HEADER TRANSCRIPTION REGULATION 16-DEC-96 1OPC TITLE OMPR DNA-BINDING DOMAIN, ESCHERICHIA COLI COMPND MOL_ID: 1; COMPND 2 MOLECULE: OMPR; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: C-TERMINAL DNA-BINDING DOMAIN; COMPND 5 SYNONYM: OMPRC; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ESCHERICHIA COLI; SOURCE 3 ORGANISM_TAXID: 562; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 6 EXPRESSION_SYSTEM_PLASMID: PET11 KEYWDS TRANSCRIPTION REGULATION, RESPONSE REGULATOR, WINGED HELIX, KEYWDS 2 OSMOREGULATION EXPDTA X-RAY DIFFRACTION AUTHOR E.MARTINEZ-HACKERT,A.M.STOCK REVDAT 3 14-FEB-24 1OPC 1 REMARK REVDAT 2 24-FEB-09 1OPC 1 VERSN REVDAT 1 01-APR-97 1OPC 0 JRNL AUTH E.MARTINEZ-HACKERT,A.M.STOCK JRNL TITL THE DNA-BINDING DOMAIN OF OMPR: CRYSTAL STRUCTURES OF A JRNL TITL 2 WINGED HELIX TRANSCRIPTION FACTOR. JRNL REF STRUCTURE V. 5 109 1997 JRNL REFN ISSN 0969-2126 JRNL PMID 9016718 JRNL DOI 10.1016/S0969-2126(97)00170-6 REMARK 2 REMARK 2 RESOLUTION. 1.95 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PROLSQ REMARK 3 AUTHORS : KONNERT,HENDRICKSON REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.95 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 5.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 97.1 REMARK 3 NUMBER OF REFLECTIONS : 7807 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 + TEST SET) : NULL REMARK 3 R VALUE (WORKING SET) : 0.228 REMARK 3 FREE R VALUE : 0.269 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 388 REMARK 3 REMARK 3 FIT/AGREEMENT OF MODEL WITH ALL DATA. REMARK 3 R VALUE (WORKING + TEST SET, NO CUTOFF) : NULL REMARK 3 R VALUE (WORKING SET, NO CUTOFF) : 0.2280 REMARK 3 FREE R VALUE (NO CUTOFF) : 0.269 REMARK 3 FREE R VALUE TEST SET SIZE (%, NO CUTOFF) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT (NO CUTOFF) : 388 REMARK 3 TOTAL NUMBER OF REFLECTIONS (NO CUTOFF) : 8195 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 805 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 85 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 16.78 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 20.70 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) : NULL REMARK 3 ESD FROM SIGMAA (A) : 0.31 REMARK 3 LOW RESOLUTION CUTOFF (A) : 5.00 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 DISTANCE RESTRAINTS. RMS SIGMA REMARK 3 BOND LENGTH (A) : 0.017 ; 0.020 REMARK 3 ANGLE DISTANCE (A) : 0.036 ; 0.040 REMARK 3 INTRAPLANAR 1-4 DISTANCE (A) : 0.037 ; 0.050 REMARK 3 H-BOND OR METAL COORDINATION (A) : NULL ; NULL REMARK 3 REMARK 3 PLANE RESTRAINT (A) : 0.016 ; 0.030 REMARK 3 CHIRAL-CENTER RESTRAINT (A**3) : 0.137 ; 0.150 REMARK 3 REMARK 3 NON-BONDED CONTACT RESTRAINTS. REMARK 3 SINGLE TORSION (A) : 0.195 ; 0.300 REMARK 3 MULTIPLE TORSION (A) : 0.268 ; 0.300 REMARK 3 H-BOND (X...Y) (A) : 0.159 ; 0.300 REMARK 3 H-BOND (X-H...Y) (A) : NULL ; NULL REMARK 3 REMARK 3 CONFORMATIONAL TORSION ANGLE RESTRAINTS. REMARK 3 SPECIFIED (DEGREES) : 31.600; 15.000 REMARK 3 PLANAR (DEGREES) : 7.900 ; 7.000 REMARK 3 STAGGERED (DEGREES) : 20.000; 15.000 REMARK 3 TRANSVERSE (DEGREES) : 22.600; 20.000 REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : 1.933 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE (A**2) : 2.605 ; 3.000 REMARK 3 SIDE-CHAIN BOND (A**2) : 1.696 ; 2.000 REMARK 3 SIDE-CHAIN ANGLE (A**2) : 2.943 ; 3.000 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: X-PLOR, PROLSQ AND REFMAC USED REMARK 4 REMARK 4 1OPC COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY BNL. REMARK 100 THE DEPOSITION ID IS D_1000175487. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : JUN-96 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.5 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) : 0.9686 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : MONOCHROMATOR REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : FUJI REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 8604 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.950 REMARK 200 RESOLUTION RANGE LOW (A) : 10.