HEADER HYDROLASE 26-FEB-09 3GF0 TITLE BIFUNCTIONAL DCTP DEAMINASE-DUTPASE MUTANT ENZYME VARIANT E145Q FROM TITLE 2 METHANOCALDOCOCCUS JANNASCHII IN COMPLEX WITH PYROPHOSPHATE AND TITLE 3 MAGNESIUM COMPND MOL_ID: 1; COMPND 2 MOLECULE: DCTP DEAMINASE, DUMP-FORMING; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: BIFUNCTIONAL DEAMINASE/DIPHOSPHATASE, MJDCD-DUT, DCD/DUT; COMPND 5 EC: 3.5.4.30; COMPND 6 ENGINEERED: YES; COMPND 7 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: METHANOCALDOCOCCUS JANNASCHII; SOURCE 3 ORGANISM_TAXID: 2190; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 6 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 8 EXPRESSION_SYSTEM_PLASMID: PET-3A KEYWDS DCTP DEAMINASE-DUTPASE, BIFUNCTIONAL HYDROLASE, MAGNESIUM, NUCLEOTIDE KEYWDS 2 METABOLISM, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR J.H.B.SIGGAARD,E.JOHANSSON,T.VOGNSEN,S.S.HELT,P.HARRIS,M.WILLEMOES REVDAT 2 01-NOV-17 3GF0 1 REMARK REVDAT 1 10-MAR-09 3GF0 0 SPRSDE 10-MAR-09 3GF0 2HXE JRNL AUTH J.H.B.SIGGAARD,E.JOHANSSON,T.VOGNSEN,S.S.HELT,P.HARRIS, JRNL AUTH 2 S.LARSEN,M.WILLEMOES JRNL TITL PRE-STEADY STATE KINETIC AND STRUCTURAL EVIDENCE FOR A JRNL TITL 2 CONCERTED BIOFUNCTIONALITY IN DCTP DEAMINASE-DUTPASE FROM JRNL TITL 3 METHANOCALDOCOCCUS JANNASCHII JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 2.62 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.5.0070 REMARK 3 AUTHORS : MURSHUDOV,VAGIN,DODSON REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.62 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 24.26 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 3 NUMBER OF REFLECTIONS : 12634 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) : 0.191 REMARK 3 FREE R VALUE : 0.229 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.800 REMARK 3 FREE R VALUE TEST SET COUNT : 636 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) : 2.62 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.69 REMARK 3 REFLECTION IN BIN (WORKING SET) : 914 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.90 REMARK 3 BIN R VALUE (WORKING SET) : 0.2310 REMARK 3 BIN FREE R VALUE SET COUNT : 40 REMARK 3 BIN FREE R VALUE : 0.2830 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1610 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 13 REMARK 3 SOLVENT ATOMS : 72 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 27.68 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : NULL REMARK 3 B22 (A**2) : NULL REMARK 3 B33 (A**2) : NULL REMARK 3 B12 (A**2) : NULL REMARK 3 B13 (A**2) : NULL REMARK 3 B23 (A**2) : NULL REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.284 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.228 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.137 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 6.133 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.932 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.919 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 1718 ; 0.023 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 2330 ; 1.976 ; 1.972 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 204 ; 7.200 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 79 ;35.397 ;24.684 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 310 ;19.536 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 6 ;17.395 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 257 ; 0.121 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 1276 ; 0.009 ; 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): 1019 ; 1.104 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 1667 ; 2.238 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 699 ; 3.638 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 663 ; 6.081 ; 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: HYDROGENS HAVE BEEN ADDED IN THE RIDING REMARK 3 POSITIONS REMARK 4 REMARK 4 3GF0 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 02-MAR-09. REMARK 100 THE DEPOSITION ID IS D_1000051777. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 23-JUL-05 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8.30 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ESRF REMARK 200 BEAMLINE : ID23-1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.0723 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : MIRRORS REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MAR CCD 165 MM REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 14787 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.620 REMARK 200 RESOLUTION RANGE LOW (A) : 25.