HEADER OXIDOREDUCTASE 21-AUG-15 5DBF TITLE CRYSTAL STRUCTURE OF IRIDOID SYNTHASE FROM CANTHARANTHUS ROSEUS IN TITLE 2 COMPLEX WITH NADPH COMPND MOL_ID: 1; COMPND 2 MOLECULE: IRIDOID SYNTHASE; COMPND 3 CHAIN: A, B; COMPND 4 FRAGMENT: UNP RESIDUES 26-388; COMPND 5 EC: 1.3.1.99; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: CATHARANTHUS ROSEUS; SOURCE 3 ORGANISM_COMMON: MADAGASCAR PERIWINKLE; SOURCE 4 ORGANISM_TAXID: 4058; 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: PET32XA/LIC KEYWDS METAL-BINDING, SUBSTRATE BINDING, ACIDOCALCISOMAL PYROPHOSPHATASE, KEYWDS 2 INHIBITOR, OXIDOREDUCTASE EXPDTA X-RAY DIFFRACTION AUTHOR Y.M.HU,W.D.LIU,Y.Y.ZHENG,Z.X.XU,T.P.KO,C.C.CHEN,R.T.GUO REVDAT 3 08-NOV-23 5DBF 1 JRNL REMARK REVDAT 2 27-JAN-16 5DBF 1 JRNL REVDAT 1 04-NOV-15 5DBF 0 JRNL AUTH Y.M.HU,W.D.LIU,S.R.MALWAL,Y.Y.ZHENG,X.X.FENG,T.P.KO, JRNL AUTH 2 C.C.CHEN,Z.X.XU,M.X.LIU,X.HAN,J.GAO,E.OLDFIELD,R.T.GUO JRNL TITL STRUCTURES OF IRIDOID SYNTHASE FROM CANTHARANTHUS ROSEUS JRNL TITL 2 WITH BOUND NAD(+) , NADPH, OR NAD(+) /10-OXOGERANIAL: JRNL TITL 3 REACTION MECHANISMS JRNL REF ANGEW.CHEM.INT.ED.ENGL. V. 54 15478 2015 JRNL REFN ESSN 1521-3773 JRNL PMID 26768532 JRNL DOI 10.1002/ANIE.201508310 REMARK 2 REMARK 2 RESOLUTION. 2.00 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0073 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) : 2.00 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 25.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 97.1 REMARK 3 NUMBER OF REFLECTIONS : 47205 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) : 0.195 REMARK 3 R VALUE (WORKING SET) : 0.192 REMARK 3 FREE R VALUE : 0.246 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.800 REMARK 3 FREE R VALUE TEST SET COUNT : 2403 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) : 2.00 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.05 REMARK 3 REFLECTION IN BIN (WORKING SET) : 3052 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 86.51 REMARK 3 BIN R VALUE (WORKING SET) : 0.3360 REMARK 3 BIN FREE R VALUE SET COUNT : 166 REMARK 3 BIN FREE R VALUE : 0.3400 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 5707 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 96 REMARK 3 SOLVENT ATOMS : 291 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 45.91 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -1.42000 REMARK 3 B22 (A**2) : 5.92000 REMARK 3 B33 (A**2) : -4.50000 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): 0.204 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.182 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.176 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 6.857 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.964 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.938 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 5959 ; 0.014 ; 0.019 REMARK 3 BOND LENGTHS OTHERS (A): 5576 ; 0.004 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 8106 ; 1.717 ; 1.962 REMARK 3 BOND ANGLES OTHERS (DEGREES): 12891 ; 1.019 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 