEQADV 5IWH HIS A 111 UNP Q7A225 EXPRESSION TAG SEQADV 5IWH HIS A 112 UNP Q7A225 EXPRESSION TAG SEQADV 5IWH HIS A 113 UNP Q7A225 EXPRESSION TAG SEQADV 5IWH HIS A 114 UNP Q7A225 EXPRESSION TAG SEQADV 5IWH HIS A 115 UNP Q7A225 EXPRESSION TAG SEQADV 5IWH HIS A 116 UNP Q7A225 EXPRESSION TAG SEQRES 1 A 117 MET GLY ILE LYS SER PHE LYS HIS LYS GLY LEU LYS LEU SEQRES 2 A 117 LEU PHE GLU LYS GLY VAL THR SER GLY VAL PRO ALA GLN SEQRES 3 A 117 ASP VAL ASP ARG ILE ASN ASP ARG LEU GLN ALA ILE ASP SEQRES 4 A 117 THR ALA THR GLU ILE GLY GLU LEU ASN ARG GLN ILE TYR SEQRES 5 A 117 LYS LEU HIS PRO LEU LYS GLY ASP ARG GLU GLY TYR TRP SEQRES 6 A 117 SER ILE THR VAL ARG ALA ASN TRP ARG ILE THR PHE GLN SEQRES 7 A 117 PHE ILE ASN GLY ASP ALA TYR ILE LEU ASN TYR GLU ASP SEQRES 8 A 117 TYR LYS LEU GLY PRO GLU GLN LYS LEU ILE SER GLU GLU SEQRES 9 A 117 ASP LEU ASN SER ALA VAL ASP HIS HIS HIS HIS HIS HIS HET CL A 201 1 HET CL A 202 1 HETNAM CL CHLORIDE ION FORMUL 2 CL 2(CL 1-) FORMUL 4 HOH *117(H2 O) HELIX 1 AA1 HIS A 7 GLY A 17 1 11 HELIX 2 AA2 PRO A 23 GLN A 25 5 3 HELIX 3 AA3 ASP A 26 ALA A 40 1 15 HELIX 4 AA4 GLU A 42 ASN A 47 5 6 HELIX 5 AA5 ARG A 48 LYS A 52 5 5 HELIX 6 AA6 LYS A 57 GLU A 61 5 5 SHEET 1 AA1 4 HIS A 54 PRO A 55 0 SHEET 2 AA1 4 TYR A 63 ARG A 69 -1 O SER A 65 N HIS A 54 SHEET 3 AA1 4 TRP A 72 ILE A 79 -1 O TRP A 72 N VAL A 68 SHEET 4 AA1 4 ASP A 82 ASP A 90 -1 O TYR A 84 N GLN A 77 SITE 1 AC1 3 SER A 4 PHE A 5 LYS A 11 SITE 1 AC2 4 LYS A 16 GLU A 42 ILE A 43 HOH A 389 CRYST1 55.776 33.166 51.492 90.00 115.49 90.00 C 1 2 1 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 0.017929 0.000000 0.008549 0.00000 SCALE2 0.000000 0.030151 0.000000 0.00000 SCALE3 0.000000 0.000000 0.021515 0.00000