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 97.1 REMARK 200 DATA REDUNDANCY : 7.100 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.04600 REMARK 200 FOR THE DATA SET : 10.8000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.95 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.00 REMARK 200 COMPLETENESS FOR SHELL (%) : 98.7 REMARK 200 DATA REDUNDANCY IN SHELL : 5.60 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : 0.08600 REMARK 200 FOR SHELL : 6.900 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: NULL REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MAD REMARK 200 SOFTWARE USED: MADSYS 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): 2.45 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PROTEIN WAS CRYSTALLIZED FROM 3% REMARK 280 POLYETHYLENEGLYCOL-MONOMETHYLETHER (PMME) 5000, 17.5% REMARK 280 ETHYLENEGLYCOL, 2.5% MPD, 30 MM MES, PH 6.5; THEN SOAKED IN 10% REMARK 280 PMME 5000, 20% ETHYLENEGLYCOL, 10% PEG 200, 200 MM AMMONIUM REMARK 280 SULFATE, 30 MM MES, PH 6.5 REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 32 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+2/3 REMARK 290 3555 -X+Y,-X,Z+1/3 REMARK 290 4555 Y,X,-Z REMARK 290 5555 X-Y,-Y,-Z+1/3 REMARK 290 6555 -X,-X+Y,-Z+2/3 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 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 38.74000 REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 19.37000 REMARK 290 SMTRY1 4 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 4 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 5 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 19.37000 REMARK 290 SMTRY1 6 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 6 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 38.74000 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: 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 ALA A 130 REMARK 465 PRO A 131 REMARK 465 SER A 132 REMARK 465 GLN A 133 REMARK 465 GLU A 134 REMARK 465 GLU A 135 REMARK 465 ALA A 136 REMARK 465 GLY A 236 REMARK 465 SER A 237 REMARK 465 LYS A 238 REMARK 465 ALA A 239 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15 REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375 REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS. REMARK 500 REMARK 500 DISTANCE CUTOFF: REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE REMARK 500 CD1 LEU A 228 CD1 LEU A 228 4556 2.13 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 ASP A 156 CB - CG - OD1 ANGL. DEV. = 6.1 DEGREES REMARK 500 ARG A 182 CD - NE - CZ ANGL. DEV. = 10.1 DEGREES REMARK 500 ARG A 182 NE - CZ - NH1 ANGL. DEV. = 4.9 DEGREES REMARK 500 GLU A 193 OE1 - CD - OE2 ANGL. DEV. = 7.9 DEGREES REMARK 500 ARG A 199 CD - NE - CZ ANGL. DEV. = 12.7 DEGREES REMARK 500 ARG A 199 NE - CZ - NH1 ANGL. DEV. = 3.1 DEGREES REMARK 500 ARG A 210 CD - NE - CZ ANGL. DEV. = 10.3 DEGREES REMARK 500 ARG A 210 NE - CZ - NH2 ANGL. DEV. = -3.5 DEGREES REMARK 500 ASP A 215 CB - CG - OD1 ANGL. DEV. = 5.5 DEGREES REMARK 500 ASP A 235 CB - CG - OD2 ANGL. DEV. = -6.4 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 THR A 162 163.51 -49.98 REMARK 500 TYR A 194 105.82 -51.98 REMARK 500 SER A 195 -73.35 -148.79 REMARK 500 LEU A 228 -77.04 -128.16 REMARK 500 REMARK 500 REMARK: NULL REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: RH REMARK 800 EVIDENCE_CODE: UNKNOWN REMARK 800 SITE_DESCRIPTION: RECOGNITION HELIX. REMARK 800 REMARK 800 SITE_IDENTIFIER: W1 REMARK 800 EVIDENCE_CODE: UNKNOWN REMARK 800 SITE_DESCRIPTION: RECOGNITION WING. REMARK 800 REMARK 800 SITE_IDENTIFIER: ALP REMARK 800 EVIDENCE_CODE: UNKNOWN REMARK 800 SITE_DESCRIPTION: ALPHA LOOP, SITE OF INTERACTION WITH RNA REMARK 800 POLYMERASE ALPHA SUBUNIT. DBREF 1OPC A 130 239 UNP P0AA16 OMPR_ECOLI 130 239 SEQRES 1 A 110 ALA PRO SER GLN GLU GLU ALA VAL ILE ALA PHE GLY LYS SEQRES 2 A 110 PHE LYS LEU ASN LEU GLY THR ARG GLU MET PHE ARG GLU SEQRES 3 A 110 ASP GLU PRO MET PRO LEU THR SER GLY GLU PHE ALA VAL SEQRES 4 A 110 LEU LYS ALA LEU VAL SER HIS PRO ARG GLU PRO LEU SER SEQRES 5 A 110 ARG ASP LYS LEU MET ASN LEU ALA ARG GLY ARG GLU TYR SEQRES 6 A 110 SER ALA MET GLU ARG SER ILE ASP VAL GLN ILE SER ARG SEQRES 7 A 110 LEU ARG ARG MET VAL GLU GLU ASP PRO ALA HIS PRO ARG SEQRES 8 A 110 TYR ILE GLN THR VAL TRP GLY LEU GLY TYR VAL PHE VAL SEQRES 9 A 110 PRO ASP GLY SER LYS ALA FORMUL 2 HOH *85(H2 O) HELIX 1 1 SER A 163 SER A 174 1 12 HELIX 2 2 ARG A 182 ALA A 189 1 8 HELIX 3 3 SER A 200 VAL A 212 1 13 SHEET 1 A 5 ILE A 138 PHE A 140 0 SHEET 2 A 5 LYS A 142 ASN A 146 -1 N LEU A 145 O ILE A 138 SHEET 3 A 5 GLU A 151 GLU A 155 -1 N PHE A 153 O LYS A 144 SHEET 4 A 5 GLU A 157 MET A 159 -1 N MET A 159 O MET A 152 SHEET 5 A 5 LEU A 180 SER A 181 1 SHEET 1 B 2 TYR A 221 VAL A 225 0 SHEET 2 B 2 LEU A 228 VAL A 233 -1 N VAL A 231 O GLN A 223 SITE 1 RH 1 SER A 200 SITE 1 W1 1 THR A 224 SITE 1 ALP 1 ARG A 190 CRYST1 59.140 59.140 58.110 90.00 90.00 120.00 P 32 2 1 6 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 0.016909 0.009762 0.000000 0.00000 SCALE2 0.000000 0.019525 0.000000 0.00000 SCALE3 0.000000 0.000000 0.017209 0.00000