HEADER OXIDOREDUCTASE 03-JUL-09 3I4Y TITLE CRYSTAL STRUCTURE DETERMINATION OF CATECHOL 1,2-DIOXYGENASE FROM TITLE 2 RHODOCOCCUS OPACUS 1CP IN COMPLEX WITH 3,5-DICHLOROCATECHOL COMPND MOL_ID: 1; COMPND 2 MOLECULE: CATECHOL 1,2-DIOXYGENASE; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: 1,2-CTD; COMPND 5 EC: 1.13.11.1 SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: RHODOCOCCUS OPACUS; SOURCE 3 ORGANISM_COMMON: NOCARDIA OPACA; SOURCE 4 ORGANISM_TAXID: 37919; SOURCE 5 STRAIN: 1CP; SOURCE 6 OTHER_DETAILS: GROWN ON BENZOATE KEYWDS BETA-SANDWICH, AROMATIC HYDROCARBONS CATABOLISM, DIOXYGENASE, IRON, KEYWDS 2 METAL-BINDING, OXIDOREDUCTASE EXPDTA X-RAY DIFFRACTION AUTHOR I.MATERA,M.FERRARONI,M.KOLOMYTSEVA,F.BRIGANTI,A.SCOZZAFAVA REVDAT 3 06-SEP-23 3I4Y 1 REMARK LINK REVDAT 2 26-MAY-10 3I4Y 1 JRNL REVDAT 1 12-JAN-10 3I4Y 0 JRNL AUTH I.MATERA,M.FERRARONI,M.KOLOMYTSEVA,L.GOLOVLEVA,A.SCOZZAFAVA, JRNL AUTH 2 F.BRIGANTI JRNL TITL CATECHOL 1,2-DIOXYGENASE FROM THE GRAM-POSITIVE RHODOCOCCUS JRNL TITL 2 OPACUS 1CP: QUANTITATIVE STRUCTURE/ACTIVITY RELATIONSHIP AND JRNL TITL 3 THE CRYSTAL STRUCTURES OF NATIVE ENZYME AND CATECHOLS JRNL TITL 4 ADDUCTS. JRNL REF J.STRUCT.BIOL. V. 170 548 2010 JRNL REFN ISSN 1047-8477 JRNL PMID 20040374 JRNL DOI 10.1016/J.JSB.2009.12.023 REMARK 2 REMARK 2 RESOLUTION. 1.85 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 REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.85 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 74.54 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 96.8 REMARK 3 NUMBER OF REFLECTIONS : 20060 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) : 0.207 REMARK 3 R VALUE (WORKING SET) : 0.204 REMARK 3 FREE R VALUE : 0.267 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 1081 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) : 1.85 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.90 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1406 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 92.06 REMARK 3 BIN R VALUE (WORKING SET) : 0.2890 REMARK 3 BIN FREE R VALUE SET COUNT : 79 REMARK 3 BIN FREE R VALUE : 0.3420 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2002 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 52 REMARK 3 SOLVENT ATOMS : 229 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 31.07 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 34.91 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.81000 REMARK 3 B22 (A**2) : 0.61000 REMARK 3 B33 (A**2) : -1.41000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.02000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.178 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.172 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.139 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 4.669 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.957 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.914 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 2121 ; 0.018 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 2886 ; 1.728 ; 1.969 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 257 ; 6.506 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 97 ;33.888 ;25.052 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 315 ;16.968 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 8 ;23.997 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 303 ; 0.142 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 1646 ; 0.008 