HEADER OXIDOREDUCTASE 10-JUL-24 9IOY TITLE ISOPHTHALATE DIOXYGENASE IN COMPLEX WITH ISOPHTHALATE COMPND MOL_ID: 1; COMPND 2 MOLECULE: RIESKE (2FE-2S) DOMAIN PROTEIN; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: ISOPHTHALATE DIOXYGENASE; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: COMAMONAS TESTOSTERONI KF-1; SOURCE 3 ORGANISM_TAXID: 399795; SOURCE 4 GENE: CTESDRAFT_PD2139; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 6 EXPRESSION_SYSTEM_TAXID: 469008 KEYWDS RIESKE OXYGENASE, NON-HEME IRON, RIESKE CENTER, MONONUCLEAR IRON, KEYWDS 2 OXIDOREDUCTASE EXPDTA X-RAY DIFFRACTION AUTHOR K.JANGID,J.K.MAHTO,P.KUMAR REVDAT 3 01-OCT-25 9IOY 1 JRNL REVDAT 2 20-AUG-25 9IOY 1 JRNL REVDAT 1 16-JUL-25 9IOY 0 JRNL AUTH J.K.MAHTO,I.MISHRA,K.JANGID,P.KUMAR JRNL TITL STRUCTURE-GUIDED ENGINEERING OF AN AROMATIC JRNL TITL 2 RING-HYDROXYLATING DIOXYGENASE FOR BROAD-SPECTRUM PHTHALATE JRNL TITL 3 DEGRADATION. JRNL REF J.BACTERIOL. V. 207 22125 2025 JRNL REFN ESSN 1098-5530 JRNL PMID 40793770 JRNL DOI 10.1128/JB.00221-25 REMARK 2 REMARK 2 RESOLUTION. 3.30 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0419 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) : 3.30 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 25.22 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 99.6 REMARK 3 NUMBER OF REFLECTIONS : 15342 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) : 0.177 REMARK 3 R VALUE (WORKING SET) : 0.175 REMARK 3 FREE R VALUE : 0.218 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.800 REMARK 3 FREE R VALUE TEST SET COUNT : 772 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) : 3.30 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 3.39 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1104 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.91 REMARK 3 BIN R VALUE (WORKING SET) : 0.1880 REMARK 3 BIN FREE R VALUE SET COUNT : 56 REMARK 3 BIN FREE R VALUE : 0.2860 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 3467 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 17 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) : 67.20 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.00000 REMARK 3 B22 (A**2) : 0.00000 REMARK 3 B33 (A**2) : 0.00000 REMARK 3 B12 (A**2) : 0.00000 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): 0.924 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.349 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.269 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 17.060 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.925 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.898 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 3583 ; 0.008 ; 0.012 REMARK 3 BOND LENGTHS OTHERS (A): 3231 ; 0.001 ; 0.016 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 4861 ; 1.958 ; 1.832 REMARK 3 BOND ANGLES OTHERS (DEGREES): 7457 ; 0.647 ; 1.762 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 434 ; 7.989 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 29 ;10.218 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 573 ;17.959 ;10.