HEADER SUGAR BINDING PROTEIN 30-MAR-11 3RCB TITLE CRYSTAL STRUCTURE OF THE K102E MUTANT OF KIJD10, A 3-KETOREDUCTASE TITLE 2 FROM ACTINOMADURA KIJANIATA IN COMPLEX WITH TDP-BENZENE AND NADP COMPND MOL_ID: 1; COMPND 2 MOLECULE: SUGAR 3-KETOREDUCTASE; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES; COMPND 5 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ACTINOMADURA KIJANIATA; SOURCE 3 ORGANISM_TAXID: 46161; SOURCE 4 GENE: KIJD10; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: ROSETTA 2; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PET28 KEYWDS SUGAR BIOSYNTHESIS, KETOREDUCTASE, TDP BINDING, NADP BINDING, SUGAR KEYWDS 2 BINDING PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR H.M.HOLDEN,R.L.KUBIAK REVDAT 4 13-SEP-23 3RCB 1 REMARK SEQADV LINK REVDAT 3 13-JUL-11 3RCB 1 JRNL REVDAT 2 22-JUN-11 3RCB 1 JRNL REVDAT 1 08-JUN-11 3RCB 0 JRNL AUTH R.L.KUBIAK,H.M.HOLDEN JRNL TITL COMBINED STRUCTURAL AND FUNCTIONAL INVESTIGATION OF A JRNL TITL 2 C-3''-KETOREDUCTASE INVOLVED IN THE BIOSYNTHESIS OF JRNL TITL 3 DTDP-L-DIGITOXOSE. JRNL REF BIOCHEMISTRY V. 50 5905 2011 JRNL REFN ISSN 0006-2960 JRNL PMID 21598943 JRNL DOI 10.1021/BI200514B REMARK 2 REMARK 2 RESOLUTION. 2.49 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.5.0066 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) : 2.49 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 65.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 97.0 REMARK 3 NUMBER OF REFLECTIONS : 18010 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) : 0.192 REMARK 3 R VALUE (WORKING SET) : 0.189 REMARK 3 FREE R VALUE : 0.253 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 959 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) : 2.49 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.55 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1139 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 85.22 REMARK 3 BIN R VALUE (WORKING SET) : 0.2380 REMARK 3 BIN FREE R VALUE SET COUNT : 72 REMARK 3 BIN FREE R VALUE : 0.2980 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2478 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 117 REMARK 3 SOLVENT ATOMS : 163 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 17.12 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.39000 REMARK 3 B22 (A**2) : 0.18000 REMARK 3 B33 (A**2) : 0.21000 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): NULL REMARK 3 ESU BASED ON FREE R VALUE (A): 0.251 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.155 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 6.844 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.924 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.867 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 2609 ; 0.010 ; 0.021 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 3557 ; 2.275 ; 1.978 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 312 ; 6.790 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 129 ;37.872 ;22.171 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 391 ;15.376 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 