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 1.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.10100 REMARK 200 FOR THE DATA SET : 26.8000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.62 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.69 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : 0.43400 REMARK 200 FOR SHELL : 5.400 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: FOURIER SYNTHESIS REMARK 200 SOFTWARE USED: FOURIER SYNTHESIS REMARK 200 STARTING MODEL: 2HXB REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 72.57 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 4.48 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 20% PEG3350, 0.2M TRIPOTASSIUM CITRATE REMARK 280 , PH 8.30, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 298K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: I 4 3 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 Z,X,Y REMARK 290 6555 Z,-X,-Y REMARK 290 7555 -Z,-X,Y REMARK 290 8555 -Z,X,-Y REMARK 290 9555 Y,Z,X REMARK 290 10555 -Y,Z,-X REMARK 290 11555 Y,-Z,-X REMARK 290 12555 -Y,-Z,X REMARK 290 13555 Y,X,-Z REMARK 290 14555 -Y,-X,-Z REMARK 290 15555 Y,-X,Z REMARK 290 16555 -Y,X,Z REMARK 290 17555 X,Z,-Y REMARK 290 18555 -X,Z,Y REMARK 290 19555 -X,-Z,-Y REMARK 290 20555 X,-Z,Y REMARK 290 21555 Z,Y,-X REMARK 290 22555 Z,-Y,X REMARK 290 23555 -Z,Y,X REMARK 290 24555 -Z,-Y,-X REMARK 290 25555 X+1/2,Y+1/2,Z+1/2 REMARK 290 26555 -X+1/2,-Y+1/2,Z+1/2 REMARK 290 27555 -X+1/2,Y+1/2,-Z+1/2 REMARK 290 28555 X+1/2,-Y+1/2,-Z+1/2 REMARK 290 29555 Z+1/2,X+1/2,Y+1/2 REMARK 290 30555 Z+1/2,-X+1/2,-Y+1/2 REMARK 290 31555 -Z+1/2,-X+1/2,Y+1/2 REMARK 290 32555 -Z+1/2,X+1/2,-Y+1/2 REMARK 290 33555 Y+1/2,Z+1/2,X+1/2 REMARK 290 34555 -Y+1/2,Z+1/2,-X+1/2 REMARK 290 35555 Y+1/2,-Z+1/2,-X+1/2 REMARK 290 36555 -Y+1/2,-Z+1/2,X+1/2 REMARK 290 37555 Y+1/2,X+1/2,-Z+1/2 REMARK 290 38555 -Y+1/2,-X+1/2,-Z+1/2 REMARK 290 39555 Y+1/2,-X+1/2,Z+1/2 REMARK 290 40555 -Y+1/2,X+1/2,Z+1/2 REMARK 290 41555 X+1/2,Z+1/2,-Y+1/2 REMARK 290 42555 -X+1/2,Z+1/2,Y+1/2 REMARK 290 43555 -X+1/2,-Z+1/2,-Y+1/2 REMARK 290 44555 X+1/2,-Z+1/2,Y+1/2 REMARK 290 45555 Z+1/2,Y+1/2,-X+1/2 REMARK 290 46555 Z+1/2,-Y+1/2,X+1/2 REMARK 290 47555 -Z+1/2,Y+1/2,X+1/2 REMARK 290 48555 -Z+1/2,-Y+1/2,-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 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 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 0.00000 REMARK 290 SMTRY2 6 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY1 7 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY2 7 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY1 8 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY2 8 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 -1.000000 0.000000 0.00000 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 0.00000 REMARK 290 SMTRY3 10 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY1 11 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 11 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY3 11 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY1 12 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 12 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY3 12 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY1 13 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 13 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 13 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 14 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 14 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 14 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 15 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 15 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 15 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 16 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 16 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 16 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 17 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 17 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY3 17 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY1 18 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 