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): NULL ; NULL ; NULL REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 490 ; 0.085 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 4351 ; 0.007 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 861 ; 0.001 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): NULL ; NULL ; NULL 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): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): NULL ; NULL ; NULL 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): 1739 ; 6.586 ; 6.448 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 1739 ; 6.578 ; 6.449 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 2172 ;10.256 ;11.585 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): 2173 ;10.256 ;11.585 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1844 ; 7.519 ; 6.961 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): 1845 ; 7.517 ; 6.960 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): 2686 ;11.671 ;12.557 REMARK 3 LONG RANGE B REFINED ATOMS (A**2): 4119 ;14.510 ;69.860 REMARK 3 LONG RANGE B OTHER ATOMS (A**2): 4120 ;14.509 ;69.860 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 9IOY COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 10-JUL-24. REMARK 100 THE DEPOSITION ID IS D_1300049216. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 30-JUL-22 REMARK 200 TEMPERATURE (KELVIN) : 100 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 MICROMAX-007 HF 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 : PIXEL REMARK 200 DETECTOR MANUFACTURER : RIGAKU HYPIX-6000HE REMARK 200 INTENSITY-INTEGRATION SOFTWARE : CRYSALISPRO REMARK 200 DATA SCALING SOFTWARE : AIMLESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 15945 REMARK 200 RESOLUTION RANGE HIGH (A) : 3.300 REMARK 200 RESOLUTION RANGE LOW (A) : 25.220 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.7 REMARK 200 DATA REDUNDANCY : 3.700 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 9.9000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 3.30 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 3.57 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.93500 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.900 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: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 76.76 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 5.29 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: AMMONIUM FLUORIDE 0.2 M, PEG 3350 20%, REMARK 280 0.1 M MES PH 6.0, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 3 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 REMARK 290 4555 X+1/2,-Y+1/2,-Z REMARK 290 5555 Z,X,Y REMARK 290 6555 Z+1/2,-X+1/2,-Y REMARK 290 7555 -Z+1/2,-X,Y+1/2 REMARK 290 8555 -Z,X+1/2,-Y+1/2 REMARK 290 9555 Y,Z,X REMARK 290 10555 -Y,Z+1/2,-X+1/2 REMARK 290 11555 Y+1/2,-Z+1/2,-X REMARK 290 12555 -Y+1/2,-Z,X+1/2 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 -1.000000 0.000000 0.000000 73.47800 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 73.47800 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 73.47800 