HEADER TRANSCRIPTION 13-MAY-09 3HGG TITLE CRYSTAL STRUCTURE OF CMER BOUND TO CHOLIC ACID 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 TRANSCRIPTION REGULATION EXPDTA X-RAY DIFFRACTION AUTHOR M.D.ROUTH,F.YANG REVDAT 3 21-FEB-24 3HGG 1 REMARK SEQADV REVDAT 2 01-NOV-17 3HGG 1 REMARK REVDAT 1 30-JUN-10 3HGG 0 JRNL AUTH M.D.ROUTH,F.YANG,C.-C.SU,F.LONG,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. 2.57 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) : 2.57 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 31.26 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.910 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.5 REMARK 3 NUMBER OF REFLECTIONS : 6730 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.215 REMARK 3 R VALUE (WORKING SET) : 0.215 REMARK 3 FREE R VALUE : 0.273 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.760 REMARK 3 FREE R VALUE TEST SET COUNT : 579 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 31.2620 - 4.0900 1.00 2909 151 0.2070 0.2530 REMARK 3 2 4.0900 - 3.2480 1.00 2944 127 0.1930 0.2540 REMARK 3 3 3.2480 - 2.8380 1.00 2930 132 0.2370 0.3010 REMARK 3 4 2.8380 - 2.5700 0.95 2790 169 0.2570 0.3020 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 : 51.76 REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.370 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : NULL REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 42.37 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 54.81 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -3.80100 REMARK 3 B22 (A**2) : 1.38800 REMARK 3 B33 (A**2) : 2.41300 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 1716 REMARK 3 ANGLE : 0.590 2315 REMARK 3 CHIRALITY : 0.048 258 REMARK 3 PLANARITY : 0.001 287 REMARK 3 DIHEDRAL : 14.079 642 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): -13.0562 0.3754 -12.4594 REMARK 3 T TENSOR REMARK 3 T11: 0.1991 T22: 0.1790 REMARK 3 T33: 0.2244 T12: 0.0048 REMARK 3 T13: -0.0475 T23: -0.0061 REMARK 3 L TENSOR REMARK 3 L11: 0.9526 L22: 0.3725 REMARK 3 L33: 0.6863 L12: -0.4547 REMARK 3 L13: -0.5050 L23: 0.2429 REMARK 3 S TENSOR REMARK 3 S11: -0.0273 S12: -0.0044 S13: -0.1068 REMARK 3 S21: -0.1138 S22: -0.0838 S23: 0.2011 REMARK 3 S31: 0.0637 S32: -0.1625 S33: 0.0933 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 3HGG 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_1000053103. 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 : SI 111 CHANNEL 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 : 6861 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.570 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 (%) : 98.2 REMARK 200 DATA REDUNDANCY : 3.800 REMARK 200 R MERGE (I) : 0.06000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 20.0000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.57 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.66 REMARK 200 COMPLETENESS FOR SHELL (%) : 83.5 REMARK 200 DATA REDUNDANCY IN SHELL : 3.60 REMARK 200 R MERGE FOR SHELL (I) : 0.21600 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 6.000 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 (%): 40.67 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.07 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 22% PEG 3350, 0.1M MAGNESIUM CHLORIDE, REMARK 280 5% JM600, 20MM SODIUM ACETATE, PH 8.5, VAPOR DIFFUSION, HANGING REMARK 280 DROP, 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 46.96150 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 18.61900 