HEADER TRANSCRIPTION REPRESSOR, DRUG BINDING 14-MAY-09 3HGY TITLE CRYSTAL STRUCTURE OF CMER BOUND TO TAUROCHOLIC ACID CAVEAT 3HGY RESIDUE TCH HAS INCORRECT STEREOCHEMISTRY AT ATOMS C3, C5, CAVEAT 2 3HGY C9, C17 COMPND MOL_ID: 1; COMPND 2 MOLECULE: CMER; COMPND 3 CHAIN: A SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: CAMPYLOBACTER JEJUNI; SOURCE 3 ORGANISM_TAXID: 197 KEYWDS ALPHA-HELICAL, HELIX-TURN-HELIX, DNA-BINDING, TRANSCRIPTION KEYWDS 2 REGULATION, TRANSCRIPTION REPRESSOR, DRUG BINDING EXPDTA X-RAY DIFFRACTION AUTHOR M.D.ROUTH,F.YANG REVDAT 4 21-FEB-24 3HGY 1 REMARK SEQADV REVDAT 3 01-NOV-17 3HGY 1 REMARK REVDAT 2 14-SEP-11 3HGY 1 CAVEAT VERSN REVDAT 1 30-JUN-10 3HGY 0 JRNL AUTH M.D.ROUTH,F.YANG,C.-C.SU,Q.ZHANG,E.W.YU JRNL TITL STRUCTURAL BASIS FOR ANIONIC LIGAND RECOGNITION BY MULTIDRUG JRNL TITL 2 BINDING PROTEINS: CRYSTAL STRUCTURES OF CMER-BILE ACID JRNL TITL 3 COMPLEXES JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 2.42 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) : 2.42 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 36.36 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 0.070 REMARK 3 COMPLETENESS FOR RANGE (%) : 92.7 REMARK 3 NUMBER OF REFLECTIONS : 7652 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.237 REMARK 3 R VALUE (WORKING SET) : 0.235 REMARK 3 FREE R VALUE : 0.289 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.680 REMARK 3 FREE R VALUE TEST SET COUNT : 358 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 36.3620 - 3.4830 0.96 2606 129 0.2210 0.2610 REMARK 3 2 3.4830 - 2.7650 0.97 2508 120 0.2460 0.3330 REMARK 3 3 2.7650 - 2.4160 0.85 2180 109 0.2840 0.3360 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 : 0.31 REMARK 3 B_SOL : 55.61 REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.420 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : NULL REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 48.77 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 73.15 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -11.34200 REMARK 3 B22 (A**2) : -5.61700 REMARK 3 B33 (A**2) : 16.95900 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 : 0.002 1722 REMARK 3 ANGLE : 0.649 2324 REMARK 3 CHIRALITY : 0.044 259 REMARK 3 PLANARITY : 0.001 288 REMARK 3 DIHEDRAL : 14.206 645 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 1 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: ALL REMARK 3 ORIGIN FOR THE GROUP (A): 13.1239 18.3520 16.2421 REMARK 3 T TENSOR REMARK 3 T11: 0.2948 T22: 0.2798 REMARK 3 T33: 0.3275 T12: 0.0148 REMARK 3 T13: 0.0546 T23: 0.0095 REMARK 3 L TENSOR REMARK 3 L11: 1.2292 L22: 0.6095 REMARK 3 L33: 0.4779 L12: -0.5207 REMARK 3 L13: 0.7639 L23: 0.0345 REMARK 3 S TENSOR REMARK 3 S11: -0.0480 S12: 0.0284 S13: 0.0887 REMARK 3 S21: -0.1114 S22: -0.0777 S23: -0.1817 REMARK 3 S31: -0.0488 S32: 0.2013 S33: -0.0000 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 3HGY COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 19-MAY-09. REMARK 100 THE DEPOSITION ID IS D_1000053121. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 21-FEB-09 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 : APS REMARK 200 BEAMLINE : 24-ID-C REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : .98 REMARK 200 MONOCHROMATOR : DOUBLE CRYSTAL SI(111) REMARK 200 OPTICS : MIRRORS 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 : 8018 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.400 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 4.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.0 REMARK 200 DATA REDUNDANCY : 4.100 REMARK 200 R MERGE (I) : 0.10200 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 10.6850 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.40 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.49 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 4.00 REMARK 200 R MERGE FOR SHELL (I) : 0.46700 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 3.100 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 (%): 41.00 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.08 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 24% PEG 3350, 0.1M TRIS 8.5, 0.1M REMARK 280 MAGNESIUM CHLORIDE, 5% JM600, 20MM SODIUM ACETATE, VAPOR REMARK 280 DIFFUSION, HANGING DROP, TEMPERATURE 298K, PH 8.5 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 46.84500 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 18.74400 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 46.84500 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 18.74400 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: 6170 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 20440 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -28.0 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 37.48800 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: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 OG SER A 35 OD1 ASP A 38 2.01 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 TYR A 47 -87.25 -132.37 REMARK 500 SER A 48 82.52 48.16 REMARK 500 ASN A 49 82.09 43.11 REMARK 500 ASP A 52 -112.69 176.82 REMARK 500 ILE A 83 -44.49 -138.96 REMARK 500 LYS A 84 -14.96 69.54 REMARK 500 ASN A 85 -129.86 -75.70 REMARK 500 ALA A 182 150.15 -47.20 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: 3HGG RELATED DB: PDB REMARK 900 THE SAME PROTEIN COMPLEXED WITH CHOLIC ACID REMARK 900 RELATED ID: 2QCO RELATED DB: PDB REMARK 900 THE SAME PROTEIN COMPLEXED WITH GLYCEROL DBREF 3HGY A 1 210 UNP Q7B8P6 Q7B8P6_CAMJE 1 210 SEQADV 3HGY HIS A -5 UNP Q7B8P6 EXPRESSION TAG SEQADV 3HGY HIS A -4 UNP Q7B8P6 EXPRESSION TAG SEQADV 3HGY HIS A -3 UNP Q7B8P6 EXPRESSION TAG SEQADV 3HGY HIS A -2 UNP Q7B8P6 EXPRESSION TAG SEQADV 3HGY HIS A -1 UNP Q7B8P6 EXPRESSION TAG SEQADV 3HGY 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 *20(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 SER A 117 1 13 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 149 1 12 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 ASN A 203 1 18 CISPEP 1 ASN A 85 GLY A 86 0 -0.18 CISPEP 2 GLU A 171 PRO A 172 0 7.74 SITE 1 AC1 8 LEU A 65 HIS A 72 ILE A 102 PHE A 103 SITE 2 AC1 8 GLN A 134 TYR A 139 LYS A 170 HOH A 221 CRYST1 93.690 37.488 57.733 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 0.010673 0.000000 0.000000 0.00000 SCALE2 0.000000 0.026675 0.000000 0.00000 SCALE3 0.000000 0.000000 0.017321 0.00000