PDB Short entry for 1DPR HEADER TRANSCRIPTION REGULATION 06-FEB-95 1DPR TITLE STRUCTURES OF THE APO-AND METAL ION ACTIVATED FORMS OF THE TITLE 2 DIPHTHERIA TOX REPRESSOR FROM CORYNEBACTERIUM DIPHTHERIAE COMPND MOL_ID: 1; COMPND 2 MOLECULE: DIPHTHERIA TOX REPRESSOR; COMPND 3 CHAIN: A, B; COMPND 4 SYNONYM: DTXR; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: CORYNEBACTERIUM DIPHTHERIAE; SOURCE 3 ORGANISM_TAXID: 1717; SOURCE 4 STRAIN: C7(-); SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 7 EXPRESSION_SYSTEM_PLASMID: PDR1 KEYWDS DIPHTHERIA, VIRULENCE, DNA-BINDING, IRON-REGULATION KEYWDS 2 REPRESSOR, TRANSCRIPTION REGULATION EXPDTA X-RAY DIFFRACTION AUTHOR N.SCHIERING,X.TAO,J.MURPHY,G.A.PETSKO,D.RINGE REVDAT 2 24-FEB-09 1DPR 1 VERSN REVDAT 1 15-SEP-95 1DPR 0 JRNL AUTH N.SCHIERING,X.TAO,H.ZENG,J.R.MURPHY,G.A.PETSKO, JRNL AUTH 2 D.RINGE JRNL TITL STRUCTURES OF THE APO- AND THE METAL ION-ACTIVATED JRNL TITL 2 FORMS OF THE DIPHTHERIA TOX REPRESSOR FROM JRNL TITL 3 CORYNEBACTERIUM DIPHTHERIAE. JRNL REF PROC.NATL.ACAD.SCI.USA V. 92 9843 1995 JRNL REFN ISSN 0027-8424 JRNL PMID 7568230 JRNL DOI 10.1073/PNAS.92.21.9843 REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH X.TAO,N.SCHIERING,H.ZENG,D.RINGE,J.MURPHY REMARK 1 TITL IRON, DTXR, AND THE REGULATION OF DIPHTHERIA TOXIN REMARK 1 TITL 2 EXPRESSION REMARK 1 REF MOL.MICROBIOL. V. 14 191 1994 REMARK 1 REFN ISSN 0950-382X REMARK 1 REFERENCE 2 REMARK 1 AUTH N.SCHIERING,X.TAO,J.MURPHY,G.PETSKO,D.RINGE REMARK 1 TITL CRYSTALLIZATION AND PRELIMINARY X-RAY STUDIES OF REMARK 1 TITL 2 THE DIPHTHERIA TOX REPRESSOR FROM CORYNEBACTERIUM REMARK 1 TITL 3 DIPHTHERIAE REMARK 1 REF J.MOL.BIOL. V. 244 654 1994 REMARK 1 REFN ISSN 0022-2836 REMARK 2 REMARK 2 RESOLUTION. 3.00 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : X-PLOR 3.1 REMARK 3 AUTHORS : BRUNGER REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 3.00 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 8.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 2.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : NULL REMARK 3 DATA CUTOFF LOW (ABS(F)) : NULL REMARK 3 COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 NUMBER OF REFLECTIONS : 7379 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : NULL REMARK 3 FREE R VALUE TEST SET SELECTION : NULL REMARK 3 R VALUE (WORKING SET) : 0.241 REMARK 3 FREE R VALUE : 0.417 REMARK 3 FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 FREE R VALUE TEST SET COUNT : NULL 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 : 2122 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 0 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 13.98 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) : 0.40 REMARK 3 ESD FROM SIGMAA (A) : NULL REMARK 3 LOW RESOLUTION CUTOFF (A) : NULL REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : NULL REMARK 3 ESD FROM C-V SIGMAA (A) : NULL REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : NULL REMARK 3 BOND ANGLES (DEGREES) : NULL REMARK 3 DIHEDRAL ANGLES (DEGREES) : NULL REMARK 3 IMPROPER ANGLES (DEGREES) : NULL 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 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 1DPR COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY BNL. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : NULL REMARK 200 TEMPERATURE (KELVIN) : NULL REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : NULL REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : NULL REMARK 200 RADIATION SOURCE : NULL REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : NULL REMARK 200 WAVELENGTH OR RANGE (A) : NULL REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : NULL REMARK 200 DETECTOR MANUFACTURER : NULL REMARK 200 INTENSITY-INTEGRATION SOFTWARE : NULL REMARK 200 DATA SCALING SOFTWARE : NULL REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 9355 REMARK 200 RESOLUTION RANGE HIGH (A) : NULL REMARK 200 RESOLUTION RANGE LOW (A) : NULL REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 83.8 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) : NULL REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : NULL REMARK 200 COMPLETENESS FOR SHELL (%) : NULL 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: NULL REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: NULL REMARK 200 SOFTWARE USED: X-PLOR 3.1 REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 52.13 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.57 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: NULL 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 146.93333 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 73.46667 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 73.46667 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 146.93333 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: REMARK 300 MTRIX REMARK 300 THE TRANSFORMATIONS PRESENTED ON MTRIX RECORDS BELOW REMARK 300 DESCRIBE NON-CRYSTALLOGRAPHIC RELATIONSHIPS AMONG THE REMARK 300 VARIOUS DOMAINS IN THIS ENTRY. APPLYING THE APPROPRIATE REMARK 300 MTRIX TRANSFORMATION TO THE RESIDUES LISTED FIRST WILL REMARK 300 YIELD APPROXIMATE COORDINATES FOR THE RESIDUES LISTED REMARK 300 SECOND. REMARK 300 REMARK 300 APPLIED TO TRANSFORMED TO REMARK 300 MTRIX RESIDUES RESIDUES RMSD REMARK 300 M1 A 3 .. A 136 B 3 .. B 136 1.491 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: 1730 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 13900 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -13.