HEADER TRANSCRIPTION 14-FEB-11 3QPS TITLE CRYSTAL STRUCTURES OF CMER-BILE ACID COMPLEXES FROM CAMPYLOBACTER TITLE 2 JEJUNI COMPND MOL_ID: 1; COMPND 2 MOLECULE: CMER; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: TRANSCRIPTIONAL REPRESSOR; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: CAMPYLOBACTER JEJUNI; SOURCE 3 ORGANISM_TAXID: 197; SOURCE 4 GENE: CMER, CMER; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS ALPHA-HELICAL, HELIX-TURN-HELIX, DNA-BINDING, TRANSCRIPTION KEYWDS 2 REGULATION, TRANSCRIPTION REPRESSOR, DRUG BINDING, TRANSCRIPTION EXPDTA X-RAY DIFFRACTION AUTHOR H.T.LEI,M.D.ROUTH,Z.SHEN,C.C.SU,Q.ZHANG,E.W.YU REVDAT 5 13-SEP-23 3QPS 1 REMARK SEQADV REVDAT 4 15-OCT-14 3QPS 1 AUTHOR REVDAT 3 29-FEB-12 3QPS 1 JRNL VERSN REVDAT 2 16-MAR-11 3QPS 1 REMARK REVDAT 1 09-MAR-11 3QPS 0 JRNL AUTH H.T.LEI,Z.SHEN,P.SURANA,M.D.ROUTH,C.C.SU,Q.ZHANG,E.W.YU JRNL TITL CRYSTAL STRUCTURES OF CMER-BILE ACID COMPLEXES FROM JRNL TITL 2 CAMPYLOBACTER JEJUNI. JRNL REF PROTEIN SCI. V. 20 712 2011 JRNL REFN ISSN 0961-8368 JRNL PMID 21328631 JRNL DOI 10.1002/PRO.602 REMARK 2 REMARK 2 RESOLUTION. 2.35 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 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) : 2.35 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 31.38 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 0.170 REMARK 3 COMPLETENESS FOR RANGE (%) : 92.6 REMARK 3 NUMBER OF REFLECTIONS : 8288 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.204 REMARK 3 R VALUE (WORKING SET) : 0.201 REMARK 3 FREE R VALUE : 0.263 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.790 REMARK 3 FREE R VALUE TEST SET COUNT : 397 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (IN BINS). REMARK 3 BIN RESOLUTION RANGE COMPL. NWORK NFREE RWORK RFREE REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.11 REMARK 3 SHRINKAGE RADIUS : 0.90 REMARK 3 K_SOL : 0.36 REMARK 3 B_SOL : 51.49 REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.340 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 25.900 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 43.24 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -2.44380 REMARK 3 B22 (A**2) : 1.70240 REMARK 3 B33 (A**2) : 0.74140 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 : 0.009 1748 REMARK 3 ANGLE : 1.377 2366 REMARK 3 CHIRALITY : 0.086 269 REMARK 3 PLANARITY : 0.004 287 REMARK 3 DIHEDRAL : 22.357 666 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 3QPS COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 15-FEB-11. REMARK 100 THE DEPOSITION ID IS D_1000063949. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 02-NOV-10 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 24-ID-E REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9792 REMARK 200 MONOCHROMATOR : DOUBLE CRYSTAL SI(111) REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 16126 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.350 REMARK 200 RESOLUTION RANGE LOW (A) : 40.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 2.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.4 REMARK 200 DATA REDUNDANCY : 3.200 REMARK 200 R MERGE (I) : 0.06300 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 11.0000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.35 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.43 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.2 REMARK 200 DATA REDUNDANCY IN SHELL : 3.20 REMARK 200 R MERGE FOR SHELL (I) : 0.42100 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> 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: PDB ENTRY 2QCO REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 39.16 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.02 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 30 % PEG 3350, 0.1 M TRIS, PH 