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 73.47800 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 73.47800 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 73.47800 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 5 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY2 5 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY1 6 0.000000 0.000000 1.000000 73.47800 REMARK 290 SMTRY2 6 -1.000000 0.000000 0.000000 73.47800 REMARK 290 SMTRY3 6 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY1 7 0.000000 0.000000 -1.000000 73.47800 REMARK 290 SMTRY2 7 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 1.000000 0.000000 73.47800 REMARK 290 SMTRY1 8 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY2 8 1.000000 0.000000 0.000000 73.47800 REMARK 290 SMTRY3 8 0.000000 -1.000000 0.000000 73.47800 REMARK 290 SMTRY1 9 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 9 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY3 9 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY1 10 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 10 0.000000 0.000000 1.000000 73.47800 REMARK 290 SMTRY3 10 -1.000000 0.000000 0.000000 73.47800 REMARK 290 SMTRY1 11 0.000000 1.000000 0.000000 73.47800 REMARK 290 SMTRY2 11 0.000000 0.000000 -1.000000 73.47800 REMARK 290 SMTRY3 11 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY1 12 0.000000 -1.000000 0.000000 73.47800 REMARK 290 SMTRY2 12 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY3 12 1.000000 0.000000 0.000000 73.47800 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: TRIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TRIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 9120 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 45750 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -115.0 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 0.000000 0.000000 -1.000000 0.00000 REMARK 350 BIOMT2 2 1.000000 0.000000 0.000000 73.47800 REMARK 350 BIOMT3 2 0.000000 -1.000000 0.000000 73.47800 REMARK 350 BIOMT1 3 0.000000 1.000000 0.000000 -73.47800 REMARK 350 BIOMT2 3 0.000000 0.000000 -1.000000 73.47800 REMARK 350 BIOMT3 3 -1.000000 0.000000 0.000000 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 -22 REMARK 465 GLY A -21 REMARK 465 SER A -20 REMARK 465 SER A -19 REMARK 465 HIS A -18 REMARK 465 HIS A -17 REMARK 465 HIS A -16 REMARK 465 HIS A -15 REMARK 465 HIS A -14 REMARK 465 HIS A -13 REMARK 465 SER A -12 REMARK 465 SER A -11 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 ASN A 251 ND2 REMARK 470 ASP A 277 CG OD1 OD2 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 CG ASP A 337 FE FE2 A 502 2.00 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 MET A -2 CG - SD - CE ANGL. DEV. = -10.6 DEGREES REMARK 500 GLU A 83 CG - CD - OE2 ANGL. DEV. = -12.1 DEGREES REMARK 500 ARG A 318 CB - CA - C ANGL. DEV. = 12.5 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 LYS A 3 -71.25 -53.92 REMARK 500 PRO A 28 97.05 -67.57 REMARK 500 ILE A 35 49.37 -104.83 REMARK 500 SER A 106 -76.29 -54.48 REMARK 500 ILE A 173 39.66 -98.62 REMARK 500 LYS A 202 44.99 -72.94 REMARK 500 