HEADER DNA BINDING PROTEIN 22-JUN-98 2TDX TITLE DIPHTHERIA TOX REPRESSOR (C102D MUTANT) COMPLEXED WITH NICKEL COMPND MOL_ID: 1; COMPND 2 MOLECULE: DIPHTHERIA TOX REPRESSOR; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: DTXR; COMPND 5 ENGINEERED: YES; COMPND 6 MUTATION: YES; COMPND 7 OTHER_DETAILS: COMPLEXED WITH NICKEL (NI) SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: CORYNEBACTERIUM DIPHTHERIAE; SOURCE 3 ORGANISM_TAXID: 1717; SOURCE 4 GENE: DTXR; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 7 EXPRESSION_SYSTEM_PLASMID: PET11C KEYWDS DNA-BINDING REGULATORY PROTEIN, DIPHTHERIA TOX REPRESSOR, KEYWDS 2 TRANSCRIPTION REGULATION, DNA-BINDING PROTEIN, IRON-REGULATED KEYWDS 3 REPRESSOR, DNA BINDING PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR A.WHITE,X.DING,H.ZHENG,N.SCHIERING,D.RINGE,J.R.MURPHY REVDAT 7 22-MAY-24 2TDX 1 REMARK REVDAT 6 09-AUG-23 2TDX 1 REMARK REVDAT 5 03-NOV-21 2TDX 1 KEYWDS REMARK SEQADV SHEET REVDAT 5 2 1 LINK REVDAT 4 13-JUL-11 2TDX 1 VERSN REVDAT 3 24-FEB-09 2TDX 1 VERSN REVDAT 2 01-APR-03 2TDX 1 JRNL REVDAT 1 14-OCT-98 2TDX 0 SPRSDE 14-OCT-98 2TDX 1TDX JRNL AUTH A.WHITE,X.DING,J.C.VANDERSPEK,J.R.MURPHY,D.RINGE JRNL TITL STRUCTURE OF THE METAL-ION-ACTIVATED DIPHTHERIA TOXIN JRNL TITL 2 REPRESSOR/TOX OPERATOR COMPLEX. JRNL REF NATURE V. 394 502 1998 JRNL REFN ISSN 0028-0836 JRNL PMID 9697776 JRNL DOI 10.1038/28893 REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH X.DING,H.ZENG,N.SCHIERING,D.RINGE,J.R.MURPHY REMARK 1 TITL IDENTIFICATION OF THE PRIMARY METAL ION-ACTIVATION SITES OF REMARK 1 TITL 2 THE DIPHTHERIA TOX REPRESSOR BY X-RAY CRYSTALLOGRAPHY AND REMARK 1 TITL 3 SITE-DIRECTED MUTATIONAL ANALYSIS REMARK 1 REF NAT.STRUCT.BIOL. V. 3 382 1996 REMARK 1 REFN ISSN 1072-8368 REMARK 1 REFERENCE 2 REMARK 1 AUTH X.QIU,C.L.VERLINDE,S.ZHANG,M.P.SCHMITT,R.K.HOLMES,W.G.HOL REMARK 1 TITL THREE-DIMENSIONAL STRUCTURE OF THE DIPHTHERIA TOXIN REMARK 1 TITL 2 REPRESSOR IN COMPLEX WITH DIVALENT CATION CO-REPRESSORS REMARK 1 REF STRUCTURE V. 3 87 1995 REMARK 1 REFN ISSN 0969-2126 REMARK 1 REFERENCE 3 REMARK 1 AUTH N.SCHIERING,X.TAO,H.ZENG,J.R.MURPHY,G.A.PETSKO,D.RINGE REMARK 1 TITL STRUCTURES OF THE APO-AND THE METAL ION-ACTIVATED FORMS OF REMARK 1 TITL 2 THE DIPHTHERIA TOX REPRESSOR FROM CORYNEBACTERIUM REMARK 1 TITL 3 DIPHTHERIAE REMARK 1 REF PROC.NATL.ACAD.SCI.USA V. 92 9843 1995 REMARK 1 REFN ISSN 0027-8424 REMARK 2 REMARK 2 RESOLUTION. 2.40 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : X-PLOR 3.851 REMARK 3 AUTHORS : BRUNGER REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.40 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 8.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 2.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : 1000000.000 REMARK 3 DATA CUTOFF LOW (ABS(F)) : 0.0010 REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 84.0 REMARK 3 NUMBER OF REFLECTIONS : 8425 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) : 0.246 REMARK 3 FREE R VALUE : 0.321 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.000 REMARK 3 FREE R VALUE TEST SET COUNT : 897 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 : 5 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 2.40 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.58 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 67.60 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 1197 REMARK 3 BIN R VALUE (WORKING SET) : 0.3000 REMARK 3 BIN FREE R VALUE : 0.3400 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 7.30 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 146 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 : 1101 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 2 REMARK 3 SOLVENT ATOMS : 26 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 27.00 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) : 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) : 0.012 REMARK 3 BOND ANGLES (DEGREES) : 1.330 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 25.40 REMARK 3 IMPROPER ANGLES (DEGREES) : 0.690 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 : PROTEIN_REP.PARAM REMARK 3 PARAMETER FILE 2 : PARAM_NI_AW.PAR REMARK 3 PARAMETER FILE 3 : NULL REMARK 3 TOPOLOGY FILE 1 : TOPH19.PEP REMARK 3 TOPOLOGY FILE 2 : TOP_NI_AW.PAR REMARK 3 TOPOLOGY FILE 3 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 2TDX 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_1000178669. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 01-JUN-95 REMARK 200 TEMPERATURE (KELVIN) : 277 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : ROTATING ANODE REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : RIGAKU RUH2R REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : RIGAKU REMARK 200 INTENSITY-INTEGRATION SOFTWARE : R-AXIS REMARK 200 DATA SCALING SOFTWARE : R-AXIS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 9464 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.320 REMARK 200 RESOLUTION RANGE LOW (A) : 55.