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B 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 MET A 1 REMARK 465 LYS A 2 REMARK 465 GLU A 137 REMARK 465 LEU A 138 REMARK 465 GLY A 139 REMARK 465 VAL A 140 REMARK 465 GLY A 141 REMARK 465 ASN A 142 REMARK 465 SER A 143 REMARK 465 ASP A 144 REMARK 465 ALA A 145 REMARK 465 ALA A 146 REMARK 465 ALA A 147 REMARK 465 PRO A 148 REMARK 465 GLY A 149 REMARK 465 THR A 150 REMARK 465 ARG A 151 REMARK 465 VAL A 152 REMARK 465 ILE A 153 REMARK 465 ASP A 154 REMARK 465 ALA A 155 REMARK 465 ALA A 156 REMARK 465 THR A 157 REMARK 465 SER A 158 REMARK 465 MET A 159 REMARK 465 PRO A 160 REMARK 465 ARG A 161 REMARK 465 LYS A 162 REMARK 465 VAL A 163 REMARK 465 ARG A 164 REMARK 465 ILE A 165 REMARK 465 VAL A 166 REMARK 465 GLN A 167 REMARK 465 ILE A 168 REMARK 465 ASN A 169 REMARK 465 GLU A 170 REMARK 465 ILE A 171 REMARK 465 PHE A 172 REMARK 465 GLN A 173 REMARK 465 VAL A 174 REMARK 465 GLU A 175 REMARK 465 THR A 176 REMARK 465 ASP A 177 REMARK 465 GLN A 178 REMARK 465 PHE A 179 REMARK 465 THR A 180 REMARK 465 GLN A 181 REMARK 465 LEU A 182 REMARK 465 LEU A 183 REMARK 465 ASP A 184 REMARK 465 ALA A 185 REMARK 465 ASP A 186 REMARK 465 ILE A 187 REMARK 465 ARG A 188 REMARK 465 VAL A 189 REMARK 465 GLY A 190 REMARK 465 SER A 191 REMARK 465 GLU A 192 REMARK 465 VAL A 193 REMARK 465 GLU A 194 REMARK 465 ILE A 195 REMARK 465 VAL A 196 REMARK 465 ASP A 197 REMARK 465 ARG A 198 REMARK 465 ASP A 199 REMARK 465 GLY A 200 REMARK 465 HIS A 201 REMARK 465 ILE A 202 REMARK 465 THR A 203 REMARK 465 LEU A 204 REMARK 465 SER A 205 REMARK 465 HIS A 206 REMARK 465 ASN A 207 REMARK 465 GLY A 208 REMARK 465 LYS A 209 REMARK 465 ASP A 210 REMARK 465 VAL A 211 REMARK 465 GLU A 212 REMARK 465 LEU A 213 REMARK 465 LEU A 214 REMARK 465 ASP A 215 REMARK 465 ASP A 216 REMARK 465 LEU A 217 REMARK 465 ALA A 218 REMARK 465 HIS A 219 REMARK 465 THR A 220 REMARK 465 ILE A 221 REMARK 465 ARG A 222 REMARK 465 ILE A 223 REMARK 465 GLU A 224 REMARK 465 GLU A 225 REMARK 465 LEU A 226 REMARK 465 MET B 1 REMARK 465 LYS B 2 REMARK 465 GLU B 137 REMARK 465 LEU B 138 REMARK 465 GLY B 139 REMARK 465 VAL B 140 REMARK 465 GLY B 141 REMARK 465 ASN B 142 REMARK 465 SER B 143 REMARK 465 ASP B 144 REMARK 465 ALA B 145 REMARK 465 ALA B 146 REMARK 465 ALA B 147 REMARK 465 PRO B 148 REMARK 465 GLY B 149 REMARK 465 THR B 150 REMARK 465 ARG B 151 REMARK 465 VAL B 152 REMARK 465 ILE B 153 REMARK 465 ASP B 154 REMARK 465 ALA B 155 REMARK 465 ALA B 156 REMARK 465 THR B 157 REMARK 465 SER B 158 REMARK 465 MET B 159 REMARK 465 PRO B 160 REMARK 465 ARG B 161 REMARK 465 LYS B 162 REMARK 465 VAL B 163 REMARK 465 ARG B 164 REMARK 465 ILE B 165 REMARK 465 VAL B 166 REMARK 465 GLN B 167 