715 ; 6.343 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 257 ;38.299 ;25.175 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 1002 ;16.767 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 14 ;18.517 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 891 ; 0.108 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 6599 ; 0.008 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): 1343 ; 0.004 ; 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): 2871 ; 3.439 ; 4.360 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 2870 ; 3.435 ; 4.358 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 3583 ; 4.668 ; 6.524 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL 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 NCS TYPE: LOCAL REMARK 3 NUMBER OF DIFFERENT NCS PAIRS : 1 REMARK 3 GROUP CHAIN1 RANGE CHAIN2 RANGE COUNT RMS WEIGHT REMARK 3 1 A 27 390 B 27 390 22340 0.080 0.050 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 U VALUES : REFINED INDIVIDUALLY REMARK 4 REMARK 4 5DBF COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 27-AUG-15. REMARK 100 THE DEPOSITION ID IS D_1000212958. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 30-MAY-15 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 4.6 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : NSRRC REMARK 200 BEAMLINE : BL15A1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.0 REMARK 200 MONOCHROMATOR : GRAPHITE REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : RAYONIX MX-300 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 49651 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.000 REMARK 200 RESOLUTION RANGE LOW (A) : 25.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 97.6 REMARK 200 DATA REDUNDANCY : 5.000 REMARK 200 R MERGE (I) : 0.06400 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 18.1000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.00 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.07 REMARK 200 COMPLETENESS FOR SHELL (%) : 91.1 REMARK 200 DATA REDUNDANCY IN SHELL : 5.00 REMARK 200 R MERGE FOR SHELL (I) : 0.39600 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER REMARK 200 STARTING MODEL: 2V6F REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 46.00 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.28 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: AMMONIUM ACETATE,SODIUM ACETATE REMARK 280 TRIHYDRATE,POLYETHYLENE GLYCOL 4000, GLYCEROL, PH 4.6, VAPOR REMARK 280 DIFFUSION, SITTING DROP, TEMPERATURE 298K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 2 2 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z+1/2 REMARK 290 3555 -X,Y,-Z+1/2 REMARK 290 4555 X,-Y,-Z REMARK 290 5555 X+1/2,Y+1/2,Z 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 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 86.30000 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 86.30000 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 45.88450 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 47.44350 