HEADER TRANSCRIPTION REGULATOR 26-JUL-07 2QQB TITLE CRYSTAL STRUCTURE OF DTXR(M10A C102D) COMPLEXED WITH NICKEL(II) COMPND MOL_ID: 1; COMPND 2 MOLECULE: DIPHTHERIA TOXIN REPRESSOR; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: IRON-DEPENDENT DIPHTHERIA TOX REGULATORY ELEMENT, TOX COMPND 5 REGULATORY FACTOR; COMPND 6 ENGINEERED: YES; COMPND 7 MUTATION: YES 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 BL21(DE3); SOURCE 6 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: BL-21(DE3) KEYWDS REPRESSOR, REGULATOR, DTXR, HELIX-TURN-HELIX, METAL ION, ACTIVATION, KEYWDS 2 DNA-BINDING, FERROUS IRON, CYTOPLASM, TRANSCRIPTION, TRANSCRIPTION KEYWDS 3 REGULATION, TRANSCRIPTION REGULATOR EXPDTA X-RAY DIFFRACTION AUTHOR J.A.D'AQUINO,J.R.LATTIMER,A.DENNINGER,K.E.D'AQUINO,D.RINGE REVDAT 6 30-AUG-23 2QQB 1 REMARK REVDAT 5 20-OCT-21 2QQB 1 REMARK SEQADV REVDAT 4 04-APR-18 2QQB 1 REMARK REVDAT 3 25-OCT-17 2QQB 1 REMARK REVDAT 2 24-FEB-09 2QQB 1 VERSN REVDAT 1 30-OCT-07 2QQB 0 JRNL AUTH J.A.D'AQUINO,J.R.LATTIMER,A.DENNINGER,K.E.D'AQUINO,D.RINGE JRNL TITL ROLE OF THE N-TERMINAL HELIX IN THE METAL ION-INDUCED JRNL TITL 2 ACTIVATION OF THE DIPHTHERIA TOXIN REPRESSOR DTXR. JRNL REF BIOCHEMISTRY V. 46 11761 2007 JRNL REFN ISSN 0006-2960 JRNL PMID 17902703 JRNL DOI 10.1021/BI7007883 REMARK 2 REMARK 2 RESOLUTION. 1.92 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.2.0019 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD WITH PHASES REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.92 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 29.87 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 90.1 REMARK 3 NUMBER OF REFLECTIONS : 15860 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) : 0.229 REMARK 3 R VALUE (WORKING SET) : 0.224 REMARK 3 FREE R VALUE : 0.311 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 853 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 20 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 1.92 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.97 REMARK 3 REFLECTION IN BIN (WORKING SET) : 537 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 41.69 REMARK 3 BIN R VALUE (WORKING SET) : 0.3150 REMARK 3 BIN FREE R VALUE SET COUNT : 25 REMARK 3 BIN FREE R VALUE : 0.4340 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1686 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 7 REMARK 3 SOLVENT ATOMS : 72 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 23.00 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 23.43 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.01000 REMARK 3 B22 (A**2) : -0.01000 REMARK 3 B33 (A**2) : 0.02000 REMARK 3 B12 (A**2) : -0.01000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.208 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.212 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.141 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 4.706 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.921 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.865 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 1755 ; 0.028 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 2387 ; 2.530 ; 1.982 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 225 ; 7.834 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 86 ;39.369 ;23.372 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 329 ;19.735 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 23 ;20.194 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 290 ; 0.212 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 1308 ; 0.010 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 914 ; 0.269 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 