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 1056 ; 0.238 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 1406 ; 0.316 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 168 ; 0.238 ; 0.200 REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): 2 ; 0.096 ; 0.200 REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): 99 ; 0.289 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 31 ; 0.208 ; 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): 1314 ; 1.057 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 2067 ; 1.695 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 952 ; 2.458 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 818 ; 3.584 ; 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: NULL REMARK 4 REMARK 4 3I4Y COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 10-JUL-09. REMARK 100 THE DEPOSITION ID IS D_1000053969. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 01-DEC-07 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : EMBL/DESY, HAMBURG REMARK 200 BEAMLINE : X12 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.0028 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARMOSAIC 225 MM CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 21143 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.850 REMARK 200 RESOLUTION RANGE LOW (A) : 74.700 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 96.8 REMARK 200 DATA REDUNDANCY : 3.600 REMARK 200 R MERGE (I) : 0.05000 REMARK 200 R SYM (I) : 0.05000 REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 15.2000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.85 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.95 REMARK 200 COMPLETENESS FOR SHELL (%) : 93.4 REMARK 200 DATA REDUNDANCY IN SHELL : 3.40 REMARK 200 R MERGE FOR SHELL (I) : 0.53900 REMARK 200 R SYM FOR SHELL (I) : 0.53900 REMARK 200 <I/SIGMA(I)> FOR SHELL : 2.200 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: 3HGI REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 42.57 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.14 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PEG 400 38%, MGCL2 0.1 M, PH 7.5, REMARK 280 VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 296K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 1 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,Y,-Z REMARK 290 3555 X+1/2,Y+1/2,Z REMARK 290 4555 -X+1/2,Y+1/2,-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 SMTRY1 2 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 2 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 3 1.000000 0.000000 0.000000 45.40900 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 18.80950 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 45.40900 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 18.80950 REMARK 290 SMTRY3 4 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 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: 8610 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 22120 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -65.0 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 -1.000000 0.000000 0.000000 -6.27354 REMARK 350 BIOMT2 2 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 74.55351 REMARK 375 REMARK 375 SPECIAL POSITION REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL REMARK 375 POSITIONS. REMARK 375 REMARK 375 ATOM RES CSSEQI REMARK 375 HOH A 291 LIES ON A SPECIAL POSITION. 