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 46.96150 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 18.61900 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: 5890 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 20120 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -26.0 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 -9 REMARK 465 HIS A -8 REMARK 465 HIS A -7 REMARK 465 HIS A -6 REMARK 465 HIS A -5 REMARK 465 HIS A -4 REMARK 465 MET A -3 REMARK 465 ASN A -2 REMARK 465 SER A -1 REMARK 465 ASN 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 O TYR A 47 CD1 ILE A 50 1.95 REMARK 500 O ASN A 49 CZ TYR A 51 2.19 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND ANGLES 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,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) 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 ATM2 ATM3 REMARK 500 SER A 48 N - CA - C ANGL. DEV. = -16.9 DEGREES REMARK 500 ILE A 50 N - CA - C ANGL. DEV. = -24.5 DEGREES REMARK 500 GLU A 171 N - CA - C ANGL. DEV. = 28.8 DEGREES 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 -77.05 -106.43 REMARK 500 SER A 48 -126.89 58.33 REMARK 500 ASN A 85 54.49 28.97 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: 2QCO RELATED DB: PDB REMARK 900 SAME PROTEIN COMPLEXED WITH GLYCEROL REMARK 900 RELATED ID: 3HGY RELATED DB: PDB REMARK 900 SAME PROTEIN COMPLEXED WITH TAUROCHOLIC ACID DBREF 3HGG A 1 210 UNP Q7B8P6 Q7B8P6_CAMJE 1 210 SEQADV 3HGG HIS A -9 UNP Q7B8P6 EXPRESSION TAG SEQADV 3HGG HIS A -8 UNP Q7B8P6 EXPRESSION TAG SEQADV 3HGG HIS A -7 UNP Q7B8P6 EXPRESSION TAG SEQADV 3HGG HIS A -6 UNP Q7B8P6 EXPRESSION TAG SEQADV 3HGG HIS A -5 UNP Q7B8P6 EXPRESSION TAG SEQADV 3HGG HIS A -4 UNP Q7B8P6 EXPRESSION TAG SEQADV 3HGG MET A -3 UNP Q7B8P6 EXPRESSION TAG SEQADV 3HGG ASN A -2 UNP Q7B8P6 EXPRESSION TAG SEQADV 3HGG SER A -1 UNP Q7B8P6 EXPRESSION TAG SEQADV 3HGG ASN A 0 UNP Q7B8P6 EXPRESSION TAG SEQRES 1 A 220 HIS HIS HIS HIS HIS HIS MET ASN SER ASN MET ASN SER SEQRES 2 A 220 ASN ARG THR PRO SER GLN LYS VAL LEU ALA ARG GLN GLU SEQRES 3 A 220 LYS ILE LYS ALA VAL ALA LEU GLU LEU PHE LEU THR LYS SEQRES 4 A 220 GLY TYR GLN GLU THR SER LEU SER ASP ILE ILE LYS LEU SEQRES 5 A 220 SER GLY GLY SER TYR SER ASN ILE TYR ASP GLY PHE LYS SEQRES 6 A 220 SER LYS GLU GLY LEU PHE PHE GLU ILE LEU ASP ASP ILE SEQRES 7 A 220 CYS LYS LYS HIS PHE HIS LEU ILE TYR SER LYS THR GLN SEQRES 8 A 220 GLU ILE LYS ASN GLY THR LEU LYS GLU ILE LEU THR SER SEQRES 9 A 220 PHE GLY LEU ALA PHE ILE GLU ILE PHE ASN GLN PRO GLU SEQRES 10 A 220 ALA VAL ALA PHE GLY LYS ILE ILE TYR SER GLN VAL TYR SEQRES 11 A 220 ASP LYS ASP ARG HIS LEU ALA ASN TRP ILE GLU ASN ASN SEQRES 12 A 220 GLN GLN ASN PHE SER TYR ASN ILE LEU MET GLY PHE PHE SEQRES 13 A 220 LYS GLN GLN ASN ASN SER TYR MET LYS LYS ASN ALA GLU SEQRES 14 A 220 LYS LEU ALA VAL LEU PHE CYS THR MET LEU LYS GLU PRO SEQRES 15 A 220 TYR HIS HIS LEU ASN VAL LEU ILE ASN ALA PRO LEU LYS SEQRES 16 A 220 ASN LYS LYS GLU GLN LYS GLU HIS VAL GLU PHE VAL VAL SEQRES 17 A 220 ASN VAL PHE LEU 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 *26(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 ASN A 181 1 25 HELIX 12 12 ASN A 186 GLY A 204 1 19 SITE 1 AC1 7 CYS A 69 PHE A 99 PHE A 137 SER A 138 SITE 2 AC1 7 LYS A 170 HIS A 175 HOH A 221 CRYST1 93.923 37.238 57.525 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 0.010647 0.000000 0.000000 0.00000 SCALE2 0.000000 0.026854 0.000000 0.00000 SCALE3 0.000000 0.000000 0.017384 0.00000