HEADER TRANSCRIPTION 18-OCT-06 2ISY TITLE CRYSTAL STRUCTURE OF THE NICKEL-ACTIVATED TWO-DOMAIN IRON-DEPENDENT TITLE 2 REGULATOR (IDER) COMPND MOL_ID: 1; COMPND 2 MOLECULE: IRON-DEPENDENT REPRESSOR IDER; COMPND 3 CHAIN: A, B; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: MYCOBACTERIUM TUBERCULOSIS; SOURCE 3 ORGANISM_TAXID: 1773; SOURCE 4 GENE: IDER,DTXR; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 6 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: BL21 (DE3); SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PAER36 KEYWDS DNA-BINDING PROTEIN, TRANSCRIPTION EXPDTA X-RAY DIFFRACTION AUTHOR G.WISEDCHAISRI,C.J.CHOU,M.WU,C.ROACH,A.E.RICE,R.K.HOLMES,C.BEESON, AUTHOR 2 W.G.HOL REVDAT 6 06-NOV-24 2ISY 1 REMARK REVDAT 5 15-NOV-23 2ISY 1 REMARK REVDAT 4 30-AUG-23 2ISY 1 REMARK SEQADV LINK REVDAT 3 18-OCT-17 2ISY 1 REMARK REVDAT 2 24-FEB-09 2ISY 1 VERSN REVDAT 1 13-FEB-07 2ISY 0 JRNL AUTH G.WISEDCHAISRI,C.J.CHOU,M.WU,C.ROACH,A.E.RICE,R.K.HOLMES, JRNL AUTH 2 C.BEESON,W.G.HOL JRNL TITL CRYSTAL STRUCTURES, METAL ACTIVATION, AND DNA-BINDING JRNL TITL 2 PROPERTIES OF TWO-DOMAIN IDER FROM MYCOBACTERIUM JRNL TITL 3 TUBERCULOSIS JRNL REF BIOCHEMISTRY V. 46 436 2007 JRNL REFN ISSN 0006-2960 JRNL PMID 17209554 JRNL DOI 10.1021/BI0609826 REMARK 2 REMARK 2 RESOLUTION. 1.96 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.2.0005 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.96 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 45.13 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 91.5 REMARK 3 NUMBER OF REFLECTIONS : 20606 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) : 0.178 REMARK 3 R VALUE (WORKING SET) : 0.176 REMARK 3 FREE R VALUE : 0.211 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 1058 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) : 1.96 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.01 REMARK 3 REFLECTION IN BIN (WORKING SET) : 820 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 51.84 REMARK 3 BIN R VALUE (WORKING SET) : 0.2240 REMARK 3 BIN FREE R VALUE SET COUNT : 40 REMARK 3 BIN FREE R VALUE : 0.2390 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2300 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 14 REMARK 3 SOLVENT ATOMS : 148 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 28.61 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 2.04000 REMARK 3 B22 (A**2) : -1.04000 REMARK 3 B33 (A**2) : -1.97000 REMARK 3 B12 (A**2) : 0.10000 REMARK 3 B13 (A**2) : -0.60000 REMARK 3 B23 (A**2) : -1.29000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.186 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.155 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.108 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 3.753 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.956 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.941 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 2416 ; 0.011 ; 0.021 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 3296 ; 1.282 ; 1.990 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 312 ; 5.046 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 115 ;30.510 ;23.478 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 425 ;16.530 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 27 ;23.683 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 383 ; 0.097 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 1831 ; 0.005 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 1220 ; 0.234 ; 0.300 REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 1669 ; 0.315 ; 0.500 REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 291 ; 0.209 ; 0.500 REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): 1 ; 0.004 ; 0.010 REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): 51 ; 0.284 ; 0.300 REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 18 ; 0.174 ; 0.500 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): 1529 ; 1.695 ; 3.000 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 2429 ; 2.629 ; 4.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 968 ; 2.651 ; 4.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 857 ; 3.688 ; 5.000 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 : 1.20 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 2ISY COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 25-OCT-06. REMARK 100 THE DEPOSITION ID IS D_1000039976. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 14-DEC-03 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8.2 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 19-ID REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.03320 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : NULL REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 20610 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.950 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 91.8 REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : 0.06000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 12.6000 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) : 2.02 REMARK 200 COMPLETENESS FOR SHELL (%) : 58.1 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.17300 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: MOLREP REMARK 200 STARTING MODEL: PDB ENTRY 1FX7 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 45.30 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.25 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.6 M NA/K PHOSPHATE PH 8.2, VAPOR REMARK 280 DIFFUSION, SITTING DROP, TEMPERATURE 298K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,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 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 ASYMMETRIC UNIT CONTAINS A BIOLOGICAL DIMER 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: 2350 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 14820 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -54.0 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 GLY A 149 REMARK 465 GLY A 150 REMARK 465 GLY A 151 REMARK 465 HIS A 152 REMARK 465 HIS A 153 REMARK 465 HIS A 154 REMARK 465 HIS A 155 REMARK 465 HIS A 156 REMARK 465 HIS A 157 REMARK 465 MET B 1 REMARK 465 GLY B 149 REMARK 465 GLY B 150 REMARK 465 GLY B 151 REMARK 465 HIS B 152 REMARK 465 HIS B 153 REMARK 465 HIS B 154 REMARK 465 HIS