31 ;20.421 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 381 ; 0.135 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2037 ; 0.008 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL 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): 1564 ; 1.166 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 2509 ; 2.130 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1045 ; 3.755 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1048 ; 5.637 ; 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 3RCB COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 08-APR-11. REMARK 100 THE DEPOSITION ID IS D_1000064755. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 26-JAN-11 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8.0 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 RU200 REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418 REMARK 200 MONOCHROMATOR : NICKEL FILTER REMARK 200 OPTICS : MONTEL MIRRORS REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : BRUKER PLATINUM 135 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : SAINT REMARK 200 DATA SCALING SOFTWARE : SADABS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 18970 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.490 REMARK 200 RESOLUTION RANGE LOW (A) : 84.270 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 96.9 REMARK 200 DATA REDUNDANCY : 4.000 REMARK 200 R MERGE (I) : 0.09600 REMARK 200 R SYM (I) : 0.09600 REMARK 200 FOR THE DATA SET : 10.6000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.49 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.58 REMARK 200 COMPLETENESS FOR SHELL (%) : 86.9 REMARK 200 DATA REDUNDANCY IN SHELL : 10.60 REMARK 200 R MERGE FOR SHELL (I) : 0.23800 REMARK 200 R SYM FOR SHELL (I) : 0.23800 REMARK 200 FOR SHELL : 3.200 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: MODEL GENERATED USING BINARY COMPLEX, PDB ENTRY REMARK 200 3RBV REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 64.47 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.46 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 1.2 M SODIUM/POTASSIUM PHOSPHATE, 100 REMARK 280 MM HEPPS, 5 MM TDP-BENZENE, 5 MM NADP, PH 8.0, VAPOR DIFFUSION, REMARK 280 HANGING DROP, TEMPERATURE 298K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: I 2 2 2 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,Y,-Z REMARK 290 4555 X,-Y,-Z REMARK 290 5555 X+1/2,Y+1/2,Z+1/2 REMARK 290 6555 -X+1/2,-Y+1/2,Z+1/2 REMARK 290 7555 -X+1/2,Y+1/2,-Z+1/2 REMARK 290 8555 X+1/2,-Y+1/2,-Z+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 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 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 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 36.18550 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 51.74850 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 72.57700 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 36.18550 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 51.74850 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 