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 45.88450 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 47.44350 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 86.30000 REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 45.88450 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 47.44350 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 86.30000 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 45.88450 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 47.44350 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2 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: 1970 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 29090 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -2.0 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 -91.76900 REMARK 350 BIOMT2 2 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 86.30000 REMARK 350 REMARK 350 BIOMOLECULE: 2 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: 1960 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 29470 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -3.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: 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 350 BIOMT1 2 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 465 REMARK 465 MISSING RESIDUES REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE REMARK 465 EXPERIMENT. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 REMARK 465 M RES C SSSEQI REMARK 465 LYS A 26 REMARK 465 GLU A 154 REMARK 465 GLY A 155 REMARK 465 SER A 156 REMARK 465 LYS A 157 REMARK 465 VAL A 158 REMARK 465 ALA A 391 REMARK 465 TRP A 392 REMARK 465 SER A 393 REMARK 465 HIS A 394 REMARK 465 PRO A 395 REMARK 465 GLN A 396 REMARK 465 PHE A 397 REMARK 465 GLU A 398 REMARK 465 LYS A 399 REMARK 465 LYS B 26 REMARK 465 GLY B 155 REMARK 465 SER B 156 REMARK 465 LYS B 157 REMARK 465 VAL B 158 REMARK 465 ALA B 391 REMARK 465 TRP B 392 REMARK 465 SER B 393 REMARK 465 HIS B 394 REMARK 465 PRO B 395 REMARK 465 GLN B 396 REMARK 465 PHE B 397 REMARK 465 GLU B 398 REMARK 465 LYS B 399 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 ILE B 92 OG SER B 96 2.16 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 O LYS A 325 O LYS A 325 4555 2.13 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 VAL A 249 CB - CA - C ANGL. DEV. = -14.9 DEGREES REMARK 500 VAL A 249 CG1 - CB - CG2 ANGL. DEV. = 10.0 DEGREES REMARK 500 VAL B 249 CB - CA - C ANGL. DEV. = -13.3 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 143 -118.57 -114.07 REMARK 500 ARG A 200 77.76 -118.80 REMARK 500 MET A 213 80.26 -151.91 REMARK 500 THR B 143 -118.42 -114.61 REMARK 500 MET B 213 82.26 -153.22 REMARK 500 REMARK 500 REMARK: NULL REMARK 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH A 636 DISTANCE = 6.29 ANGSTROMS REMARK 525 HOH A 637 DISTANCE = 6.64 ANGSTROMS REMARK 525 HOH A 638 DISTANCE = 6.68 ANGSTROMS REMARK 525 HOH A 639 DISTANCE = 7.08 ANGSTROMS REMARK 525 HOH A 640 DISTANCE = 7.34 ANGSTROMS REMARK 525 HOH A 641 DISTANCE = 7.48 ANGSTROMS REMARK 525 HOH A 642 DISTANCE = 7.59 ANGSTROMS