10 20 30 40 50 60 70 80 1P2F - Header ----|----|----|----|----|----|----|----|----|----|----|----|----|----|----|----| Asymmetric UnitHEADER TRANSCRIPTION 15-APR-03 1P2F
TITLE CRYSTAL STRUCTURE ANALYSIS OF RESPONSE REGULATOR DRRB, A TITLE 2 THERMOTOGA MARITIMA OMPR/PHOB HOMOLOG
COMPND MOL_ID: 1; COMPND 2 MOLECULE: RESPONSE REGULATOR; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: RESPONSE REGULATOR DRRB; COMPND 5 ENGINEERED: YES
SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: THERMOTOGA MARITIMA; SOURCE 3 ORGANISM_TAXID: 2336; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 5 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 6 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 8 EXPRESSION_SYSTEM_PLASMID: PDB1
KEYWDS RESPONSE REGULATOR, DRRB, OMPR/PHOB, TRANSCRIPTION
EXPDTA X-RAY DIFFRACTION
AUTHOR V.L.ROBINSON,T.WU,A.M.STOCK
REVDAT 3 24-FEB-09 1P2F 1 VERSN REVDAT 2 29-JUL-03 1P2F 1 JRNL REMARK REVDAT 1 29-APR-03 1P2F 0
JRNL AUTH V.L.ROBINSON,T.WU,A.M.STOCK JRNL TITL STRUCTURAL ANALYSIS OF THE DOMAIN INTERFACE IN JRNL TITL 2 DRRB, A RESPONSE REGULATOR OF THE OMPR/PHOB JRNL TITL 3 SUBFAMILY JRNL REF J.BACTERIOL. V. 185 4186 2003 JRNL REFN ISSN 0021-9193 JRNL PMID 12837793 JRNL DOI 10.1128/JB.185.14.4186-4194.2003
REMARK 1
REMARK 2 REMARK 2 RESOLUTION. 1.80 ANGSTROMS.
REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS REMARK 3 AUTHORS : BRUNGER,ADAMS,CLORE,DELANO,GROS,GROSSE- REMARK 3 : KUNSTLEVE,JIANG,KUSZEWSKI,NILGES, PANNU, REMARK 3 : READ,RICE,SIMONSON,WARREN REMARK 3 REMARK 3 REFINEMENT TARGET : ENGH & HUBER REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.80 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 20.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : NULL REMARK 3 DATA CUTOFF LOW (ABS(F)) : NULL REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 97.0 REMARK 3 NUMBER OF REFLECTIONS : 25071 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING SET) : 0.198 REMARK 3 FREE R VALUE : 0.224 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.700 REMARK 3 FREE R VALUE TEST SET COUNT : 2683 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : NULL REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : NULL REMARK 3 BIN RESOLUTION RANGE HIGH (A) : NULL REMARK 3 BIN RESOLUTION RANGE LOW (A) : NULL REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 REFLECTIONS IN BIN (WORKING SET) : NULL REMARK 3 BIN R VALUE (WORKING SET) : NULL REMARK 3 BIN FREE R VALUE : NULL REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 BIN FREE R VALUE TEST SET COUNT : NULL REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : NULL REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1784 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 163 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 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.21 REMARK 3 ESD FROM SIGMAA (A) : 0.14 REMARK 3 LOW RESOLUTION CUTOFF (A) : 1.80 REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : 0.24 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.17 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.006 REMARK 3 BOND ANGLES (DEGREES) : 1.26 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 22.90 REMARK 3 IMPROPER ANGLES (DEGREES) : 0.72 REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : NULL REMARK 3 KSOL : NULL REMARK 3 BSOL : NULL REMARK 3 REMARK 3 NCS MODEL : NULL REMARK 3 REMARK 3 NCS RESTRAINTS. RMS SIGMA/WEIGHT REMARK 3 GROUP 1 POSITIONAL (A) : NULL ; NULL REMARK 3 GROUP 1 B-FACTOR (A**2) : NULL ; NULL REMARK 3 REMARK 3 PARAMETER FILE 1 : NULL REMARK 3 TOPOLOGY FILE 1 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL
REMARK 4 REMARK 4 1P2F COMPLIES WITH FORMAT V. 3.15, 01-DEC-08
REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 18-APR-03. REMARK 100 THE RCSB ID CODE IS RCSB018927.
REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 11-NOV-02 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.3 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : NSLS REMARK 200 BEAMLINE : X4A REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9786 REMARK 200 MONOCHROMATOR : KOHZU DOUBLE CRYSTAL REMARK 200 MONOCHROMATOR WITH A REMARK 200 SAGITTALLY FOCUSED SECOND REMARK 200 CRYSTAL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 4 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 44556 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.800 REMARK 200 RESOLUTION RANGE LOW (A) : 30.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 2.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 97.4 REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : NULL REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.80 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.86 REMARK 200 COMPLETENESS FOR SHELL (%) : 87.6 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SAD REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: SAD REMARK 200 SOFTWARE USED: CNS REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL
REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 49.40 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.45 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: SODIUM AND POTASSIUM PHOSPHATE, PH REMARK 280 6.3, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 335K
REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 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 28.94500 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 38.82000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 29.69500 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 38.82000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 28.94500 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 29.69500 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 300 REMARK: THE BIOLOGICAL ASSEMBLY IS A MONOMER
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 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 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 GLY A 218 REMARK 465 GLU A 219 REMARK 465 ARG A 220
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 PRO A 199 43.21 -59.12 REMARK 500 TRP A 209 20.80 49.72 REMARK 500 REMARK 500 REMARK: NULL
REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1KGS RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF DRRD, AN OMPR/PHOB HOMOLOG FROM REMARK 900 THERMOTOGA MARITIMA
DBREF 1P2F A 1 220 UNP Q9WXY0 Q9WXY0_THEMA 1 220
SEQADV 1P2F MSE A 1 UNP Q9WXY0 MET 1 CLONING ARTIFACT SEQADV 1P2F MSE A 2 UNP Q9WXY0 MET 2 CLONING ARTIFACT SEQADV 1P2F MSE A 52 UNP Q9WXY0 MET 52 CLONING ARTIFACT SEQADV 1P2F MSE A 64 UNP Q9WXY0 MET 64 CLONING ARTIFACT SEQADV 1P2F MSE A 214 UNP Q9WXY0 MET 214 CLONING ARTIFACT