1152 ; 0.302 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 95 ; 0.218 ; 0.200 REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): 86 ; 0.237 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 17 ; 0.340 ; 0.200 REMARK 3 SYMMETRY H-BOND OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 MAIN-CHAIN BOND REFINED ATOMS (A**2): 1149 ; 1.301 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 1782 ; 1.885 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 693 ; 3.225 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 599 ; 4.264 ; 4.500 REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 RIGID-BOND RESTRAINTS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; FREE ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; BONDED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 NCS RESTRAINTS STATISTICS REMARK 3 NUMBER OF DIFFERENT NCS GROUPS : NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.40 REMARK 3 ION PROBE RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: HYDROGENS HAVE BEEN ADDED IN THE RIDING REMARK 3 POSITIONS REMARK 4 REMARK 4 2QQB COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 10-SEP-07. REMARK 100 THE DEPOSITION ID IS D_1000043921. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 05-APR-06 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : SEALED TUBE REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : OXFORD DIFFRACTION ENHANCE ULTRA 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 : CCD REMARK 200 DETECTOR MANUFACTURER : OXFORD ONYX CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 15860 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.920 REMARK 200 RESOLUTION RANGE LOW (A) : 29.870 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 90.0 REMARK 200 DATA REDUNDANCY : 7.200 REMARK 200 R MERGE (I) : 0.11400 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 6.0100 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.92 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.97 REMARK 200 COMPLETENESS FOR SHELL (%) : 41.7 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: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER REMARK 200 STARTING MODEL: 1P92 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 46.92 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.32 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.2 M SODIUM PHOSPHATE, 20% PEG 3350, REMARK 280 5 MM NICKEL CHLORIDE, PH 7.5, VAPOR DIFFUSION, HANGING DROP, REMARK 280 TEMPERATURE 298K 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 34.86067 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 69.72133 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 69.72133 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 34.86067 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: 2610 ANGSTROM**2 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 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 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 ASP A 199 REMARK 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 HIS A 201 CG ND1 CD2 CE1 NE2 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 ARG A 27 NE - CZ - NH2 ANGL. DEV. = -3.4 DEGREES REMARK 500 ARG A 33 CG - CD - NE ANGL. DEV. = -17.0 DEGREES REMARK 500 ARG A 33 NE - CZ - NH1 ANGL. DEV. = 4.3 DEGREES REMARK 500 ARG A 33 NE - CZ - NH2 ANGL. DEV. = -8.1 DEGREES REMARK 500 ARG A 60 NE - CZ - NH2 ANGL. DEV. = -3.4 DEGREES REMARK 500 ARG A 69 NE - CZ - NH1 ANGL. DEV. = -3.4 DEGREES REMARK 500 ARG A 69 NE - CZ - NH2 ANGL. DEV. = 3.8 DEGREES REMARK 500 LEU A 81 CA - CB - CG ANGL. DEV. = 15.5 DEGREES REMARK 500 ARG A 151 NE - CZ - NH1 ANGL. DEV. = 3.3 DEGREES REMARK 500 