REMARK 525 HOH A 643 DISTANCE = 8.16 ANGSTROMS REMARK 525 HOH A 644 DISTANCE = 9.37 ANGSTROMS REMARK 525 HOH B 644 DISTANCE = 6.76 ANGSTROMS REMARK 525 HOH B 645 DISTANCE = 7.59 ANGSTROMS REMARK 525 HOH B 646 DISTANCE = 8.10 ANGSTROMS REMARK 525 HOH B 647 DISTANCE = 8.24 ANGSTROMS REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue NDP A 401 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue NDP B 401 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 5DBG RELATED DB: PDB REMARK 900 RELATED ID: 5DBI RELATED DB: PDB DBREF 5DBF A 26 388 UNP K7WDL7 IRIS_CATRO 26 388 DBREF 5DBF B 26 388 UNP K7WDL7 IRIS_CATRO 26 388 SEQADV 5DBF ALA A 389 UNP K7WDL7 EXPRESSION TAG SEQADV 5DBF SER A 390 UNP K7WDL7 EXPRESSION TAG SEQADV 5DBF ALA A 391 UNP K7WDL7 EXPRESSION TAG SEQADV 5DBF TRP A 392 UNP K7WDL7 EXPRESSION TAG SEQADV 5DBF SER A 393 UNP K7WDL7 EXPRESSION TAG SEQADV 5DBF HIS A 394 UNP K7WDL7 EXPRESSION TAG SEQADV 5DBF PRO A 395 UNP K7WDL7 EXPRESSION TAG SEQADV 5DBF GLN A 396 UNP K7WDL7 EXPRESSION TAG SEQADV 5DBF PHE A 397 UNP K7WDL7 EXPRESSION TAG SEQADV 5DBF GLU A 398 UNP K7WDL7 EXPRESSION TAG SEQADV 5DBF LYS A 399 UNP K7WDL7 EXPRESSION TAG SEQADV 5DBF ALA B 389 UNP K7WDL7 EXPRESSION TAG SEQADV 5DBF SER B 390 UNP K7WDL7 EXPRESSION TAG SEQADV 5DBF ALA B 391 UNP K7WDL7 EXPRESSION TAG SEQADV 5DBF TRP B 392 UNP K7WDL7 EXPRESSION TAG SEQADV 5DBF SER B 393 UNP K7WDL7 EXPRESSION TAG SEQADV 5DBF HIS B 394 UNP K7WDL7 EXPRESSION TAG SEQADV 5DBF PRO B 395 UNP K7WDL7 EXPRESSION TAG SEQADV 5DBF GLN B 396 UNP K7WDL7 EXPRESSION TAG SEQADV 5DBF PHE B 397 UNP K7WDL7 EXPRESSION TAG SEQADV 5DBF GLU B 398 UNP K7WDL7 EXPRESSION TAG SEQADV 5DBF LYS B 399 UNP K7WDL7 EXPRESSION TAG SEQRES 1 A 374 LYS SER TYR LYS SER VAL ALA LEU VAL VAL GLY VAL THR SEQRES 2 A 374 GLY ILE VAL GLY SER SER LEU ALA GLU VAL LEU LYS LEU SEQRES 3 A 374 PRO ASP THR PRO GLY GLY PRO TRP LYS VAL TYR GLY VAL SEQRES 4 A 374 ALA ARG ARG PRO CYS PRO VAL TRP LEU ALA LYS LYS PRO SEQRES 5 A 374 VAL GLU TYR ILE GLN CYS ASP VAL SER ASP ASN GLN GLU SEQRES 6 A 374 THR ILE SER LYS LEU SER PRO LEU LYS ASP ILE THR HIS SEQRES 7 A 374 ILE PHE TYR VAL SER TRP ILE GLY SER GLU ASP CYS GLN SEQRES 8 A 374 THR ASN ALA THR MET PHE LYS ASN ILE LEU ASN SER VAL SEQRES 9 A 374 ILE PRO ASN ALA SER ASN LEU GLN HIS VAL CYS LEU GLN SEQRES 10 A 374 THR GLY ILE LYS HIS TYR PHE GLY ILE PHE GLU GLU GLY SEQRES 11 A 374 SER LYS VAL VAL PRO HIS ASP SER PRO PHE THR GLU ASP SEQRES 12 A 374 LEU PRO ARG LEU ASN VAL PRO ASN PHE TYR HIS ASP LEU SEQRES 13 A 374 GLU ASP ILE LEU TYR GLU GLU THR GLY LYS ASN ASN LEU SEQRES 14 A 374 THR TRP SER VAL HIS ARG PRO ALA LEU VAL PHE GLY PHE SEQRES 15 A 374 SER PRO CYS SER MET MET ASN ILE VAL SER THR LEU CYS SEQRES 16 A 374 VAL TYR ALA THR ILE CYS LYS HIS GLU ASN LYS ALA LEU SEQRES 17 A 374 VAL TYR PRO GLY SER LYS ASN SER TRP ASN CYS TYR ALA SEQRES 18 A 374 ASP ALA VAL ASP ALA ASP LEU VAL ALA GLU HIS GLU ILE SEQRES 19 A 374 TRP ALA ALA VAL ASP PRO LYS ALA LYS ASN GLN VAL LEU SEQRES 20 A 374 ASN CYS ASN ASN GLY ASP VAL PHE LYS TRP LYS HIS ILE SEQRES 21 A 374 TRP LYS LYS