ALA A 203 -86.43 -148.94 REMARK 500 ASN A 225 105.08 -44.56 REMARK 500 ALA A 253 151.76 -48.03 REMARK 500 ASP A 263 -155.33 -143.82 REMARK 500 THR A 358 -1.70 -56.38 REMARK 500 ARG A 366 -70.42 -50.08 REMARK 500 GLU A 411 -70.68 -69.07 REMARK 500 LYS A 418 30.61 -94.26 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 ARG A 24 0.13 SIDE CHAIN REMARK 500 ARG A 72 0.07 SIDE CHAIN REMARK 500 ARG A 159 0.14 SIDE CHAIN REMARK 500 ARG A 354 0.12 SIDE CHAIN REMARK 500 ARG A 367 0.11 SIDE CHAIN 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 FES A 501 FE1 REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 69 SG REMARK 620 2 FES A 501 S1 93.0 REMARK 620 3 FES A 501 S2 120.7 104.3 REMARK 620 4 CYS A 88 SG 127.1 113.6 96.9 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 FES A 501 FE2 REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 71 ND1 REMARK 620 2 FES A 501 S1 124.6 REMARK 620 3 FES A 501 S2 129.8 103.3 REMARK 620 4 HIS A 91 ND1 67.5 116.4 106.2 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 FE2 A 502 FE REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 177 NE2 REMARK 620 2 HIS A 182 NE2 95.5 REMARK 620 3 ASP A 337 OD1 100.2 91.0 REMARK 620 4 ASP A 337 OD2 170.6 92.3 74.4 REMARK 620 N 1 2 3 DBREF 9IOY A 1 424 UNP B7WRK8 B7WRK8_COMTK 1 424 SEQADV 9IOY MET A -22 UNP B7WRK8 INITIATING METHIONINE SEQADV 9IOY GLY A -21 UNP B7WRK8 EXPRESSION TAG SEQADV 9IOY SER A -20 UNP B7WRK8 EXPRESSION TAG SEQADV 9IOY SER A -19 UNP B7WRK8 EXPRESSION TAG SEQADV 9IOY HIS A -18 UNP B7WRK8 EXPRESSION TAG SEQADV 9IOY HIS A -17 UNP B7WRK8 EXPRESSION TAG SEQADV 9IOY HIS A -16 UNP B7WRK8 EXPRESSION TAG SEQADV 9IOY HIS A -15 UNP B7WRK8 EXPRESSION TAG SEQADV 9IOY HIS A -14 UNP B7WRK8 EXPRESSION TAG SEQADV 9IOY HIS A -13 UNP B7WRK8 EXPRESSION TAG SEQADV 9IOY SER A -12 UNP B7WRK8 EXPRESSION TAG SEQADV 9IOY SER A -11 UNP B7WRK8 EXPRESSION TAG SEQADV 9IOY GLU A -10 UNP B7WRK8 EXPRESSION TAG SEQADV 9IOY ASN A -9 UNP B7WRK8 EXPRESSION TAG SEQADV 9IOY LEU A -8 UNP B7WRK8 EXPRESSION TAG SEQADV 9IOY TYR A -7 UNP B7WRK8 EXPRESSION TAG SEQADV 9IOY PHE A -6 UNP B7WRK8 EXPRESSION TAG SEQADV 9IOY GLN A -5 UNP B7WRK8 EXPRESSION TAG SEQADV 9IOY GLY A -4 UNP B7WRK8 EXPRESSION TAG SEQADV 9IOY HIS A -3 UNP B7WRK8 EXPRESSION TAG SEQADV 9IOY MET A -2 UNP B7WRK8 EXPRESSION TAG SEQADV 9IOY ALA A -1 UNP B7WRK8 EXPRESSION TAG SEQADV 9IOY SER A 0 UNP B7WRK8 EXPRESSION TAG SEQRES 1 A 447 MET GLY SER SER HIS HIS HIS HIS HIS HIS SER SER GLU SEQRES 2 A 447 ASN LEU TYR PHE GLN GLY HIS MET ALA SER MET ASN LYS SEQRES 3 A 447 GLU MET SER GLU THR LEU THR ARG VAL GLY PRO ASN THR SEQRES 4 A 447 ARG MET GLY ASN LEU LEU ARG ARG TYR TRP VAL PRO ALA SEQRES 5 A 447 LEU MET SER SER GLU ILE ALA GLU ALA ASP GLY PRO GLN SEQRES 6 A 447 VAL ARG VAL GLN LEU LEU GLY GLU LYS LEU LEU ALA PHE SEQRES 7 A 447 ARG ASN THR ASP GLY LYS ALA CYS LEU ILE SER GLU PHE SEQRES 8 A 447 CYS SER HIS ARG GLY VAL SER LEU TYR PHE GLY ARG ASN SEQRES 9 A 447 GLU GLU ASN GLY ILE ARG CYS ALA TYR HIS GLY VAL LYS SEQRES 10 A 447 PHE ASP GLY ASP GLY GLN CYS VAL ASP VAL PRO SER SER SEQRES 11 A 447 PRO GLN SER CYS ALA ARG MET HIS ILE LYS