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 1.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 80.6 REMARK 200 DATA REDUNDANCY : 2.800 REMARK 200 R MERGE (I) : 0.04100 REMARK 200 R SYM (I) : NULL REMARK 200 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 FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: NULL REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: DIFFERENCE FOURIER REMARK 200 SOFTWARE USED: X-PLOR 3.851 REMARK 200 STARTING MODEL: APO-DTXR (PDB ENTRY 1DPR) REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 70.00 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 4.03 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: NULL REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 31 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+1/3 REMARK 290 3555 -X+Y,-X,Z+2/3 REMARK 290 4555 Y,X,-Z REMARK 290 5555 X-Y,-Y,-Z+2/3 REMARK 290 6555 -X,-X+Y,-Z+1/3 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 35.23333 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 70.46667 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 70.46667 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 35.23333 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,PQS REMARK 350 TOTAL BURIED SURFACE AREA: 2420 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 13450 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -62.0 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 -0.500000 0.866025 0.000000 0.00000 REMARK 350 BIOMT2 2 0.866025 0.500000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 105.70000 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 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 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 VAL A 5 -47.02 69.42 REMARK 500 SER A 37 -163.50 -69.04 REMARK 500 PRO A 39 0.07 -67.94 REMARK 500 SER A 58 36.65 -69.75 REMARK 500 ASP A 59 15.15 -152.19 REMARK 500 PRO A 66 -24.99 -38.68 REMARK 500 GLU A 105 -19.75 -44.82 REMARK 500 LEU A 138 -78.55 -58.65 REMARK 500 REMARK 500 REMARK: NULL REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NI A 552 NI REMARK 620 N RES CSSEQI ATOM REMARK 620 1 MET A 10 SD REMARK 620 2 ASP A 102 O 177.7 REMARK 620 3 ASP A 102 OD1 90.6 87.6 REMARK 620 4 GLU A 105 OE2 91.7 89.7 90.8 REMARK 620 5 HIS A 106 NE2 89.6 92.2 179.4 88.6 REMARK 620 6 HOH A 251 O 88.7 89.9 90.0 179.1 90.6 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NI A 551 NI REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 79 NE2 REMARK 620 2 GLU A 83 OE2 84.5 REMARK 620 3 HIS A 98 ND1 104.4 93.8 REMARK 620 N 1 2 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: NI2 REMARK 800 EVIDENCE_CODE: UNKNOWN REMARK 800 SITE_DESCRIPTION: PRIMARY METAL-ION BINDING SITE (2). REMARK 800 REMARK 800 SITE_IDENTIFIER: NI1 REMARK 800 EVIDENCE_CODE: UNKNOWN REMARK 800 SITE_DESCRIPTION: ANCILLARY METAL-ION BINDING SITE (1). REMARK 800 REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NI A 551 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NI A 552 DBREF 2TDX A 1 226 UNP P33120 DTXR_CORDI 1 226 SEQADV 2TDX ASP A 102 UNP P33120 CYS 102 ENGINEERED MUTATION 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 ASP 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 HET NI A 551 1 HET NI A 552 1 HETNAM NI NICKEL (II) ION FORMUL 2 NI 2(NI 2+) FORMUL 4 HOH *26(H2 O) HELIX 1 A THR A 7 GLU A 21 1 15 HELIX 2 B ARG A 27 ARG A 33 1 7 HELIX 3 C GLY A 38 MET A 48 1 11 HELIX 4 D PRO A 66 ASP A 88 1 23 HELIX 5 E ILE A 94 TRP A 104 1 11 HELIX 6 F ASP A 110 VAL A 119 1 10 SHEET 1 1 2 VAL A 54 VAL A 56 0 SHEET 2 1 2 LEU A 62 MET A 64 -1 LINK SD MET A 10 NI NI A 552 1555 1555 2.45 LINK NE2 HIS A 79 NI NI A 551 1555 1555 2.09 LINK OE2 GLU A 83 NI NI A 551 1555 1555 2.15 LINK ND1 HIS A 98 NI NI A 551 1555 1555 2.10 LINK O ASP A 102 NI NI A 552 1555 1555 2.11 LINK OD1 ASP A 102 NI NI A 552 1555 1555 2.04 LINK OE2 GLU A 105 NI NI A 552 1555 1555 2.16 LINK NE2 HIS A 106 NI NI A 552 1555 1555 2.15 LINK O HOH A 251 NI NI A 552 1555 1555 2.09 SITE 1 NI2 6 NI A 552 MET A 10 ASP A 102 GLU A 105 SITE 2 NI2 6 HIS A 106 HOH A 251 SITE 1 NI1 4 NI A 551 HIS A 79 GLU A 83 HIS A 98 SITE 1 AC1 3 HIS A 79 GLU A 83 HIS A 98 SITE 1 AC2 5 MET A 10 ASP A 102 GLU A 105 HIS A 106 SITE 2 AC2 5 HOH A 251 CRYST1 64.500 64.500 105.700 90.00 90.00 120.00 P 31 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 0.015504 0.008951 0.000000 0.00000 SCALE2 0.000000 0.017902 0.000000 0.00000 SCALE3 0.000000 0.000000 0.009461 0.00000