REMARK 465 ILE B 168 REMARK 465 ASN B 169 REMARK 465 GLU B 170 REMARK 465 ILE B 171 REMARK 465 PHE B 172 REMARK 465 GLN B 173 REMARK 465 VAL B 174 REMARK 465 GLU B 175 REMARK 465 THR B 176 REMARK 465 ASP B 177 REMARK 465 GLN B 178 REMARK 465 PHE B 179 REMARK 465 THR B 180 REMARK 465 GLN B 181 REMARK 465 LEU B 182 REMARK 465 LEU B 183 REMARK 465 ASP B 184 REMARK 465 ALA B 185 REMARK 465 ASP B 186 REMARK 465 ILE B 187 REMARK 465 ARG B 188 REMARK 465 VAL B 189 REMARK 465 GLY B 190 REMARK 465 SER B 191 REMARK 465 GLU B 192 REMARK 465 VAL B 193 REMARK 465 GLU B 194 REMARK 465 ILE B 195 REMARK 465 VAL B 196 REMARK 465 ASP B 197 REMARK 465 ARG B 198 REMARK 465 ASP B 199 REMARK 465 GLY B 200 REMARK 465 HIS B 201 REMARK 465 ILE B 202 REMARK 465 THR B 203 REMARK 465 LEU B 204 REMARK 465 SER B 205 REMARK 465 HIS B 206 REMARK 465 ASN B 207 REMARK 465 GLY B 208 REMARK 465 LYS B 209 REMARK 465 ASP B 210 REMARK 465 VAL B 211 REMARK 465 GLU B 212 REMARK 465 LEU B 213 REMARK 465 LEU B 214 REMARK 465 ASP B 215 REMARK 465 ASP B 216 REMARK 465 LEU B 217 REMARK 465 ALA B 218 REMARK 465 HIS B 219 REMARK 465 THR B 220 REMARK 465 ILE B 221 REMARK 465 ARG B 222 REMARK 465 ILE B 223 REMARK 465 GLU B 224 REMARK 465 GLU B 225 REMARK 465 LEU B 226 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 ARG A 50 NE ARG A 50 CZ 0.086 REMARK 500 SER A 58 CA SER A 58 CB 0.108 REMARK 500 HIS A 79 NE2 HIS A 79 CD2 -0.075 REMARK 500 HIS A 106 NE2 HIS A 106 CD2 -0.070 REMARK 500 HIS B 79 NE2 HIS B 79 CD2 -0.067 REMARK 500 HIS B 106 NE2 HIS B 106 CD2 -0.087 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 3 N - CA - C ANGL. DEV. = -16.5 DEGREES REMARK 500 LEU A 4 CA - CB - CG ANGL. DEV. = 20.3 DEGREES REMARK 500 ASP A 6 CB - CG - OD1 ANGL. DEV. = 7.5 DEGREES REMARK 500 TYR A 11 CB - CG - CD2 ANGL. DEV. = -4.2 DEGREES REMARK 500 ARG A 13 NE - CZ - NH2 ANGL. DEV. = -3.1 DEGREES REMARK 500 TYR A 16 CB - CG - CD2 ANGL. DEV. = -3.9 DEGREES REMARK 500 GLU A 17 CA - CB - CG ANGL. DEV. = 15.7 DEGREES REMARK 500 GLU A 19 CA - CB - CG ANGL. DEV. = 15.8 DEGREES REMARK 500 LEU A 26 CB - CG - CD1 ANGL. DEV. = -11.4 DEGREES REMARK 500 ARG A 33 NE - CZ - NH1 ANGL. DEV. = 4.9 DEGREES REMARK 500 ARG A 33 NE - CZ - NH2 ANGL. DEV. = -5.5 DEGREES REMARK 500 GLN A 43 CA - CB - CG ANGL. DEV. = 16.4 DEGREES REMARK 500 ARG A 47 NE - CZ - NH1 ANGL. DEV. = 3.4 DEGREES REMARK 500 ARG A 47 NE - CZ - NH2 ANGL. DEV. = -6.0 DEGREES REMARK 500 MET A 48 CA - CB - CG ANGL. DEV. = 15.7 DEGREES REMARK 500 ARG A 50 NH1 - CZ - NH2 ANGL. DEV. = -6.9 DEGREES REMARK 500 ARG A 50 NE - CZ - NH1 ANGL. DEV. = 7.7 DEGREES REMARK 500 MET A 64 CG - SD - CE ANGL. DEV. = 13.5 DEGREES REMARK 500 GLN A 63 CA - C - N ANGL. DEV. = -19.3 DEGREES REMARK 500 ARG A 69 NE - CZ - NH1 