72.57700 REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 36.18550 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 51.74850 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 72.57700 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 36.18550 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 51.74850 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 72.57700 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: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA 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 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 501 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 MET A -17 REMARK 465 GLY A -16 REMARK 465 SER A -15 REMARK 465 SER A -14 REMARK 465 HIS A -13 REMARK 465 HIS A -12 REMARK 465 HIS A -11 REMARK 465 HIS A -10 REMARK 465 HIS A -9 REMARK 465 HIS A -8 REMARK 465 GLU A -7 REMARK 465 ASN A -6 REMARK 465 LEU A -5 REMARK 465 TYR A -4 REMARK 465 PHE A -3 REMARK 465 GLN A -2 REMARK 465 GLY A -1 REMARK 465 HIS A 0 REMARK 465 MET A 1 REMARK 465 GLU A 2 REMARK 465 ASN A 3 REMARK 465 PRO A 4 REMARK 465 ALA A 5 REMARK 465 ASN A 6 REMARK 465 ALA A 7 REMARK 465 LYS A 164 REMARK 465 PRO A 165 REMARK 465 GLN A 166 REMARK 465 GLY A 167 REMARK 465 ASP A 168 REMARK 465 ILE A 169 REMARK 465 ARG A 170 REMARK 465 TYR A 171 REMARK 465 GLN A 172 REMARK 465 ALA A 173 REMARK 465 ASP A 174 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 ALA A 263 O HOH A 412 2.08 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 ARG A 23 NE - CZ - NH1 ANGL. DEV. = -3.1 DEGREES REMARK 500 ARG A 50 NE - CZ - NH2 ANGL. DEV. = -5.4 DEGREES REMARK 500 ARG A 121 NE - CZ - NH1 ANGL. DEV. = 3.5 DEGREES REMARK 500 LEU A 181 CB - CG - CD1 ANGL. DEV. = -10.4 DEGREES REMARK 500 ARG A 327 NE - CZ - NH2 ANGL. DEV. = -3.2 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 ASP A 71 32.73 -84.23 REMARK 500 ASP A 198 36.80 -98.19 REMARK 500 ASN A 242 74.09 -163.05 REMARK 500 REMARK 500 REMARK: NULL REMARK 615 REMARK 615 ZERO OCCUPANCY ATOM REMARK 615 THE FOLLOWING RESIDUES HAVE ATOMS MODELED WITH ZERO REMARK 615 OCCUPANCY. THE LOCATION AND PROPERTIES OF THESE ATOMS REMARK 615 MAY NOT BE RELIABLE. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 615 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 615 M RES C SSEQI REMARK 615 NAP A 333 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 NA A 335 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ARG A 323 O REMARK 620 2 THR A 324 O 75.5 REMARK 620 3 ALA A 326 O 107.5 93.7 REMARK 620 4 ASP A 328 OD2 107.4 174.3 80.9 REMARK 620 5 HOH A 420 O 152.7 77.9 68.3 98.6 REMARK 620 N 1 2 3 4 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CL A 334 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NA A 335 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PO4 A 336 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE TLO A 337 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE TLO A 338 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3RC1 RELATED DB: PDB REMARK 900 SAME PROTEIN, TERNARY COMPLEX WITH TDP-BENZENE AND