HEADER TRANSCRIPTION 15-FEB-11 3QQA 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 3 21-FEB-24 3QQA 1 REMARK SEQADV REVDAT 2 29-FEB-12 3QQA 1 JRNL VERSN REVDAT 1 16-MAR-11 3QQA 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. 2.20 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) : 2.20 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 31.59 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 0.210 REMARK 3 COMPLETENESS FOR RANGE (%) : 95.0 REMARK 3 NUMBER OF REFLECTIONS : 10457 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.225 REMARK 3 R VALUE (WORKING SET) : 0.222 REMARK 3 FREE R VALUE : 0.284 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.830 REMARK 3 FREE R VALUE TEST SET COUNT : 505 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 31.5976 - 3.4848 0.96 2641 134 0.2049 0.2513 REMARK 3 2 3.4848 - 2.7665 0.97 2522 128 0.2304 0.3157 REMARK 3 3 2.7665 - 2.4170 0.96 2468 126 0.2429 0.3103 REMARK 3 4 2.4170 - 2.1960 0.91 2321 117 0.2524 0.3489 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 : 0.35 REMARK 3 B_SOL : 56.42 REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.400 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 28.380 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) : -2.14600 REMARK 3 B22 (A**2) : 3.50220 REMARK 3 B33 (A**2) : -1.35620 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 : 0.006 1708 REMARK 3 ANGLE : 1.069 2305 REMARK 3 CHIRALITY : 0.069 257 REMARK 3 PLANARITY : 0.003 285 REMARK 3 DIHEDRAL : 19.405 640 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 3QQA COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 17-FEB-11. REMARK 100 THE DEPOSITION ID IS D_1000063967. 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) : 298 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 : 10812 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.200 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 2.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.2 REMARK 200 DATA REDUNDANCY : 4.700 REMARK 200 R MERGE (I) : 0.04500 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 16.0000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.20 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.28 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.8 REMARK 200 DATA REDUNDANCY IN SHELL : 4.80 REMARK 200 R MERGE FOR SHELL (I) : 0.25500 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: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 39.68 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.04 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 30 % PEG3350, 0.1 M TRIS, AND 0.16 M REMARK 280 MGCL2, PH 8.0, 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 46.99600 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 18.88700 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 46.99600 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 18.88700 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: 5840 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 19850 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -34.0 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 -37.77400 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 ASN A 206 REMARK 465 SER A 207 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: COVALENT BOND LENGTHS REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 RES CSSEQI ATM2 DEVIATION REMARK 500 LYS A 170 CE LYS A 170 NZ 0.151 REMARK 500 REMARK 500 REMARK: NULL 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 ASN A 49 -21.67 76.09 REMARK 500 ILE A 50 -72.21 -90.63 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 TCH A 211 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3QPS RELATED DB: PDB REMARK 900 RELATED ID: 3OQU RELATED DB: PDB DBREF 3QQA A 1 210 UNP Q7B8P6 Q7B8P6_CAMJE 1 210 SEQADV 3QQA HIS A -5 UNP Q7B8P6 EXPRESSION TAG SEQADV 3QQA HIS A -4 UNP Q7B8P6 EXPRESSION TAG SEQADV 3QQA HIS A -3 UNP Q7B8P6 EXPRESSION TAG SEQADV 3QQA HIS A -2 UNP Q7B8P6 EXPRESSION TAG SEQADV 3QQA HIS A -1 UNP Q7B8P6 EXPRESSION TAG SEQADV 3QQA 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 TCH A 211 35 HETNAM TCH TAUROCHOLIC ACID FORMUL 2 TCH C26 H45 N O7 S FORMUL 3 HOH *54(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 SER A 56 ILE A 83 1 28 HELIX 4 4 THR A 87 ASN A 104 1 18 HELIX 5 5 GLN A 105 GLN A 118 1 14 HELIX 6 6 ARG A 124 ASN A 133 1 10 HELIX 7 7 GLN A 134 PHE A 137 5 4 HELIX 8 8 SER A 138 GLN A 149 1 12 HELIX 9 9 ASN A 151 ASN A 157 1 7 HELIX 10 10 ASN A 157 GLU A 171 1 15 HELIX 11 11 PRO A 172 ASN A 181 1 10 HELIX 12 12 ASN A 186 GLY A 204 1 19 CISPEP 1 GLU A 171 PRO A 172 0 3.45 SITE 1 AC1 7 TYR A 51 HIS A 72 PHE A 103 ALA A 108 SITE 2 AC1 7 GLN A 134 HIS A 175 HOH A 257 CRYST1 93.992 37.774 57.642 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 0.010639 0.000000 0.000000 0.00000 SCALE2 0.000000 0.026473 0.000000 0.00000 SCALE3 0.000000 0.000000 0.017348 0.00000