ANGL. DEV. = 7.1 DEGREES REMARK 500 ARG A 69 NE - CZ - NH2 ANGL. DEV. = -6.5 DEGREES REMARK 500 ARG A 77 NE - CZ - NH1 ANGL. DEV. = 5.4 DEGREES REMARK 500 ARG A 77 NE - CZ - NH2 ANGL. DEV. = -4.9 DEGREES REMARK 500 ARG A 84 NE - CZ - NH2 ANGL. DEV. = -3.3 DEGREES REMARK 500 ARG A 103 CA - CB - CG ANGL. DEV. = -13.9 DEGREES REMARK 500 ARG A 103 NE - CZ - NH2 ANGL. DEV. = -3.8 DEGREES REMARK 500 TRP A 104 CD1 - CG - CD2 ANGL. DEV. = 5.2 DEGREES REMARK 500 TRP A 104 CE2 - CD2 - CG ANGL. DEV. = -5.6 DEGREES REMARK 500 VAL A 107 CB - CA - C ANGL. DEV. = 11.8 DEGREES REMARK 500 VAL A 107 N - CA - CB ANGL. DEV. = -16.8 DEGREES REMARK 500 VAL A 107 N - CA - C ANGL. DEV. = -17.8 DEGREES REMARK 500 VAL A 112 CA - CB - CG1 ANGL. DEV. = 11.1 DEGREES REMARK 500 VAL A 112 CA - CB - CG2 ANGL. DEV. = -14.2 DEGREES REMARK 500 ARG A 115 NE - CZ - NH1 ANGL. DEV. = 4.2 DEGREES REMARK 500 ARG A 115 NE - CZ - NH2 ANGL. DEV. = -3.5 DEGREES REMARK 500 THR B 8 CA - CB - CG2 ANGL. DEV. = 9.0 DEGREES REMARK 500 THR B 7 CA - C - N ANGL. DEV. = 14.9 DEGREES REMARK 500 TYR B 11 CB - CG - CD2 ANGL. DEV. = -4.0 DEGREES REMARK 500 ARG B 13 NE - CZ - NH1 ANGL. DEV. = 4.9 DEGREES REMARK 500 ARG B 13 NE - CZ - NH2 ANGL. DEV. = -5.5 DEGREES REMARK 500 LEU B 26 N - CA - CB ANGL. DEV. = -13.2 DEGREES REMARK 500 ARG B 27 NE - CZ - NH2 ANGL. DEV. = -3.0 DEGREES REMARK 500 ARG B 29 CA - CB - CG ANGL. DEV. = 19.9 DEGREES REMARK 500 ARG B 29 NE - CZ - NH1 ANGL. DEV. = 3.3 DEGREES REMARK 500 ILE B 30 CA - C - N ANGL. DEV. = 13.5 DEGREES REMARK 500 GLU B 35 CB - CA - C ANGL. DEV. = 12.2 DEGREES REMARK 500 GLU B 35 N - CA - CB ANGL. DEV. = -11.7 DEGREES REMARK 500 GLU B 35 CA - CB - CG ANGL. DEV. = 14.5 DEGREES REMARK 500 ARG B 47 NE - CZ - NH1 ANGL. DEV. = 3.8 DEGREES REMARK 500 ARG B 47 NE - CZ - NH2 ANGL. DEV. = -4.1 DEGREES REMARK 500 REMARK 500 THIS ENTRY HAS 78 ANGLE DEVIATIONS. 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 ARG A 27 -33.36 -31.20 REMARK 500 GLU A 35 -3.94 47.78 REMARK 500 SER A 58 -85.52 11.81 REMARK 500 SER A 61 -69.45 54.58 REMARK 500 LEU A 85 -70.77 -72.66 REMARK 500 THR A 87 -60.84 -108.46 REMARK 500 ILE A 90 -93.85 -112.01 REMARK 500 LEU A 92 66.97 -48.99 REMARK 500 ASP A 93 -84.08 51.44 REMARK 500 ILE A 94 -49.22 159.21 REMARK 500 LYS A 96 -36.93 -168.92 REMARK 500 VAL A 107 -120.72 -110.34 REMARK 500 MET A 108 70.07 45.77 REMARK 500 LYS A 121 49.60 -100.02 REMARK 500 ASP A 122 82.99 156.42 REMARK 500 PHE A 128 67.42 -103.66 REMARK 500 ASN A 130 114.34 -22.62 REMARK 500 ILE A 132 96.59 -45.43 REMARK 500 LEU A 135 88.55 134.80 REMARK 500 LEU B 4 -72.16 -31.46 REMARK 500 ALA B 31 6.71 -57.35 REMARK 500 PRO B 39 -70.44 -3.95 REMARK 500 ALA B 57 -155.70 -142.65 REMARK 500 SER B 58 -88.47 -86.22 REMARK 500 