NADP; CLOSED REMARK 900 CONFORMATION REMARK 900 RELATED ID: 3RC2 RELATED DB: PDB REMARK 900 SAME PROTEIN, TERNARY COMPLEX WITH TDP-BENZENE AND NADP; OPEN REMARK 900 CONFORMATION REMARK 900 RELATED ID: 3RC7 RELATED DB: PDB REMARK 900 SAME PROTEIN, Y186F MUTANT WITH TDP-BENZENE AND NADP REMARK 900 RELATED ID: 3RC9 RELATED DB: PDB REMARK 900 SAME PROTEIN, K102A MUTANT WITH TDP-BENZENE AND NADP REMARK 900 RELATED ID: 3RBV RELATED DB: PDB REMARK 900 SAME PROTEIN, BINARY COMPLEX WITH NADP DBREF 3RCB A 1 332 UNP B3TMR8 B3TMR8_9ACTO 1 332 SEQADV 3RCB MET A -17 UNP B3TMR8 EXPRESSION TAG SEQADV 3RCB GLY A -16 UNP B3TMR8 EXPRESSION TAG SEQADV 3RCB SER A -15 UNP B3TMR8 EXPRESSION TAG SEQADV 3RCB SER A -14 UNP B3TMR8 EXPRESSION TAG SEQADV 3RCB HIS A -13 UNP B3TMR8 EXPRESSION TAG SEQADV 3RCB HIS A -12 UNP B3TMR8 EXPRESSION TAG SEQADV 3RCB HIS A -11 UNP B3TMR8 EXPRESSION TAG SEQADV 3RCB HIS A -10 UNP B3TMR8 EXPRESSION TAG SEQADV 3RCB HIS A -9 UNP B3TMR8 EXPRESSION TAG SEQADV 3RCB HIS A -8 UNP B3TMR8 EXPRESSION TAG SEQADV 3RCB GLU A -7 UNP B3TMR8 EXPRESSION TAG SEQADV 3RCB ASN A -6 UNP B3TMR8 EXPRESSION TAG SEQADV 3RCB LEU A -5 UNP B3TMR8 EXPRESSION TAG SEQADV 3RCB TYR A -4 UNP B3TMR8 EXPRESSION TAG SEQADV 3RCB PHE A -3 UNP B3TMR8 EXPRESSION TAG SEQADV 3RCB GLN A -2 UNP B3TMR8 EXPRESSION TAG SEQADV 3RCB GLY A -1 UNP B3TMR8 EXPRESSION TAG SEQADV 3RCB HIS A 0 UNP B3TMR8 EXPRESSION TAG SEQADV 3RCB GLU A 102 UNP B3TMR8 LYS 102 ENGINEERED MUTATION SEQRES 1 A 350 MET GLY SER SER HIS HIS HIS HIS HIS HIS GLU ASN LEU SEQRES 2 A 350 TYR PHE GLN GLY HIS MET GLU ASN PRO ALA ASN ALA ASN SEQRES 3 A 350 PRO ILE ARG VAL GLY VAL ILE GLY CYS ALA ASP ILE ALA SEQRES 4 A 350 TRP ARG ARG ALA LEU PRO ALA LEU GLU ALA GLU PRO LEU SEQRES 5 A 350 THR GLU VAL THR ALA ILE ALA SER ARG ARG TRP ASP ARG SEQRES 6 A 350 ALA LYS ARG PHE THR GLU ARG PHE GLY GLY GLU PRO VAL SEQRES 7 A 350 GLU GLY TYR PRO ALA LEU LEU GLU ARG ASP ASP VAL ASP SEQRES 8 A 350 ALA VAL TYR VAL PRO LEU PRO ALA VAL LEU HIS ALA GLU SEQRES 9 A 350 TRP ILE ASP ARG ALA LEU ARG ALA GLY LYS HIS VAL LEU SEQRES 10 A 350 ALA GLU GLU PRO LEU THR THR ASP ARG PRO GLN ALA GLU SEQRES 11 A 350 ARG LEU PHE ALA VAL ALA ARG GLU ARG GLY LEU LEU LEU SEQRES 12 A 350 MET GLU ASN PHE MET PHE LEU HIS HIS PRO GLN HIS ARG SEQRES 13 A 350 GLN VAL ALA ASP MET LEU ASP GLU GLY VAL ILE GLY GLU SEQRES 14 A 350 ILE ARG SER PHE ALA ALA SER PHE THR ILE PRO PRO LYS SEQRES 15 A 350 PRO GLN GLY ASP ILE ARG TYR GLN ALA ASP VAL GLY GLY SEQRES 16 A 350 GLY ALA LEU LEU ASP ILE GLY VAL TYR PRO ILE ARG ALA SEQRES 17 A 350 ALA GLY LEU PHE LEU GLY ALA ASP LEU GLU PHE VAL GLY SEQRES 18 A 350 ALA VAL LEU ARG HIS GLU ARG ASP ARG ASP VAL VAL VAL SEQRES 19 A 350 GLY GLY ASN ALA LEU LEU THR THR ARG GLN GLY VAL THR SEQRES 20 A 350 ALA GLN LEU THR PHE GLY MET GLU HIS ALA TYR THR ASN SEQRES 21 A 350 ASN TYR GLU PHE ARG GLY SER THR GLY ARG LEU TRP MET SEQRES 22 A 350 ASN ARG VAL PHE THR PRO PRO ALA THR TYR GLN PRO VAL SEQRES 23 A 350 VAL HIS ILE GLU ARG GLN ASP HIS ALA GLU GLN PHE VAL SEQRES 24 A 350 LEU PRO ALA HIS ASP GLN PHE ALA LYS SER ILE ARG ALA SEQRES 25 A 350 