8.0, REMARK 280 0.16M MGCL2, VAPOR DIFFUSION, TEMPERATURE 298K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 2 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 46.97750 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 18.68500 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 46.97750 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 18.68500 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: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 5720 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 19760 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -29.0 KCAL/MOL 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 350 BIOMT1 2 -1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 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 A -5 REMARK 465 HIS A -4 REMARK 465 HIS A -3 REMARK 465 HIS A -2 REMARK 465 HIS A -1 REMARK 465 HIS A 0 REMARK 465 MET A 1 REMARK 465 ASN A 2 REMARK 465 SER A 3 REMARK 465 ASN A 4 REMARK 465 ARG A 5 REMARK 465 SER A 208 REMARK 465 LYS A 209 REMARK 465 ALA A 210 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 SER A 48 -85.83 -94.81 REMARK 500 GLU A 82 47.35 -69.58 REMARK 500 ASN A 133 47.37 -160.06 REMARK 500 ASN A 150 45.54 -74.86 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 CHD A 211 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3QQA RELATED DB: PDB REMARK 900 RELATED ID: 3OQU RELATED DB: PDB DBREF 3QPS A 1 210 UNP Q7B8P6 Q7B8P6_CAMJE 1 210 SEQADV 3QPS HIS A -5 UNP Q7B8P6 EXPRESSION TAG SEQADV 3QPS HIS A -4 UNP Q7B8P6 EXPRESSION TAG SEQADV 3QPS HIS A -3 UNP Q7B8P6 EXPRESSION TAG SEQADV 3QPS HIS A -2 UNP Q7B8P6 EXPRESSION TAG SEQADV 3QPS HIS A -1 UNP Q7B8P6 EXPRESSION TAG SEQADV 3QPS HIS A 0 UNP Q7B8P6 EXPRESSION TAG SEQRES 1 A 216 HIS HIS HIS HIS HIS HIS MET ASN SER ASN ARG THR PRO SEQRES 2 A 216 SER GLN LYS VAL LEU ALA ARG GLN GLU LYS ILE LYS ALA SEQRES 3 A 216 VAL ALA LEU GLU LEU PHE LEU THR LYS GLY TYR GLN GLU SEQRES 4 A 216 THR SER LEU SER ASP ILE ILE LYS LEU SER GLY GLY SER SEQRES 5 A 216 TYR SER ASN ILE TYR ASP GLY PHE LYS SER LYS GLU GLY SEQRES 6 A 216 LEU PHE PHE GLU ILE LEU ASP ASP ILE CYS LYS LYS HIS SEQRES 7 A 216 PHE HIS LEU ILE TYR SER LYS THR GLN GLU ILE LYS ASN SEQRES 8 A 216 GLY THR LEU LYS GLU ILE LEU THR SER PHE GLY LEU ALA SEQRES 9 A 216 PHE ILE GLU ILE PHE ASN GLN PRO GLU ALA VAL ALA PHE SEQRES 10 A 216 GLY LYS ILE ILE TYR SER GLN VAL TYR ASP LYS ASP ARG SEQRES 11 A 216 HIS LEU ALA ASN TRP ILE GLU ASN ASN GLN GLN ASN PHE SEQRES 12 A 216 SER TYR ASN ILE LEU MET GLY PHE PHE LYS GLN GLN ASN SEQRES 13 A 216 ASN SER TYR MET LYS LYS ASN ALA GLU LYS LEU ALA VAL SEQRES 14 A 216 LEU PHE CYS THR MET LEU LYS GLU PRO TYR HIS HIS LEU SEQRES 15 A 216 ASN VAL LEU ILE ASN ALA PRO LEU LYS ASN LYS LYS GLU SEQRES 16 A 216 GLN LYS GLU HIS VAL GLU PHE VAL VAL ASN VAL PHE LEU SEQRES 17 A 216 ASN GLY ILE ASN SER SER LYS ALA HET CHD A 211 29 HETNAM CHD CHOLIC ACID FORMUL 2 CHD C24 H40 O5 FORMUL 3 HOH *50(H2 O) HELIX 1 1 THR A 6 LYS A 29 1 24 HELIX 2 2 SER A 35 GLY A 44 1 10 HELIX 3 3 GLY A 45 TYR A 47 5 3 HELIX 4 4 SER A 56 GLU A 82 1 27 HELIX 5 5 THR A 87 ASN A 104 1 18 HELIX 6 6 GLN A 105 GLN A 118 1 14 HELIX 7 7 ARG A 124 ASN A 132 1 9 HELIX 8 8 ASN A 133 PHE A 137 5 5 HELIX 9 9 SER A 138 GLN A 148 1 11 HELIX 10 10 ASN A 151 ASN A 157 1 7 HELIX 11 11 ASN A 157 GLU A 171 1 15 HELIX 12 12 PRO A 172 ASN A 181 1 10 HELIX 13 13 ASN A 186 GLY A 204 1 19 CISPEP 1 GLU A 171 PRO A 172 0 7.15 SITE 1 AC1 10 LEU A 65 ALA A 108 GLY A 112 TRP A 129 SITE 2 AC1 10 PHE A 137 CYS A 166 HIS A 175 HOH A 249 SITE 3 AC1 10 HOH A 253 HOH A 261 CRYST1 93.955 37.370 57.792 90.00 90.00 90.00 P 21 21 2 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 0.010643 0.000000 0.000000 0.00000 SCALE2 0.000000 0.026759 0.000000 0.00000 SCALE3 0.000000 0.000000 0.017303 0.00000