ASP B 59 -95.39 -42.13 REMARK 500 SER B 61 -84.76 75.00 REMARK 500 LEU B 62 109.56 -59.71 REMARK 500 ARG B 69 -79.80 -54.02 REMARK 500 THR B 70 -32.57 -30.00 REMARK 500 ARG B 84 -54.69 151.92 REMARK 500 THR B 87 -78.55 -104.89 REMARK 500 ILE B 89 -71.81 -96.48 REMARK 500 ASP B 93 -13.50 -24.10 REMARK 500 ILE B 94 -122.09 85.32 REMARK 500 ASN B 95 -51.09 8.67 REMARK 500 VAL B 97 -38.93 -21.28 REMARK 500 GLU B 105 7.34 -59.22 REMARK 500 ASP B 122 120.66 118.74 REMARK 500 VAL B 123 -108.48 -106.64 REMARK 500 SER B 124 -69.30 63.19 REMARK 500 ASN B 130 144.09 65.04 REMARK 500 PRO B 133 -83.73 -84.45 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: NON-CIS, NON-TRANS REMARK 500 REMARK 500 THE FOLLOWING PEPTIDE BONDS DEVIATE SIGNIFICANTLY FROM BOTH REMARK 500 CIS AND TRANS CONFORMATION. CIS BONDS, IF ANY, ARE LISTED REMARK 500 ON CISPEP RECORDS. TRANS IS DEFINED AS 180 +/- 30 AND REMARK 500 CIS IS DEFINED AS 0 +/- 30 DEGREES. REMARK 500 MODEL OMEGA REMARK 500 GLY B 38 PRO B 39 144.04 REMARK 500 ASN B 130 PRO B 131 -135.08 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: PLANAR GROUPS REMARK 500 REMARK 500 PLANAR GROUPS IN THE FOLLOWING RESIDUES HAVE A TOTAL REMARK 500 RMS DISTANCE OF ALL ATOMS FROM THE BEST-FIT PLANE REMARK 500 BY MORE THAN AN EXPECTED VALUE OF 6*RMSD, WITH AN REMARK 500 RMSD 0.02 ANGSTROMS, OR AT LEAST ONE ATOM HAS REMARK 500 AN RMSD GREATER THAN THIS VALUE REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI RMS TYPE REMARK 500 TYR A 16 0.07 SIDE_CHAIN REMARK 500 REMARK 500 REMARK: NULL REMARK 650 REMARK 650 HELIX REMARK 650 HELIX REMARK 650 DETERMINATION METHOD: DSSP AND O. REMARK 700 REMARK 700 SHEET REMARK 700 SHEET REMARK 700 SHEET_ID: 1; DETERMINATION METHOD: DSSP AND O. REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: A1 REMARK 800 EVIDENCE_CODE: AUTHOR REMARK 800 SITE_DESCRIPTION: LIGANDS FOR NI(II) REMARK 800 SITE_IDENTIFIER: B1 REMARK 800 EVIDENCE_CODE: AUTHOR REMARK 800 SITE_DESCRIPTION: LIGANDS FOR NI(II) DBREF 1DPR A 1 226 UNP P33120 DTXR_CORDI 1 226 DBREF 1DPR B 1 226 UNP P33120 DTXR_CORDI 1 226 SEQRES 1 A 226 MET LYS ASP LEU VAL ASP THR THR GLU MET TYR LEU ARG SEQRES 2 A 226 THR ILE TYR GLU LEU GLU GLU GLU GLY VAL THR PRO LEU SEQRES 3 A 226 ARG ALA ARG ILE ALA GLU ARG LEU GLU GLN SER GLY PRO SEQRES 4 A 226 THR VAL SER GLN THR VAL ALA ARG MET GLU ARG ASP GLY SEQRES 5 A 226 LEU VAL VAL VAL ALA SER ASP ARG SER LEU GLN MET THR SEQRES 6 A 226 PRO THR GLY ARG THR LEU ALA THR ALA VAL MET ARG LYS SEQRES 7 A 226 HIS ARG LEU ALA GLU ARG LEU LEU THR ASP ILE ILE GLY SEQRES 8 A 226 LEU ASP ILE ASN LYS VAL HIS ASP GLU ALA CYS ARG TRP SEQRES 9 A 226 GLU HIS VAL MET SER ASP GLU VAL GLU ARG ARG LEU VAL SEQRES 10 A 226 LYS VAL LEU LYS ASP VAL SER ARG SER PRO