PHE ALA GLN ALA VAL LEU SER GLY GLU HIS PRO ARG GLU SEQRES 26 A 350 TRP SER GLU ASP SER LEU ARG GLN ALA SER LEU VAL ASP SEQRES 27 A 350 ALA VAL ARG THR GLY ALA ARG ASP ILE TYR PHE PRO HET NAP A 333 48 HET CL A 334 1 HET NA A 335 1 HET PO4 A 336 5 HET TLO A 337 31 HET TLO A 338 31 HETNAM NAP NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE HETNAM CL CHLORIDE ION HETNAM NA SODIUM ION HETNAM PO4 PHOSPHATE ION HETNAM TLO 5'-O-[(S)-HYDROXY{[(S)-HYDROXY(PHENOXY) HETNAM 2 TLO PHOSPHORYL]OXY}PHOSPHORYL]THYMIDINE HETSYN NAP 2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE HETSYN TLO THYMIDINE DIPHOSPHATE PHENOL FORMUL 2 NAP C21 H28 N7 O17 P3 FORMUL 3 CL CL 1- FORMUL 4 NA NA 1+ FORMUL 5 PO4 O4 P 3- FORMUL 6 TLO 2(C16 H20 N2 O11 P2) FORMUL 8 HOH *163(H2 O) HELIX 1 1 ALA A 18 ARG A 24 1 7 HELIX 2 2 ARG A 24 GLU A 32 1 9 HELIX 3 3 ARG A 44 GLY A 56 1 13 HELIX 4 4 GLY A 62 ARG A 69 1 8 HELIX 5 5 PRO A 80 ALA A 94 1 15 HELIX 6 6 ASP A 107 ARG A 121 1 15 HELIX 7 7 PHE A 129 HIS A 134 5 6 HELIX 8 8 PRO A 135 GLU A 146 1 12 HELIX 9 9 GLY A 178 ILE A 183 1 6 HELIX 10 10 GLY A 184 GLY A 196 1 13 HELIX 11 11 ASP A 286 GLY A 302 1 17 HELIX 12 12 PRO A 305 ALA A 326 1 22 SHEET 1 A 6 GLU A 58 GLU A 61 0 SHEET 2 A 6 THR A 35 SER A 42 1 N ILE A 40 O VAL A 60 SHEET 3 A 6 ILE A 10 ILE A 15 1 N VAL A 12 O GLU A 36 SHEET 4 A 6 ALA A 74 VAL A 77 1 O ALA A 74 N GLY A 13 SHEET 5 A 6 HIS A 97 GLU A 101 1 O HIS A 97 N VAL A 75 SHEET 6 A 6 LEU A 125 ASN A 128 1 O ASN A 128 N ALA A 100 SHEET 1 B 9 HIS A 276 VAL A 281 0 SHEET 2 B 9 VAL A 268 ARG A 273 -1 N ARG A 273 O HIS A 276 SHEET 3 B 9 ARG A 252 ASN A 256 -1 N TRP A 254 O HIS A 270 SHEET 4 B 9 THR A 241 GLY A 248 -1 N PHE A 246 O LEU A 253 SHEET 5 B 9 ILE A 152 THR A 160 -1 N ARG A 153 O ARG A 247 SHEET 6 B 9 THR A 229 GLY A 235 1 O GLN A 231 N PHE A 155 SHEET 7 B 9 VAL A 214 THR A 223 -1 N ALA A 220 O LEU A 232 SHEET 8 B 9 GLU A 200 GLU A 209 -1 N GLU A 209 O VAL A 214 SHEET 9 B 9 ARG A 327 PHE A 331 1 O ILE A 329 N HIS A 208 LINK O ARG A 323 NA NA A 335 1555 1555 2.87 LINK O THR A 324 NA NA A 335 1555 1555 2.41 LINK O ALA A 326 NA NA A 335 1555 1555 2.58 LINK OD2 ASP A 328 NA NA A 335 1555 1555 2.59 LINK NA NA A 335 O HOH A 420 1555 1555 2.98 CISPEP 1 GLU A 102 PRO A 103 0 -5.65 CISPEP 2 PHE A 331 PRO A 332 0 -12.54 SITE 1 AC1 2 ASN A 256 HIS A 270 SITE 1 AC2 5 ARG A 323 THR A 324 ALA A 326 ASP A 328 SITE 2 AC2 5 HOH A 420 SITE 1 AC3 4 HIS A 285 LYS A 290 HOH A 368 HOH A 438 SITE 1 AC4 12 ARG A 23 ARG A 24 PHE A 159 PRO A 162 SITE 2 AC4 12 TYR A 186 TYR A 240 ARG A 257 THR A 260 SITE 3 AC4 12 GLN A 274 HOH A 353 HOH A 394 HOH A 418 SITE 1 AC5 18 MET A 126 LEU A 132 HIS A 133 HIS A 137 SITE 2 AC5 18 ARG A 138 ALA A 141 ARG A 189 LEU A 193 SITE 3 AC5 18 PHE A 194 GLU A 307 TRP A 308 ASP A 311 SITE 4 AC5 18 HOH A 359 HOH A 393 HOH A 411 HOH A 434 SITE 5 AC5 18 HOH A 442 HOH A 464 CRYST1 72.371 103.497 145.154 90.00 90.00 90.00 I 2 2 2 8 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 0.013818 0.000000 0.000000 0.00000 SCALE2 0.000000 0.009662 0.000000 0.00000 SCALE3 0.000000 0.000000 0.006889 0.00000