LEU ALA GLU GLU PHE GLY ILE GLU MET VAL SEQRES 22 A 374 GLY TYR VAL GLU GLY LYS GLU GLN VAL SER LEU ALA GLU SEQRES 23 A 374 LEU MET LYS ASP LYS ASP GLN VAL TRP ASP GLU ILE VAL SEQRES 24 A 374 LYS LYS ASN ASN LEU VAL PRO THR LYS LEU LYS GLU ILE SEQRES 25 A 374 ALA ALA PHE TRP PHE ALA ASP ILE ALA PHE CYS SER GLU SEQRES 26 A 374 ASN LEU ILE SER SER MET ASN LYS SER LYS GLU LEU GLY SEQRES 27 A 374 PHE LEU GLY PHE ARG ASN SER MET LYS SER PHE VAL SER SEQRES 28 A 374 CYS ILE ASP LYS MET ARG ASP TYR ARG PHE ILE PRO ALA SEQRES 29 A 374 SER ALA TRP SER HIS PRO GLN PHE GLU LYS SEQRES 1 B 374 LYS SER TYR LYS SER VAL ALA LEU VAL VAL GLY VAL THR SEQRES 2 B 374 GLY ILE VAL GLY SER SER LEU ALA GLU VAL LEU LYS LEU SEQRES 3 B 374 PRO ASP THR PRO GLY GLY PRO TRP LYS VAL TYR GLY VAL SEQRES 4 B 374 ALA ARG ARG PRO CYS PRO VAL TRP LEU ALA LYS LYS PRO SEQRES 5 B 374 VAL GLU TYR ILE GLN CYS ASP VAL SER ASP ASN GLN GLU SEQRES 6 B 374 THR ILE SER LYS LEU SER PRO LEU LYS ASP ILE THR HIS SEQRES 7 B 374 ILE PHE TYR VAL SER TRP ILE GLY SER GLU ASP CYS GLN SEQRES 8 B 374 THR ASN ALA THR MET PHE LYS ASN ILE LEU ASN SER VAL SEQRES 9 B 374 ILE PRO ASN ALA SER ASN LEU GLN HIS VAL CYS LEU GLN SEQRES 10 B 374 THR GLY ILE LYS HIS TYR PHE GLY ILE PHE GLU GLU GLY SEQRES 11 B 374 SER LYS VAL VAL PRO HIS ASP SER PRO PHE THR GLU ASP SEQRES 12 B 374 LEU PRO ARG LEU ASN VAL PRO ASN PHE TYR HIS ASP LEU SEQRES 13 B 374 GLU ASP ILE LEU TYR GLU GLU THR GLY LYS ASN ASN LEU SEQRES 14 B 374 THR TRP SER VAL HIS ARG PRO ALA LEU VAL PHE GLY PHE SEQRES 15 B 374 SER PRO CYS SER MET MET ASN ILE VAL SER THR LEU CYS SEQRES 16 B 374 VAL TYR ALA THR ILE CYS LYS HIS GLU ASN LYS ALA LEU SEQRES 17 B 374 VAL TYR PRO GLY SER LYS ASN SER TRP ASN CYS TYR ALA SEQRES 18 B 374 ASP ALA VAL ASP ALA ASP LEU VAL ALA GLU HIS GLU ILE SEQRES 19 B 374 TRP ALA ALA VAL ASP PRO LYS ALA LYS ASN GLN VAL LEU SEQRES 20 B 374 ASN CYS ASN ASN GLY ASP VAL PHE LYS TRP LYS HIS ILE SEQRES 21 B 374 TRP LYS LYS LEU ALA GLU GLU PHE GLY ILE GLU MET VAL SEQRES 22 B 374 GLY TYR VAL GLU GLY LYS GLU GLN VAL SER LEU ALA GLU SEQRES 23 B 374 LEU MET LYS ASP LYS ASP GLN VAL TRP ASP GLU ILE VAL SEQRES 24 B 374 LYS LYS ASN ASN LEU VAL PRO THR LYS LEU LYS GLU ILE SEQRES 25 B 374 ALA ALA PHE TRP PHE ALA ASP ILE ALA PHE CYS SER GLU SEQRES 26 B 374 ASN LEU ILE SER SER MET ASN LYS SER LYS GLU LEU GLY SEQRES 27 B 374 PHE LEU GLY PHE ARG ASN SER MET LYS SER PHE VAL SER SEQRES 28 B 374 CYS ILE ASP LYS MET ARG ASP TYR ARG PHE ILE PRO ALA SEQRES 29 B 374 SER ALA TRP SER HIS PRO GLN PHE GLU LYS HET NDP A 401 48 HET NDP B 401 48 HETNAM NDP NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE HETNAM 2 NDP PHOSPHATE FORMUL 3 NDP 2(C21 H30 N7 O17 P3) FORMUL 5 HOH *291(H2 O) HELIX 1 AA1 VAL A 41 LEU A 49 1 9 HELIX 2 AA2 PRO A 70 LYS A 75 1 6 HELIX 3 AA3 ASP A 87 SER A 96 1 10 HELIX 4 AA4 ASP A 114 ILE A 130 1 17 HELIX 5 AA5 GLY A 144 PHE A 149 5 6 HELIX 6 AA6 ASN A 176 ASN A 192 1 17 HELIX 7 AA7 ASN A 214 GLU A 229 1 16 HELIX 8 AA8 SER A 238 CYS A 244 1 7 HELIX 9 AA9 ALA A 251 ASP A 264 1 14 HELIX 10 AB1 PRO A 265 LYS A 268 5 4 HELIX 