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 GLY A 11 REMARK 465 SER A 12 REMARK 465 GLY A 13 REMARK 465 SER A 14 REMARK 465 ALA A 15 REMARK 465 ALA A 16 REMARK 465 THR A 17 REMARK 465 ASP A 18 REMARK 465 LYS A 19 REMARK 465 PHE A 20 REMARK 465 LYS A 21 REMARK 465 ALA A 22 REMARK 465 GLU A 23 REMARK 465 ARG A 24 REMARK 480 REMARK 480 ZERO OCCUPANCY ATOM REMARK 480 THE FOLLOWING RESIDUES HAVE ATOMS MODELED WITH ZERO REMARK 480 OCCUPANCY. THE LOCATION AND PROPERTIES OF THESE ATOMS REMARK 480 MAY NOT BE RELIABLE. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 480 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 480 M RES C SSEQI ATOMS REMARK 480 LYS A 117 CE NZ REMARK 480 GLU A 182 CB CG CD OE1 OE2 REMARK 480 ILE A 198 CG2 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 O HOH A 313 O HOH A 370 1.97 REMARK 500 O ASN A 274 O HOH A 446 1.99 REMARK 500 O HOH A 313 O HOH A 470 2.00 REMARK 500 O HOH A 455 O HOH A 474 2.12 REMARK 500 N ALA A 25 O HOH A 445 2.19 REMARK 500 CD1 LEU A 77 CL10 35C A 1 2.19 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15 REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375 REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS. REMARK 500 REMARK 500 DISTANCE CUTOFF: REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE REMARK 500 OE1 GLU A 32 O HOH A 491 4556 2.19 REMARK 500 REMARK 500 REMARK: NULL 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 LYS A 117 CD LYS A 117 CE -0.700 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 LYS A 117 CD - CE - NZ ANGL. DEV. = 17.1 DEGREES REMARK 500 GLU A 182 CB - CA - C ANGL. DEV. = 21.6 DEGREES REMARK 500 ILE A 198 CG1 - CB - CG2 ANGL. DEV. = -22.7 DEGREES REMARK 500 ILE A 198 CA - CB - CG2 ANGL. DEV. = -14.3 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 THR A 29 129.77 -32.87 REMARK 500 PHE A 165 23.70 -140.43 REMARK 500 ALA A 166 105.40 -166.74 REMARK 500 ASP A 181 -176.42 -68.66 REMARK 500 THR A 190 -151.61 -146.95 REMARK 500 PRO A 215 41.93 -87.45 REMARK 500 ASP A 260 79.63 -118.40 REMARK 500 REMARK 500 REMARK: NULL REMARK 610 REMARK 610 MISSING HETEROATOM REMARK 610 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 610 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 610 I=INSERTION CODE): REMARK 610 M RES C SSEQI REMARK 610 6PL A 282 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 FE A 281 FE REMARK 620 N RES CSSEQI ATOM REMARK 620 1 35C A 1 O7 REMARK 620 2 35C A 1 O7 16.3 REMARK 620 3 35C A 1 O8 78.9 69.1 REMARK 620 4 35C A 1 O8 81.5 75.7 16.1 REMARK 620 5 TYR A 162 OH 96.1 99.7 155.1 171.1 REMARK 620 6 HIS A 220 NE2 105.7 120.5 107.7 91.7 97.2 REMARK 620 7 HIS A 222 NE2 156.2 140.0 83.6 86.1 93.0 94.9 REMARK 620 N 1 2 3 4 5 6 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE FE A 281 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE 35C A 1 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE 6PL A 282 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3HGI RELATED DB: PDB DBREF 3I4Y A 11 280 UNP P95607 CATA_RHOOP 1 270 SEQRES 1 A 270 GLY SER GLY SER ALA ALA THR ASP LYS PHE LYS ALA GLU SEQRES 2 A 270 ARG ALA THR ALA ASP THR SER PRO GLU ARG LEU ALA ALA SEQRES 3 A 270 ILE ALA LYS ASP ALA LEU GLY ALA LEU ASN ASP VAL ILE SEQRES 4 A 270 LEU LYS HIS GLY VAL THR TYR PRO GLU TYR ARG VAL PHE SEQRES 5 A 270 LYS GLN TRP LEU ILE ASP VAL GLY GLU GLY GLY GLU TRP SEQRES 6 A 270 PRO LEU PHE LEU ASP VAL PHE ILE GLU HIS SER VAL GLU SEQRES 7 A 270 GLU VAL LEU ALA ARG SER ARG LYS GLY THR MET GLY SER SEQRES 8 A 270 