ARG A 151 NE - CZ - NH2 ANGL. DEV. = -5.5 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 VAL A 5 -65.53 61.68 REMARK 500 SER A 58 -63.89 -28.57 REMARK 500 ARG A 60 1.80 86.12 REMARK 500 ARG A 60 9.44 80.21 REMARK 500 VAL A 189 -73.87 51.21 REMARK 500 SER A 191 91.67 149.26 REMARK 500 VAL A 196 -100.75 -128.85 REMARK 500 ASP A 197 179.19 155.52 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 A 190 SER A 191 -44.55 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 551 NI REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 79 NE2 REMARK 620 2 GLU A 83 OE2 83.1 REMARK 620 3 HIS A 98 ND1 97.9 96.4 REMARK 620 4 PO4 A 600 O2 94.1 92.2 166.0 REMARK 620 5 HOH A 613 O 96.0 171.4 92.2 79.3 REMARK 620 N 1 2 3 4 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 ASP A 102 O REMARK 620 2 ASP A 102 OD1 90.6 REMARK 620 3 GLU A 105 OE2 103.6 83.3 REMARK 620 4 HIS A 106 NE2 93.6 171.7 102.6 REMARK 620 5 HOH A 608 O 164.5 77.8 85.4 96.7 REMARK 620 6 HOH A 612 O 86.9 83.9 163.5 89.2 81.8 REMARK 620 N 1 2 3 4 5 REMARK 800 REMARK 800 SITE 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 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PO4 A 600 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1XCV RELATED DB: PDB REMARK 900 RELATED ID: 1P92 RELATED DB: PDB REMARK 900 RELATED ID: 1DDN RELATED DB: PDB REMARK 900 RELATED ID: 2TDX RELATED DB: PDB REMARK 900 RELATED ID: 2QQ9 RELATED DB: PDB REMARK 900 RELATED ID: 2QQA RELATED DB: PDB DBREF 2QQB A 1 226 UNP P33120 DTXR_CORDI 1 226 SEQADV 2QQB ALA A 10 UNP P33120 MET 10 ENGINEERED MUTATION SEQADV 2QQB ASP A 102 UNP P33120 CYS 102 ENGINEERED MUTATION SEQADV 2QQB ALA A 147 UNP P33120 VAL 147 VARIANT SEQADV 2QQB LEU A 214 UNP P33120 ILE 214 VARIANT SEQRES 1 A 226 MET LYS ASP LEU VAL ASP THR THR GLU ALA 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 HET PO4 A 600 5 HETNAM NI NICKEL (II) ION HETNAM PO4 PHOSPHATE ION FORMUL 2 NI 2(NI 2+) FORMUL 4 PO4 O4 P 3- FORMUL 5 HOH *72(H2 O) HELIX 1 1 ASP A 6 GLU A 21 1 16 HELIX 2 2 LEU A 26 GLU A 35 1 10 HELIX 3 3 SER A 37 ASP A 51 1 15 HELIX 4 4 THR A 65 ILE A 89 1 25 HELIX 5 5 ASP A 93 GLU A 105 1 13 HELIX 6 6 SER A 109 LEU A 120 1 12 HELIX 7 7 ARG A 151 ALA A 156 1 6 HELIX 8 8 ASN A 169 GLN A 173 5 5 HELIX 9 9 GLN A 178 ALA A 185 1 8 HELIX 10 10 LEU A 214 ILE A 221 1 8 SHEET 1 A 2 VAL A 54 VAL A 56 0 SHEET 2 A 2 LEU A 62 MET A 64 -1 O GLN A 63 N VAL A 55 SHEET 1 B 5 ASP A 210 LEU A 213 0 SHEET 2 B 5 ILE A 202 SER A 205 -1 N ILE A 202 O LEU A 213 SHEET 3 B 5 GLU A 192 ILE A 195 -1 N GLU A 194 O SER A 205 SHEET 4 B 5 ARG A 161 GLN A 167 -1 N VAL A 163 O VAL A 193 SHEET 5 B 5 ARG A 222 GLU A 224 -1 O ARG A 222 N VAL A 166 LINK NE2 HIS A 79 NI NI A 551 1555 1555 2.06 LINK OE2 GLU A 83 NI NI A 551 1555 1555 2.27 LINK ND1 HIS A 98 NI NI A 551 1555 1555 2.36 LINK O ASP A 102 NI NI A 552 1555 1555 2.22 LINK OD1 ASP A 102 NI NI A 552 1555 1555 2.32 LINK OE2 GLU A 105 NI NI A 552 1555 1555 2.30 LINK NE2 HIS A 106 NI NI A 552 1555 1555 2.07 LINK NI NI A 551 O2 PO4 A 600 1555 1555 2.20 LINK NI NI A 551 O HOH A 613 1555 1555 2.30 LINK NI NI A 552 O HOH A 608 1555 1555 2.32 LINK NI NI A 552 O HOH A 612 1555 1555 2.11 CISPEP 1 VAL A 189 GLY A 190 0 7.75 CISPEP 2 ASN A 207 GLY A 208 0 -1.75 SITE 1 AC1 5 HIS A 79 GLU A 83 HIS A 98 PO4 A 600 SITE 2 AC1 5 HOH A 613 SITE 1 AC2 5 ASP A 102 GLU A 105 HIS A 106 HOH A 608 SITE 2 AC2 5 HOH A 612 SITE 1 AC3 8 HIS A 79 ARG A 80 GLU A 83 SER A 126 SITE 2 AC3 8 PHE A 128 ASN A 130 NI A 551 HOH A 613 CRYST1 62.320 62.320 104.582 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 0.016046 0.009264 0.000000 0.00000 SCALE2 0.000000 0.018528 0.000000 0.00000 SCALE3 0.000000 0.000000 0.009562 0.00000