GLY TYR PRO SEQRES 12 A 447 CYS VAL GLU ARG GLY GLY ILE VAL TRP THR TYR MET GLY SEQRES 13 A 447 PRO GLU GLU HIS LYS PRO SER PRO PRO GLU LEU GLU TRP SEQRES 14 A 447 CYS THR LEU PRO PRO GLU HIS VAL PHE VAL SER LYS ARG SEQRES 15 A 447 LEU GLN TYR SER ASN TRP LEU GLN ALA MET GLU GLY GLY SEQRES 16 A 447 ILE ASP THR ALA HIS VAL SER TYR VAL HIS ARG PHE GLU SEQRES 17 A 447 VAL ASP THR ASP PRO MET HIS GLN GLY VAL LYS ALA LEU SEQRES 18 A 447 ASP TYR ILE LYS ALA ASP GLY ASN VAL LYS PHE GLU ILE SEQRES 19 A 447 GLU GLN THR PRO PHE GLY LEU SER LEU PHE GLY ARG ARG SEQRES 20 A 447 ASN GLY GLU PRO ASP SER TYR TYR TRP ARG ILE THR GLN SEQRES 21 A 447 TRP LEU PHE PRO TRP PHE THR LEU ILE ALA PRO PHE GLY SEQRES 22 A 447 ASN HIS ALA LEU GLY GLY HIS VAL TRP VAL PRO ILE ASP SEQRES 23 A 447 ASP HIS ASN CYS TRP ALA TRP SER ILE ASN TRP GLN PRO SEQRES 24 A 447 ASP GLN PRO LEU THR LYS GLU GLU ARG GLN SER MET GLU SEQRES 25 A 447 GLU GLY LYS GLY ILE HIS VAL GLU TYR GLU GLU PRO GLY SEQRES 26 A 447 SER PHE ILE PRO LYS ALA ASN ARG ASN ASN ASP TYR GLY SEQRES 27 A 447 MET ASP ARG VAL ALA GLN ARG GLU GLU ARG SER TYR SER SEQRES 28 A 447 GLY ILE PHE GLY PHE SER ALA GLN ASP TYR SER LEU GLN SEQRES 29 A 447 GLU SER MET GLY PRO ILE GLN ASP HIS ALA ALA GLU ARG SEQRES 30 A 447 LEU LEU PRO THR ASP LYS ALA ILE VAL MET ALA ARG ARG SEQRES 31 A 447 MET LEU ASN GLU ALA ALA LEU GLY LEU GLU GLN GLY GLU SEQRES 32 A 447 THR PRO PRO ALA LEU ASP ALA SER GLU GLN HIS VAL ARG SEQRES 33 A 447 PRO ALA GLY VAL LEU LEU PRO ARG ASP GLN ASP PRO VAL SEQRES 34 A 447 ALA TRP ALA ARG GLU GLU LEU ALA ASP ALA THR LYS LYS SEQRES 35 A 447 PRO VAL PHE SER LEU HET FES A 501 4 HET FE2 A 502 1 HET 8G0 A 503 12 HETNAM FES FE2/S2 (INORGANIC) CLUSTER HETNAM FE2 FE (II) ION HETNAM 8G0 BENZENE-1,3-DICARBOXYLIC ACID FORMUL 2 FES FE2 S2 FORMUL 3 FE2 FE 2+ FORMUL 4 8G0 C8 H6 O4 HELIX 1 AA1 ASN A 2 ARG A 11 1 10 HELIX 2 AA2 THR A 16 ARG A 24 1 9 HELIX 3 AA3 SER A 75 GLY A 79 5 5 HELIX 4 AA4 SER A 107 MET A 114 5 8 HELIX 5 AA5 GLU A 123 GLY A 125 5 3 HELIX 6 AA6 PRO A 134 LYS A 138 5 5 HELIX 7 AA7 LEU A 144 LEU A 149 1 6 HELIX 8 AA8 PRO A 150 GLU A 152 5 3 HELIX 9 AA9 ASN A 164 GLY A 171 1 8 HELIX 10 AB1 GLY A 172 ASP A 174 5 3 HELIX 11 AB2 THR A 175 VAL A 181 1 7 HELIX 12 AB3 PHE A 184 ASP A 189 1 6 HELIX 13 AB4 LYS A 196 LYS A 202 1 7 HELIX 14 AB5 THR A 281 GLU A 290 1 10 HELIX 15 AB6 ASN A 312 MET A 316 5 5 HELIX 16 AB7 ASP A 317 GLU A 323 1 7 HELIX 17 AB8 GLY A 332 MET A 344 1 13 HELIX 18 AB9 ASP A 349 GLU A 353 5 5 HELIX 19 AC1 LEU A 356 THR A 358 5 3 HELIX 20 AC2 ASP A 359 GLN A 378 1 20 HELIX 21 AC3 ASP A 404 LEU A 413 1 10 HELIX 22 AC4 ASP A 415 LYS A 419 5 5 SHEET 1 AA1 2 TYR A -7 PHE A -6 0 SHEET 2 AA1 2 HIS A -3 MET A -2 -1 O HIS A -3 N PHE A -6 SHEET 1 AA2 3 VAL A 27 MET A 31 0 SHEET 2 AA2 3 ILE A 127 THR A 130 -1 O THR A 130 N VAL A 27 SHEET 3 AA2 3 CYS A 121 VAL A 122 -1 N VAL A 122 O TRP A 129 SHEET 1 AA3 4 VAL A 43 LEU A 47 0 SHEET 2 AA3 4 GLU A 50 ARG A 56 -1 O LEU A 52 N VAL A 45 SHEET 3 AA3 4 ALA A 62 SER A 66 -1 O ILE A 65 N LEU A 53 SHEET 4 AA3 4 GLY A 118 TYR A 119 -1 O TYR A 119 N LEU A 64 SHEET 1 AA4 3 ARG A 80 ASN A 81 0 