11 AB2 LYS A 281 PHE A 293 1 13 HELIX 12 AB3 SER A 308 MET A 313 1 6 HELIX 13 AB4 LYS A 316 ASN A 328 1 13 HELIX 14 AB5 LYS A 333 ALA A 338 1 6 HELIX 15 AB6 ALA A 339 PHE A 347 1 9 HELIX 16 AB7 MET A 356 LEU A 362 1 7 HELIX 17 AB8 ASN A 369 TYR A 384 1 16 HELIX 18 AB9 VAL B 41 LEU B 49 1 9 HELIX 19 AC1 PRO B 70 LYS B 75 1 6 HELIX 20 AC2 ASP B 87 SER B 96 1 10 HELIX 21 AC3 ASP B 114 ILE B 130 1 17 HELIX 22 AC4 GLY B 144 PHE B 149 5 6 HELIX 23 AC5 ASN B 176 ASN B 192 1 17 HELIX 24 AC6 ASN B 214 GLU B 229 1 16 HELIX 25 AC7 SER B 238 CYS B 244 1 7 HELIX 26 AC8 ALA B 251 ASP B 264 1 14 HELIX 27 AC9 PRO B 265 LYS B 268 5 4 HELIX 28 AD1 LYS B 281 PHE B 293 1 13 HELIX 29 AD2 SER B 308 MET B 313 1 6 HELIX 30 AD3 LYS B 316 ASN B 328 1 13 HELIX 31 AD4 LYS B 333 ALA B 338 1 6 HELIX 32 AD5 ALA B 339 PHE B 347 1 9 HELIX 33 AD6 MET B 356 LEU B 362 1 7 HELIX 34 AD7 ASN B 369 TYR B 384 1 16 SHEET 1 AA1 7 GLU A 79 GLN A 82 0 SHEET 2 AA1 7 TRP A 59 ALA A 65 1 N GLY A 63 O ILE A 81 SHEET 3 AA1 7 SER A 30 VAL A 35 1 N VAL A 34 O TYR A 62 SHEET 4 AA1 7 HIS A 103 TYR A 106 1 O PHE A 105 N LEU A 33 SHEET 5 AA1 7 HIS A 138 GLN A 142 1 O CYS A 140 N TYR A 106 SHEET 6 AA1 7 THR A 195 PRO A 201 1 O HIS A 199 N LEU A 141 SHEET 7 AA1 7 GLN A 270 CYS A 274 1 O LEU A 272 N VAL A 198 SHEET 1 AA2 2 LEU A 203 PHE A 205 0 SHEET 2 AA2 2 ALA A 248 ASP A 250 1 O VAL A 249 N PHE A 205 SHEET 1 AA3 2 LEU A 233 VAL A 234 0 SHEET 2 AA3 2 MET A 297 VAL A 298 1 O VAL A 298 N LEU A 233 SHEET 1 AA4 7 GLU B 79 GLN B 82 0 SHEET 2 AA4 7 TRP B 59 ALA B 65 1 N GLY B 63 O ILE B 81 SHEET 3 AA4 7 SER B 30 VAL B 35 1 N VAL B 34 O TYR B 62 SHEET 4 AA4 7 HIS B 103 TYR B 106 1 O PHE B 105 N LEU B 33 SHEET 5 AA4 7 HIS B 138 GLN B 142 1 O CYS B 140 N TYR B 106 SHEET 6 AA4 7 THR B 195 PRO B 201 1 O HIS B 199 N LEU B 141 SHEET 7 AA4 7 GLN B 270 CYS B 274 1 O LEU B 272 N VAL B 198 SHEET 1 AA5 2 LEU B 203 PHE B 205 0 SHEET 2 AA5 2 ALA B 248 ASP B 250 1 O VAL B 249 N PHE B 205 SHEET 1 AA6 2 LEU B 233 VAL B 234 0 SHEET 2 AA6 2 MET B 297 VAL B 298 1 O VAL B 298 N LEU B 233 CISPEP 1 GLY A 57 PRO A 58 0 -1.00 CISPEP 2 SER A 163 PRO A 164 0 9.65 CISPEP 3 GLY B 57 PRO B 58 0 -3.59 CISPEP 4 SER B 163 PRO B 164 0 9.38 SITE 1 AC1 24 GLY A 36 THR A 38 GLY A 39 ILE A 40 SITE 2 AC1 24 ALA A 65 ARG A 66 ARG A 67 CYS A 83 SITE 3 AC1 24 ASP A 84 VAL A 85 SER A 108 TRP A 109 SITE 4 AC1 24 MET A 121 GLN A 142 THR A 143 TYR A 178 SITE 5 AC1 24 PRO A 201 ALA A 202 VAL A 204 SER A 211 SITE 6 AC1 24 MET A 212 MET A 213 HOH A 516 HOH A 535 SITE 1 AC2 25 GLY B 36 THR B 38 GLY B 39 ILE B 40 SITE 2 AC2 25 ALA B 65 ARG B 66 ARG B 67 CYS B 83 SITE 3 AC2 25 ASP B 84 VAL B 85 SER B 108 TRP B 109 SITE 4 AC2 25 MET B 121 GLN B 142 THR B 143 TYR B 178 SITE 5 AC2 25 PRO B 201 ALA B 202 VAL B 204 SER B 211 SITE 6 AC2 25 MET B 212 MET B 213 HOH B 511 HOH B 552 SITE 7 AC2 25 HOH B 569 CRYST1 91.769 94.887 172.600 90.00 90.00 90.00 C 2 2 21 16 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 0.010897 0.000000 0.000000 0.00000 SCALE2 0.000000 0.010539 0.000000 0.00000 SCALE3 0.000000 0.000000 0.005794 0.00000