B 155 REMARK 465 HIS B 156 REMARK 465 HIS B 157 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 ARG A 60 CG CD NE CZ NH1 NH2 REMARK 470 ARG B 29 CG CD NE CZ NH1 NH2 REMARK 470 GLU B 32 CG CD OE1 OE2 REMARK 470 ARG B 47 CG CD NE CZ NH1 NH2 REMARK 470 ARG B 55 CG CD NE CZ NH1 NH2 REMARK 470 ARG B 60 CG CD NE CZ NH1 NH2 REMARK 470 TYR B 146 CG CD1 CD2 CE1 CE2 CZ OH REMARK 470 GLN B 148 CB CG CD OE1 NE2 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 NH2 ARG B 84 O HOH B 2024 2.05 REMARK 500 OE2 GLU A 19 O HOH A 2059 2.08 REMARK 500 OH TYR A 16 O HOH A 2061 2.17 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 -55.95 74.28 REMARK 500 ASN A 121 53.61 71.44 REMARK 500 VAL B 5 -57.38 66.54 REMARK 500 ARG B 60 -18.52 83.90 REMARK 500 THR B 65 -179.58 -66.44 REMARK 500 ASN B 121 60.86 62.79 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 A1002 NI REMARK 620 N RES CSSEQI ATOM REMARK 620 1 MET A 10 SD REMARK 620 2 CSO A 102 OD 88.4 REMARK 620 3 CSO A 102 O 177.9 90.8 REMARK 620 4 GLU A 105 OE2 86.1 93.5 95.9 REMARK 620 5 HIS A 106 NE2 89.8 176.0 90.8 90.0 REMARK 620 6 HOH A2043 O 91.0 78.8 87.0 171.8 97.7 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NI A1001 NI REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 79 NE2 REMARK 620 2 GLU A 83 OE2 89.2 REMARK 620 3 HIS A 98 ND1 90.9 104.2 REMARK 620 4 PO4 A2001 O4 95.5 85.1 168.8 REMARK 620 5 HOH A2017 O 93.6 167.3 88.2 82.3 REMARK 620 6 HOH A2020 O 178.6 89.5 89.0 84.8 87.7 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NI B1002 NI REMARK 620 N RES CSSEQI ATOM REMARK 620 1 MET B 10 SD REMARK 620 2 CSO B 102 O 178.4 REMARK 620 3 CSO B 102 OD 82.8 95.7 REMARK 620 4 GLU B 105 OE2 92.0 88.6 87.1 REMARK 620 5 HIS B 106 NE2 93.4 88.0 173.1 98.7 REMARK 620 6 HOH B2013 O 91.6 87.6 84.4 170.4 90.0 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NI B1001 NI REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS B 79 NE2 REMARK 620 2 GLU B 83 OE2 88.7 REMARK 620 3 HIS B 98 ND1 94.6 103.1 REMARK 620 4 PO4 B2001 O3 94.5 83.0 169.2 REMARK 620 5 HOH B2017 O 94.4 169.1 87.1 86.3 REMARK 620 6 HOH B2046 O 176.9 88.2 86.2 85.1 88.6 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 1001 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NI A 1002 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NI B 1001 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NI B 1002 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PO4 A 2001 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PO4 B 2001 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1FX7 RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF THE COBALT-ACTIVATED FULL-LENGTH IDER REMARK 900 RELATED ID: 1U8R RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF A FULL-LENGTH IDER-DNA COMPLEX REMARK 900 RELATED ID: 2ISZ RELATED DB: PDB REMARK 900 RELATED ID: 2IT0 RELATED DB: PDB DBREF 2ISY A 1 140 UNP P0A672 IDER_MYCTU 1 140 DBREF 2ISY B 1 140 UNP P0A672 IDER_MYCTU 1 140 SEQADV 2ISY CSO A 102 UNP P0A672 CYS 102 MODIFIED RESIDUE SEQADV 2ISY ALA A 141 UNP P0A672 EXPRESSION TAG SEQADV 2ISY SER A 142 UNP P0A672 EXPRESSION TAG SEQADV 2ISY GLU A 143 UNP P0A672 EXPRESSION