SHEET 2 AA4 3 ILE A 86 ARG A 87 -1 O ARG A 87 N ARG A 80 SHEET 3 AA4 3 LYS A 94 PHE A 95 -1 O PHE A 95 N ILE A 86 SHEET 1 AA5 7 VAL A 154 GLN A 161 0 SHEET 2 AA5 7 CYS A 267 TRP A 274 -1 O SER A 271 N SER A 157 SHEET 3 AA5 7 LEU A 254 PRO A 261 -1 N VAL A 260 O TRP A 268 SHEET 4 AA5 7 PHE A 243 ILE A 246 -1 N THR A 244 O HIS A 257 SHEET 5 AA5 7 SER A 230 LEU A 239 -1 N GLN A 237 O LEU A 245 SHEET 6 AA5 7 GLY A 217 GLU A 227 -1 N ARG A 224 O TYR A 232 SHEET 7 AA5 7 LYS A 208 THR A 214 -1 N LYS A 208 O ARG A 223 SHEET 1 AA6 6 VAL A 154 GLN A 161 0 SHEET 2 AA6 6 CYS A 267 TRP A 274 -1 O SER A 271 N SER A 157 SHEET 3 AA6 6 LEU A 254 PRO A 261 -1 N VAL A 260 O TRP A 268 SHEET 4 AA6 6 PHE A 243 ILE A 246 -1 N THR A 244 O HIS A 257 SHEET 5 AA6 6 SER A 230 LEU A 239 -1 N GLN A 237 O LEU A 245 SHEET 6 AA6 6 ALA A 395 PRO A 400 -1 O ALA A 395 N ILE A 235 LINK SG CYS A 69 FE1 FES A 501 1555 1555 2.17 LINK ND1 HIS A 71 FE2 FES A 501 1555 1555 2.19 LINK SG CYS A 88 FE1 FES A 501 1555 1555 2.20 LINK ND1 HIS A 91 FE2 FES A 501 1555 1555 2.26 LINK NE2 HIS A 177 FE FE2 A 502 1555 1555 1.84 LINK NE2 HIS A 182 FE FE2 A 502 1555 1555 2.05 LINK OD1 ASP A 337 FE FE2 A 502 1555 1555 1.90 LINK OD2 ASP A 337 FE FE2 A 502 1555 1555 1.73 CISPEP 1 PHE A 240 PRO A 241 0 -10.49 CRYST1 146.956 146.956 146.956 90.00 90.00 90.00 P 21 3 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 0.006805 0.000000 0.000000 0.00000 SCALE2 0.000000 0.006805 0.000000 0.00000 SCALE3 0.000000 0.000000 0.006805 0.00000 TER 3468 LEU A 424 HETATM 3469 FE1 FES A 501 -22.522 15.137 56.683 1.00 48.62 FE HETATM 3470 FE2 FES A 501 -22.268 15.630 59.285 1.00 49.70 FE HETATM 3471 S1 FES A 501 -24.012 16.171 57.962 1.00 44.18 S HETATM 3472 S2 FES A 501 -20.683 15.170 57.864 1.00 57.18 S HETATM 3473 FE FE2 A 502 -46.263 13.117 19.629 1.00 87.69 FE HETATM 3474 O01 8G0 A 503 -46.457 6.752 17.953 1.00 57.81 O HETATM 3475 C02 8G0 A 503 -45.877 7.331 16.970 1.00 55.25 C HETATM 3476 O03 8G0 A 503 -46.161 7.142 15.781 1.00 47.64 O HETATM 3477 C04 8G0 A 503 -44.813 8.357 17.265 1.00 56.41 C HETATM 3478 C05 8G0 A 503 -44.256 9.128 16.247 1.00 52.33 C HETATM 3479 C06 8G0 A 503 -43.302 10.086 16.548 1.00 52.02 C HETATM 3480 C07 8G0 A 503 -42.895 10.276 17.861 1.00 54.05 C HETATM 3481 C08 8G0 A 503 -43.460 9.533 18.900 1.00 59.22 C HETATM 3482 C09 8G0 A 503 -42.985 9.691 20.365 1.00 60.62 C HETATM 3483 O10 8G0 A 503 -43.285 8.800 21.207 1.00 58.02 O HETATM 3484 O11 8G0 A 503 -42.304 10.686 20.656 1.00 62.64 O HETATM 3485 C12 8G0 A 503 -44.402 8.559 18.581 1.00 62.91 C CONECT 629 3469 CONECT 642 3470 CONECT 782 3469 CONECT 806 3470 CONECT 1481 3473 CONECT 1523 3473 CONECT 2798 3473 CONECT 2799 3473 CONECT 3469 629 782 3471 3472 CONECT 3470 642 806 3471 3472 CONECT 3471 3469 3470 CONECT 3472 3469 3470 CONECT 3473 1481 1523 2798 2799 CONECT 3474 3475 CONECT 3475 3474 3476 3477 CONECT 3476 3475 CONECT 3477 3475 3478 3485 CONECT 3478 3477 3479 CONECT 3479 3478 3480 CONECT 3480 3479 3481 CONECT 3481 3480 3482 3485 CONECT 3482 3481 3483 3484 CONECT 3483 3482 CONECT 3484 3482 CONECT 3485 3477 3481 MASTER 417 0 3 22 25 0 0 6 3484 1 25 35 END