18 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY3 18 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY1 19 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 19 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY3 19 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY1 20 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 20 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY3 20 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY1 21 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY2 21 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 21 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY1 22 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY2 22 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 22 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY1 23 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY2 23 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 23 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY1 24 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY2 24 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 24 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY1 25 1.000000 0.000000 0.000000 85.78450 REMARK 290 SMTRY2 25 0.000000 1.000000 0.000000 85.78450 REMARK 290 SMTRY3 25 0.000000 0.000000 1.000000 85.78450 REMARK 290 SMTRY1 26 -1.000000 0.000000 0.000000 85.78450 REMARK 290 SMTRY2 26 0.000000 -1.000000 0.000000 85.78450 REMARK 290 SMTRY3 26 0.000000 0.000000 1.000000 85.78450 REMARK 290 SMTRY1 27 -1.000000 0.000000 0.000000 85.78450 REMARK 290 SMTRY2 27 0.000000 1.000000 0.000000 85.78450 REMARK 290 SMTRY3 27 0.000000 0.000000 -1.000000 85.78450 REMARK 290 SMTRY1 28 1.000000 0.000000 0.000000 85.78450 REMARK 290 SMTRY2 28 0.000000 -1.000000 0.000000 85.78450 REMARK 290 SMTRY3 28 0.000000 0.000000 -1.000000 85.78450 REMARK 290 SMTRY1 29 0.000000 0.000000 1.000000 85.78450 REMARK 290 SMTRY2 29 1.000000 0.000000 0.000000 85.78450 REMARK 290 SMTRY3 29 0.000000 1.000000 0.000000 85.78450 REMARK 290 SMTRY1 30 0.000000 0.000000 1.000000 85.78450 REMARK 290 SMTRY2 30 -1.000000 0.000000 0.000000 85.78450 REMARK 290 SMTRY3 30 0.000000 -1.000000 0.000000 85.78450 REMARK 290 SMTRY1 31 0.000000 0.000000 -1.000000 85.78450 REMARK 290 SMTRY2 31 -1.000000 0.000000 0.000000 85.78450 REMARK 290 SMTRY3 31 0.000000 1.000000 0.000000 85.78450 REMARK 290 SMTRY1 32 0.000000 0.000000 -1.000000 85.78450 REMARK 290 SMTRY2 32 1.000000 0.000000 0.000000 85.78450 REMARK 290 SMTRY3 32 0.000000 -1.000000 0.000000 85.78450 REMARK 290 SMTRY1 33 0.000000 1.000000 0.000000 85.78450 REMARK 290 SMTRY2 33 0.000000 0.000000 1.000000 85.78450 REMARK 290 SMTRY3 33 1.000000 0.000000 0.000000 85.78450 REMARK 290 SMTRY1 34 0.000000 -1.000000 0.000000 85.78450 REMARK 290 SMTRY2 34 0.000000 0.000000 1.000000 85.78450 REMARK 290 SMTRY3 34 -1.000000 0.000000 0.000000 85.78450 REMARK 290 SMTRY1 35 0.000000 1.000000 0.000000 85.78450 REMARK 290 SMTRY2 35 0.000000 0.000000 -1.000000 85.78450 REMARK 290 SMTRY3 35 -1.000000 0.000000 0.000000 85.78450 REMARK 290 SMTRY1 36 0.000000 -1.000000 0.000000 85.78450 REMARK 290 SMTRY2 36 0.000000 0.000000 -1.000000 85.78450 REMARK 290 SMTRY3 36 1.000000 0.000000 0.000000 85.78450 REMARK 290 SMTRY1 37 0.000000 1.000000 0.000000 85.78450 REMARK 290 SMTRY2 37 1.000000 0.000000 0.000000 85.78450 REMARK 290 SMTRY3 37 0.000000 0.000000 -1.000000 85.78450 REMARK 290 SMTRY1 38 0.000000 -1.000000 0.000000 85.78450 REMARK 290 SMTRY2 38 -1.000000 0.000000 0.000000 85.78450 REMARK 290 SMTRY3 38 0.000000 0.000000 -1.000000 85.78450 REMARK 290 SMTRY1 39 0.000000 1.000000 0.000000 85.78450 REMARK 290 SMTRY2 39 -1.000000 0.000000 0.000000 85.78450 REMARK 290 SMTRY3 39 0.000000 0.000000 1.000000 85.78450 REMARK 290 SMTRY1 40 0.000000 -1.000000 0.000000 85.78450 REMARK 290 SMTRY2 40 1.000000 0.000000 0.000000 85.78450 REMARK 290 SMTRY3 40 0.000000 0.000000 1.000000 85.78450 REMARK 290 SMTRY1 41 1.000000 0.000000 0.000000 85.78450 REMARK 290 SMTRY2 41 0.000000 0.000000 1.000000 85.78450 REMARK 290 SMTRY3 41 0.000000 -1.000000 0.000000 85.78450 REMARK 290 SMTRY1 42 -1.000000 0.000000 0.000000 85.78450 REMARK 290 SMTRY2 42 0.000000 0.000000 1.000000 85.78450 REMARK 290 SMTRY3 42 0.000000 1.000000 0.000000 85.78450 REMARK 290 SMTRY1 43 -1.000000 0.000000 0.000000 85.78450 REMARK 290 SMTRY2 43 