TAG SEQADV 2ISY ASN A 144 UNP P0A672 EXPRESSION TAG SEQADV 2ISY LEU A 145 UNP P0A672 EXPRESSION TAG SEQADV 2ISY TYR A 146 UNP P0A672 EXPRESSION TAG SEQADV 2ISY PHE A 147 UNP P0A672 EXPRESSION TAG SEQADV 2ISY GLN A 148 UNP P0A672 EXPRESSION TAG SEQADV 2ISY GLY A 149 UNP P0A672 EXPRESSION TAG SEQADV 2ISY GLY A 150 UNP P0A672 EXPRESSION TAG SEQADV 2ISY GLY A 151 UNP P0A672 EXPRESSION TAG SEQADV 2ISY HIS A 152 UNP P0A672 EXPRESSION TAG SEQADV 2ISY HIS A 153 UNP P0A672 EXPRESSION TAG SEQADV 2ISY HIS A 154 UNP P0A672 EXPRESSION TAG SEQADV 2ISY HIS A 155 UNP P0A672 EXPRESSION TAG SEQADV 2ISY HIS A 156 UNP P0A672 EXPRESSION TAG SEQADV 2ISY HIS A 157 UNP P0A672 EXPRESSION TAG SEQADV 2ISY CSO B 102 UNP P0A672 CYS 102 MODIFIED RESIDUE SEQADV 2ISY ALA B 141 UNP P0A672 EXPRESSION TAG SEQADV 2ISY SER B 142 UNP P0A672 EXPRESSION TAG SEQADV 2ISY GLU B 143 UNP P0A672 EXPRESSION TAG SEQADV 2ISY ASN B 144 UNP P0A672 EXPRESSION TAG SEQADV 2ISY LEU B 145 UNP P0A672 EXPRESSION TAG SEQADV 2ISY TYR B 146 UNP P0A672 EXPRESSION TAG SEQADV 2ISY PHE B 147 UNP P0A672 EXPRESSION TAG SEQADV 2ISY GLN B 148 UNP P0A672 EXPRESSION TAG SEQADV 2ISY GLY B 149 UNP P0A672 EXPRESSION TAG SEQADV 2ISY GLY B 150 UNP P0A672 EXPRESSION TAG SEQADV 2ISY GLY B 151 UNP P0A672 EXPRESSION TAG SEQADV 2ISY HIS B 152 UNP P0A672 EXPRESSION TAG SEQADV 2ISY HIS B 153 UNP P0A672 EXPRESSION TAG SEQADV 2ISY HIS B 154 UNP P0A672 EXPRESSION TAG SEQADV 2ISY HIS B 155 UNP P0A672 EXPRESSION TAG SEQADV 2ISY HIS B 156 UNP P0A672 EXPRESSION TAG SEQADV 2ISY HIS B 157 UNP P0A672 EXPRESSION TAG SEQRES 1 A 157 MET ASN GLU LEU VAL ASP THR THR GLU MET TYR LEU ARG SEQRES 2 A 157 THR ILE TYR ASP LEU GLU GLU GLU GLY VAL THR PRO LEU SEQRES 3 A 157 ARG ALA ARG ILE ALA GLU ARG LEU ASP GLN SER GLY PRO SEQRES 4 A 157 THR VAL SER GLN THR VAL SER ARG MET GLU ARG ASP GLY SEQRES 5 A 157 LEU LEU ARG VAL ALA GLY ASP ARG HIS LEU GLU LEU THR SEQRES 6 A 157 GLU LYS GLY ARG ALA LEU ALA ILE ALA VAL MET ARG LYS SEQRES 7 A 157 HIS ARG LEU ALA GLU ARG LEU LEU VAL ASP VAL ILE GLY SEQRES 8 A 157 LEU PRO TRP GLU GLU VAL HIS ALA GLU ALA CSO ARG TRP SEQRES 9 A 157 GLU HIS VAL MET SER GLU ASP VAL GLU ARG ARG LEU VAL SEQRES 10 A 157 LYS VAL LEU ASN ASN PRO THR THR SER PRO PHE GLY ASN SEQRES 11 A 157 PRO ILE PRO GLY LEU VAL GLU LEU GLY VAL ALA SER GLU SEQRES 12 A 157 ASN LEU TYR PHE GLN GLY GLY GLY HIS HIS HIS HIS HIS SEQRES 13 A 157 HIS SEQRES 1 B 157 MET ASN GLU LEU VAL ASP THR THR GLU MET TYR LEU ARG SEQRES 2 B 157 THR ILE TYR ASP LEU GLU GLU GLU GLY VAL THR PRO LEU SEQRES 3 B 157 ARG ALA ARG ILE ALA GLU ARG LEU ASP GLN SER GLY PRO SEQRES 4 B 157 THR VAL SER GLN THR VAL SER ARG MET GLU ARG ASP GLY SEQRES 5 B 157 LEU LEU ARG VAL ALA GLY ASP ARG HIS LEU GLU LEU THR SEQRES 6 B 157 GLU LYS GLY ARG ALA LEU ALA ILE ALA VAL MET ARG LYS SEQRES 7 B 157 HIS ARG LEU ALA GLU ARG LEU LEU VAL ASP VAL ILE GLY SEQRES 8 B 157 LEU PRO TRP GLU GLU VAL HIS ALA GLU ALA CSO ARG TRP SEQRES 9 B 157 GLU HIS VAL MET SER GLU ASP VAL GLU ARG ARG LEU VAL SEQRES 10 B 157 LYS VAL LEU ASN ASN PRO THR THR SER PRO PHE GLY ASN SEQRES 11 B 157 PRO ILE PRO GLY LEU VAL GLU LEU GLY VAL ALA SER GLU SEQRES 12 B 157 ASN LEU TYR PHE GLN GLY GLY GLY