SEQRES 1 A 220 MSE MSE TRP LYS ILE ALA VAL VAL ASP ASP ASP LYS ASN SEQRES 2 A 220 ILE LEU LYS LYS VAL SER GLU LYS LEU GLN GLN LEU GLY SEQRES 3 A 220 ARG VAL LYS THR PHE LEU THR GLY GLU ASP PHE LEU ASN SEQRES 4 A 220 ASP GLU GLU ALA PHE HIS VAL VAL VAL LEU ASP VAL MSE SEQRES 5 A 220 LEU PRO ASP TYR SER GLY TYR GLU ILE CYS ARG MSE ILE SEQRES 6 A 220 LYS GLU THR ARG PRO GLU THR TRP VAL ILE LEU LEU THR SEQRES 7 A 220 LEU LEU SER ASP ASP GLU SER VAL LEU LYS GLY PHE GLU SEQRES 8 A 220 ALA GLY ALA ASP ASP TYR VAL THR LYS PRO PHE ASN PRO SEQRES 9 A 220 GLU ILE LEU LEU ALA ARG VAL LYS ARG PHE LEU GLU ARG SEQRES 10 A 220 GLU LYS LYS GLY LEU TYR ASP PHE GLY ASP LEU LYS ILE SEQRES 11 A 220 ASP ALA THR GLY PHE THR VAL PHE LEU LYS GLY LYS ARG SEQRES 12 A 220 ILE HIS LEU PRO LYS LYS GLU PHE GLU ILE LEU LEU PHE SEQRES 13 A 220 LEU ALA GLU ASN ALA GLY LYS VAL VAL THR ARG GLU LYS SEQRES 14 A 220 LEU LEU GLU THR PHE TRP GLU ASP PRO VAL SER PRO ARG SEQRES 15 A 220 VAL VAL ASP THR VAL ILE LYS ARG ILE ARG LYS ALA ILE SEQRES 16 A 220 GLU ASP ASP PRO ASN ARG PRO ARG TYR ILE LYS THR ILE SEQRES 17 A 220 TRP GLY VAL GLY TYR MSE PHE THR GLY GLY GLU ARG
MODRES 1P2F MSE A 1 MET SELENOMETHIONINE MODRES 1P2F MSE A 2 MET SELENOMETHIONINE MODRES 1P2F MSE A 52 MET SELENOMETHIONINE MODRES 1P2F MSE A 64 MET SELENOMETHIONINE MODRES 1P2F MSE A 214 MET SELENOMETHIONINE
HET MSE A 1 11 HET MSE A 2 8 HET MSE A 52 8 HET MSE A 64 8 HET MSE A 214 8
HETNAM MSE SELENOMETHIONINE
FORMUL 1 MSE 5(C5 H11 N O2 SE) FORMUL 2 HOH *163(H2 O)
HELIX 1 1 ASP A 11 GLN A 23 1 13 HELIX 2 2 THR A 33 ASP A 40 1 8 HELIX 3 3 SER A 57 ARG A 69 1 13 HELIX 4 4 ASP A 82 GLY A 93 1 12 HELIX 5 5 ASN A 103 GLU A 118 1 16 HELIX 6 6 PRO A 147 ASN A 160 1 14 HELIX 7 7 ARG A 167 TRP A 175 1 9 HELIX 8 8 PRO A 181 GLU A 196 1 16
SHEET 1 A 5 GLY A 26 PHE A 31 0 SHEET 2 A 5 TRP A 3 VAL A 8 1 N ILE A 5 O ARG A 27 SHEET 3 A 5 VAL A 46 ASP A 50 1 O VAL A 48 N ALA A 6 SHEET 4 A 5 TRP A 73 THR A 78 1 O ILE A 75 N LEU A 49 SHEET 5 A 5 ASP A 96 THR A 99 1 O ASP A 96 N LEU A 76 SHEET 1 B 4 LEU A 122 PHE A 125 0 SHEET 2 B 4 LEU A 128 ASP A 131 -1 O ILE A 130 N TYR A 123 SHEET 3 B 4 THR A 136 LEU A 139 -1 O THR A 136 N ASP A 131 SHEET 4 B 4 LYS A 142 ARG A 143 -1 O LYS A 142 N LEU A 139 SHEET 1 C 3 VAL A 165 THR A 166 0 SHEET 2 C 3 GLY A 212 PHE A 215 -1 O TYR A 213 N VAL A 165 SHEET 3 C 3 ILE A 205 ILE A 208 -1 N LYS A 206 O MSE A 214
LINK C MSE A 1 N MSE A 2 1555 1555 1.33 LINK C MSE A 2 N TRP A 3 1555 1555 1.33 LINK C VAL A 51 N MSE A 52 1555 1555 1.33 LINK C MSE A 52 N LEU A 53 1555 1555 1.33 LINK C ARG A 63 N MSE A 64 1555 1555 1.33 LINK C MSE A 64 N ILE A 65 1555 1555 1.33 LINK C TYR A 213 N MSE A 214 1555 1555 1.33 LINK C MSE A 214 N PHE A 215 1555 1555 1.33
CISPEP 1 LYS A 100 PRO A 101 0 -0.18
CRYST1 57.890 59.390 77.640 90.00 90.00 90.00 P 21 21 21 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 0.017274 0.000000 0.000000 0.00000
SCALE2 0.000000 0.016838 0.000000 0.00000
SCALE3 0.000000 0.000000 0.012880 0.00000