PHE GLY ASN SEQRES 11 A 226 PRO ILE PRO GLY LEU ASP GLU LEU GLY VAL GLY ASN SER SEQRES 12 A 226 ASP ALA ALA ALA PRO GLY THR ARG VAL ILE ASP ALA ALA SEQRES 13 A 226 THR SER MET PRO ARG LYS VAL ARG ILE VAL GLN ILE ASN SEQRES 14 A 226 GLU ILE PHE GLN VAL GLU THR ASP GLN PHE THR GLN LEU SEQRES 15 A 226 LEU ASP ALA ASP ILE ARG VAL GLY SER GLU VAL GLU ILE SEQRES 16 A 226 VAL ASP ARG ASP GLY HIS ILE THR LEU SER HIS ASN GLY SEQRES 17 A 226 LYS ASP VAL GLU LEU LEU ASP ASP LEU ALA HIS THR ILE SEQRES 18 A 226 ARG ILE GLU GLU LEU SEQRES 1 B 226 MET LYS ASP LEU VAL ASP THR THR GLU MET TYR LEU ARG SEQRES 2 B 226 THR ILE TYR GLU LEU GLU GLU GLU GLY VAL THR PRO LEU SEQRES 3 B 226 ARG ALA ARG ILE ALA GLU ARG LEU GLU GLN SER GLY PRO SEQRES 4 B 226 THR VAL SER GLN THR VAL ALA ARG MET GLU ARG ASP GLY SEQRES 5 B 226 LEU VAL VAL VAL ALA SER ASP ARG SER LEU GLN MET THR SEQRES 6 B 226 PRO THR GLY ARG THR LEU ALA THR ALA VAL MET ARG LYS SEQRES 7 B 226 HIS ARG LEU ALA GLU ARG LEU LEU THR ASP ILE ILE GLY SEQRES 8 B 226 LEU ASP ILE ASN LYS VAL HIS ASP GLU ALA CYS ARG TRP SEQRES 9 B 226 GLU HIS VAL MET SER ASP GLU VAL GLU ARG ARG LEU VAL SEQRES 10 B 226 LYS VAL LEU LYS ASP VAL SER ARG SER PRO PHE GLY ASN SEQRES 11 B 226 PRO ILE PRO GLY LEU ASP GLU LEU GLY VAL GLY ASN SER SEQRES 12 B 226 ASP ALA ALA ALA PRO GLY THR ARG VAL ILE ASP ALA ALA SEQRES 13 B 226 THR SER MET PRO ARG LYS VAL ARG ILE VAL GLN ILE ASN SEQRES 14 B 226 GLU ILE PHE GLN VAL GLU THR ASP GLN PHE THR GLN LEU SEQRES 15 B 226 LEU ASP ALA ASP ILE ARG VAL GLY SER GLU VAL GLU ILE SEQRES 16 B 226 VAL ASP ARG ASP GLY HIS ILE THR LEU SER HIS ASN GLY SEQRES 17 B 226 LYS ASP VAL GLU LEU LEU ASP ASP LEU ALA HIS THR ILE SEQRES 18 B 226 ARG ILE GLU GLU LEU HELIX 1 A ASP A 3 GLU A 20 1 18 HELIX 2 B ARG A 27 ARG A 33 1 7 HELIX 3 C GLY A 38 ARG A 50 1 13 HELIX 4 D PRO A 66 ASP A 88 1 23 HELIX 5 E VAL A 97 HIS A 106 1 10 HELIX 6 F ASP A 110 VAL A 119 1 10 HELIX 7 A' ASP B 3 GLU B 20 1 18 HELIX 8 B' ARG B 27 ARG B 33 1 7 HELIX 9 C' GLY B 38 ARG B 50 1 13 HELIX 10 D' PRO B 66 ASP B 88 1 23 HELIX 11 E' VAL B 97 HIS B 106 1 10 HELIX 12 F' ASP B 110 VAL B 119 1 10 SHEET 1 1 2 LEU A 53 ALA A 57 0 SHEET 2 1 2 SER A 61 MET A 64 -1 N GLN A 63 O VAL A 55 SHEET 1 1' 2 LEU B 53 ALA B 57 0 SHEET 2 1' 2 SER B 61 MET B 64 -1 N GLN B 63 O VAL B 55 SITE 1 A1 3 HIS A 79 GLU A 83 HIS A 98 SITE 1 B1 3 HIS B 79 GLU B 83 HIS B 98 CRYST1 64.000 64.000 220.400 90.00 90.00 120.00 P 32 2 1 12 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 0.015625 0.009021 0.000000 0.00000 SCALE2 0.000000 0.018042 0.000000 0.00000 SCALE3 0.000000 0.000000 0.004537 0.00000 MTRIX1 1 -0.507000 0.861000 0.032000 0.28700 1 MTRIX2 1 0.860000 0.503000 0.084000 -5.62200 1 MTRIX3 1 0.057000 0.070000 -0.996000 107.46800 1