ILE GLU GLY PRO TYR TYR ILE GLU ASN SER PRO GLU LEU SEQRES 9 A 270 PRO SER LYS CYS THR LEU PRO MET ARG GLU GLU ASP GLU SEQRES 10 A 270 LYS ILE THR PRO LEU VAL PHE SER GLY GLN VAL THR ASP SEQRES 11 A 270 LEU ASP GLY ASN GLY LEU ALA GLY ALA LYS VAL GLU LEU SEQRES 12 A 270 TRP HIS ALA ASP ASN ASP GLY TYR TYR SER GLN PHE ALA SEQRES 13 A 270 PRO HIS LEU PRO GLU TRP ASN LEU ARG GLY THR ILE ILE SEQRES 14 A 270 ALA ASP GLU GLU GLY ARG TYR GLU ILE THR THR ILE GLN SEQRES 15 A 270 PRO ALA PRO TYR GLN ILE PRO THR ASP GLY PRO THR GLY SEQRES 16 A 270 GLN PHE ILE GLU ALA GLN ASN GLY HIS PRO TRP ARG PRO SEQRES 17 A 270 ALA HIS LEU HIS LEU ILE VAL SER ALA PRO GLY LYS GLU SEQRES 18 A 270 SER VAL THR THR GLN LEU TYR PHE LYS GLY GLY GLU TRP SEQRES 19 A 270 ILE ASP SER ASP VAL ALA SER ALA THR LYS PRO GLU LEU SEQRES 20 A 270 ILE LEU ASP PRO LYS THR GLY ASP ASP GLY LYS ASN TYR SEQRES 21 A 270 VAL THR TYR ASN PHE VAL LEU ASP PRO ALA HET FE A 281 1 HET 35C A 1 20 HET 6PL A 282 41 HETNAM FE FE (III) ION HETNAM 35C 3,5-DICHLOROBENZENE-1,2-DIOL HETNAM 6PL (4S,7R)-4-HYDROXY-N,N,N-TRIMETHYL-9-OXO-7- HETNAM 2 6PL [(PALMITOYLOXY)METHYL]-3,5,8-TRIOXA-4- HETNAM 3 6PL PHOSPHAHEXACOSAN-1-AMINIUM 4-OXIDE HETSYN 6PL 1-PALMITOYL-2-STEAROYL-SN-GLYCERO-3-PHOSPHOCHOLINE FORMUL 2 FE FE 3+ FORMUL 3 35C C6 H4 CL2 O2 FORMUL 4 6PL C42 H85 N O8 P 1+ FORMUL 5 HOH *229(H2 O) HELIX 1 1 SER A 30 GLY A 53 1 24 HELIX 2 2 THR A 55 GLY A 72 1 18 HELIX 3 3 GLU A 74 ILE A 83 1 10 HELIX 4 4 ILE A 83 SER A 94 1 12 HELIX 5 5 GLU A 125 ILE A 129 5 5 HELIX 6 6 GLY A 202 GLN A 211 1 10 HELIX 7 7 LYS A 254 GLU A 256 5 3 SHEET 1 A 6 GLU A 113 LEU A 114 0 SHEET 2 A 6 ARG A 175 ALA A 180 1 O ILE A 179 N LEU A 114 SHEET 3 A 6 ALA A 149 TRP A 154 -1 N VAL A 151 O ILE A 178 SHEET 4 A 6 LEU A 221 SER A 226 -1 O ILE A 224 N GLU A 152 SHEET 5 A 6 VAL A 233 PHE A 239 -1 O THR A 235 N LEU A 223 SHEET 6 A 6 ILE A 258 LEU A 259 1 O LEU A 259 N TYR A 238 SHEET 1 B 5 LYS A 117 THR A 119 0 SHEET 2 B 5 ARG A 185 ILE A 191 1 O THR A 189 N CYS A 118 SHEET 3 B 5 PRO A 131 THR A 139 -1 N PHE A 134 O ILE A 188 SHEET 4 B 5 ASN A 269 THR A 272 1 O ASN A 269 N VAL A 133 SHEET 5 B 5 LYS A 262 THR A 263 -1 N LYS A 262 O TYR A 270 SHEET 1 C 4 LYS A 117 THR A 119 0 SHEET 2 C 4 ARG A 185 ILE A 191 1 O THR A 189 N CYS A 118 SHEET 3 C 4 PRO A 131 THR A 139 -1 N PHE A 134 O ILE A 188 SHEET 4 C 4 PHE A 275 VAL A 276 1 O PHE A 275 N THR A 139 SHEET 1 D 2 TYR A 196 GLN A 197 0 SHEET 2 D 2 TRP A 216 ARG A 217 -1 O ARG A 217 N TYR A 196 SHEET 1 E 2 LYS A 230 GLU A 231 0 SHEET 2 E 2 ASP A 278 PRO A 279 -1 O ASP A 278 N GLU A 231 LINK O7 B35C A 1 FE FE A 281 1555 1555 1.94 LINK O7 A35C A 1 FE FE A 281 1555 1555 2.12 LINK O8 B35C A 1 FE FE A 281 1555 1555 2.13 LINK O8 A35C A 1 FE FE A 281 1555 1555 2.34 LINK OH TYR A 162 FE FE A 281 1555 1555 1.83 LINK NE2 HIS A 220 FE FE A 281 1555 1555 2.18 LINK NE2 HIS A 222 FE FE A 281 1555 1555 2.07 SITE 1 AC1 4 35C A 1 TYR A 162 HIS A 220 HIS A 222 SITE 1 AC2 12 LEU A 77 VAL A 81 ILE A 102 GLY A 104 SITE 2 AC2 12 PRO A 105 TYR A 106 TYR A 162 TYR A 196 SITE 3 AC2 12 ARG A 217 HIS A 220 HIS A 222 FE A 281 SITE 1 AC3 12 ALA A 25 THR A 26 THR A 29 LEU A 45 SITE 2 AC3 12 VAL A 48 GLU A 58 VAL A 61 PHE A 62 SITE 3 AC3 12 TRP A 65 LEU A 79 GLN A 206 PHE A 207 CRYST1 90.818 37.619 74.817 90.00 94.81 90.00 C 1 2 1 4 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 0.011011 0.000000 0.000926 0.00000 SCALE2 0.000000 0.026582 0.000000 0.00000 SCALE3 0.000000 0.000000 0.013413 0.00000