HIS HIS HIS HIS HIS SEQRES 13 B 157 HIS MODRES 2ISY CSO A 102 CYS S-HYDROXYCYSTEINE MODRES 2ISY CSO B 102 CYS S-HYDROXYCYSTEINE HET CSO A 102 9 HET CSO B 102 9 HET NI A1001 1 HET NI A1002 1 HET PO4 A2001 5 HET NI B1001 1 HET NI B1002 1 HET PO4 B2001 5 HETNAM CSO S-HYDROXYCYSTEINE HETNAM NI NICKEL (II) ION HETNAM PO4 PHOSPHATE ION FORMUL 1 CSO 2(C3 H7 N O3 S) FORMUL 3 NI 4(NI 2+) FORMUL 5 PO4 2(O4 P 3-) FORMUL 9 HOH *148(H2 O) HELIX 1 1 ASP A 6 GLU A 21 1 16 HELIX 2 2 LEU A 26 ASP A 35 1 10 HELIX 3 3 SER A 37 ASP A 51 1 15 HELIX 4 4 THR A 65 VAL A 89 1 25 HELIX 5 5 PRO A 93 GLU A 105 1 13 HELIX 6 6 SER A 109 LEU A 120 1 12 HELIX 7 7 GLY A 134 GLY A 139 1 6 HELIX 8 8 ASP B 6 GLU B 21 1 16 HELIX 9 9 LEU B 26 LEU B 34 1 9 HELIX 10 10 SER B 37 ASP B 51 1 15 HELIX 11 11 THR B 65 VAL B 89 1 25 HELIX 12 12 PRO B 93 GLU B 105 1 13 HELIX 13 13 SER B 109 LEU B 120 1 12 HELIX 14 14 GLY B 134 GLY B 139 1 6 SHEET 1 A 2 LEU A 54 VAL A 56 0 SHEET 2 A 2 LEU A 62 LEU A 64 -1 O GLU A 63 N ARG A 55 SHEET 1 B 2 LEU B 54 VAL B 56 0 SHEET 2 B 2 LEU B 62 LEU B 64 -1 O GLU B 63 N ARG B 55 LINK C ALA A 101 N CSO A 102 1555 1555 1.33 LINK C CSO A 102 N ARG A 103 1555 1555 1.34 LINK C ALA B 101 N CSO B 102 1555 1555 1.34 LINK C CSO B 102 N ARG B 103 1555 1555 1.34 LINK SD MET A 10 NI NI A1002 1555 1555 2.42 LINK NE2 HIS A 79 NI NI A1001 1555 1555 2.22 LINK OE2 GLU A 83 NI NI A1001 1555 1555 2.14 LINK ND1 HIS A 98 NI NI A1001 1555 1555 2.15 LINK OD ACSO A 102 NI NI A1002 1555 1555 1.91 LINK O CSO A 102 NI NI A1002 1555 1555 2.15 LINK OE2 GLU A 105 NI NI A1002 1555 1555 2.04 LINK NE2 HIS A 106 NI NI A1002 1555 1555 2.07 LINK NI NI A1001 O4 PO4 A2001 1555 1555 2.17 LINK NI NI A1001 O HOH A2017 1555 1555 2.37 LINK NI NI A1001 O HOH A2020 1555 1555 2.19 LINK NI NI A1002 O HOH A2043 1555 1555 2.21 LINK SD MET B 10 NI NI B1002 1555 1555 2.47 LINK NE2 HIS B 79 NI NI B1001 1555 1555 2.08 LINK OE2 GLU B 83 NI NI B1001 1555 1555 2.11 LINK ND1 HIS B 98 NI NI B1001 1555 1555 2.11 LINK O CSO B 102 NI NI B1002 1555 1555 2.08 LINK OD ACSO B 102 NI NI B1002 1555 1555 2.12 LINK OE2 GLU B 105 NI NI B1002 1555 1555 2.12 LINK NE2 HIS B 106 NI NI B1002 1555 1555 1.98 LINK NI NI B1001 O3 PO4 B2001 1555 1555 2.25 LINK NI NI B1001 O HOH B2017 1555 1555 2.08 LINK NI NI B1001 O HOH B2046 1555 1555 2.19 LINK NI NI B1002 O HOH B2013 1555 1555 2.18 SITE 1 AC1 6 HIS A 79 GLU A 83 HIS A 98 PO4 A2001 SITE 2 AC1 6 HOH A2017 HOH A2020 SITE 1 AC2 5 MET A 10 CSO A 102 GLU A 105 HIS A 106 SITE 2 AC2 5 HOH A2043 SITE 1 AC3 6 HIS B 79 GLU B 83 HIS B 98 PO4 B2001 SITE 2 AC3 6 HOH B2017 HOH B2046 SITE 1 AC4 5 MET B 10 CSO B 102 GLU B 105 HIS B 106 SITE 2 AC4 5 HOH B2013 SITE 1 AC5 11 HIS A 79 ARG A 80 GLU A 83 SER A 126 SITE 2 AC5 11 PHE A 128 ASN A 130 NI A1001 HOH A2017 SITE 3 AC5 11 HOH A2020 HOH A2041 HOH A2054 SITE 1 AC6 10 HIS B 79 ARG B 80 GLU B 83 SER B 126 SITE 2 AC6 10 PHE B 128 ASN B 130 NI B1001 HOH B2017 SITE 3 AC6 10 HOH B2042 HOH B2046 CRYST1 41.954 44.743 49.641 110.18 96.57 108.29 P 1 2 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 0.023836 0.007878 0.006478 0.00000 SCALE2 0.000000 0.023539 0.010390 0.00000 SCALE3 0.000000 0.000000 0.022165 0.00000