0.000000 0.000000 -1.000000 85.78450 REMARK 290 SMTRY3 43 0.000000 -1.000000 0.000000 85.78450 REMARK 290 SMTRY1 44 1.000000 0.000000 0.000000 85.78450 REMARK 290 SMTRY2 44 0.000000 0.000000 -1.000000 85.78450 REMARK 290 SMTRY3 44 0.000000 1.000000 0.000000 85.78450 REMARK 290 SMTRY1 45 0.000000 0.000000 1.000000 85.78450 REMARK 290 SMTRY2 45 0.000000 1.000000 0.000000 85.78450 REMARK 290 SMTRY3 45 -1.000000 0.000000 0.000000 85.78450 REMARK 290 SMTRY1 46 0.000000 0.000000 1.000000 85.78450 REMARK 290 SMTRY2 46 0.000000 -1.000000 0.000000 85.78450 REMARK 290 SMTRY3 46 1.000000 0.000000 0.000000 85.78450 REMARK 290 SMTRY1 47 0.000000 0.000000 -1.000000 85.78450 REMARK 290 SMTRY2 47 0.000000 1.000000 0.000000 85.78450 REMARK 290 SMTRY3 47 1.000000 0.000000 0.000000 85.78450 REMARK 290 SMTRY1 48 0.000000 0.000000 -1.000000 85.78450 REMARK 290 SMTRY2 48 0.000000 -1.000000 0.000000 85.78450 REMARK 290 SMTRY3 48 -1.000000 0.000000 0.000000 85.78450 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: 14340 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 21580 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -179.0 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 171.56900 REMARK 350 BIOMT2 2 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 -1.000000 0.000000 171.56900 REMARK 350 BIOMT1 3 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT2 3 0.000000 0.000000 -1.000000 171.56900 REMARK 350 BIOMT3 3 -1.000000 0.000000 0.000000 171.56900 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 278 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 ASN A 200 REMARK 465 HIS A 201 REMARK 465 LYS A 202 REMARK 465 LYS A 203 REMARK 465 ASP A 204 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 OD1 ASN A 87 O HOH A 313 2.10 REMARK 500 O HOH A 306 O HOH A 342 2.16 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 GLU A 105 CG GLU A 105 CD 0.102 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 TYR A 56 CB - CA - C ANGL. DEV. = -14.0 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 ASN A 63 -53.63 -128.51 REMARK 500 ASN A 73 81.74 46.44 REMARK 500 THR A 130 39.92 39.51 REMARK 500 ALA A 131 -126.11 -116.69 REMARK 500 ASP A 150 -64.02 -127.66 REMARK 500 TYR A 187 12.97 91.11 REMARK 500 GLN A 188 143.06 -33.82 REMARK 500 SER A 190 -152.57 -144.00 REMARK 500 PRO A 193 -179.37 -61.79 REMARK 500 REMARK 500 REMARK: NULL REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG A 205 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG A 206 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG A 207 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG A 276 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE POP A 277 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1OGH RELATED DB: PDB REMARK 900 SAME PROTEIN IN DIFFERENT SPACE GROUP WITH NOTHING BOUND REMARK 900 RELATED ID: 2HXD RELATED DB: PDB REMARK 900 MUTANT ENZYME VARIANT E145A DCD-DUT IN COMPLEX WITH ALPHA,BETA- REMARK 900 IMIDO DUTP AND MAGNESIUM REMARK 900 RELATED ID: 2HXB RELATED DB: PDB REMARK 900 SAME PROTEIN AND SPACE GROUP, WILDTYPE WITH NOTHING BOUND DBREF 3GF0 A 1 204 UNP Q57872 DCD_METJA 1 204 SEQADV 3GF0 GLN A 145 UNP Q57872 GLU 145 ENGINEERED SEQRES 1 A 204 MET ILE LEU SER ASP LYS ASP ILE ILE ASP TYR VAL THR SEQRES 2 A 204 SER LYS ARG ILE ILE ILE LYS PRO PHE ASN LYS ASP PHE SEQRES 3 A 204 VAL GLY PRO CYS SER TYR ASP VAL THR LEU GLY ASP GLU SEQRES 4 A 204 PHE ILE ILE TYR ASP ASP GLU VAL TYR ASP LEU SER LYS SEQRES 5 A 204 GLU LEU ASN TYR LYS ARG ILE LYS ILE LYS ASN SER ILE SEQRES 6 A 204 LEU VAL CYS PRO LEU ASN TYR ASN LEU THR GLU GLU LYS SEQRES 7 A 204 ILE ASN TYR PHE LYS GLU LYS TYR ASN VAL ASP TYR VAL SEQRES 8 A 204 VAL GLU GLY GLY VAL LEU GLY THR THR ASN GLU TYR ILE SEQRES 9 A 204 GLU LEU PRO ASN ASP ILE SER ALA GLN TYR GLN GLY ARG SEQRES 10 A 204 SER SER LEU GLY ARG VAL PHE LEU THR SER HIS GLN THR SEQRES 11 A 204 ALA GLY TRP ILE ASP ALA GLY PHE LYS GLY LYS ILE THR SEQRES 12 A 204 LEU GLN ILE VAL ALA PHE ASP LYS PRO VAL ILE LEU TYR SEQRES 13 A 204 LYS ASN GLN ARG ILE GLY GLN LEU ILE PHE SER LYS LEU SEQRES 14 A 204 LEU SER PRO ALA ASP VAL GLY TYR SER GLU ARG LYS THR SEQRES 15 A 204 SER LYS TYR ALA TYR GLN LYS SER VAL MET PRO SER LEU SEQRES 16 A 204 ILE HIS LEU ASP ASN HIS LYS LYS ASP HET MG A 205 1 HET MG A 206 1 HET MG A 207 1 HET MG A 276 1 HET POP A 277 9 HETNAM MG MAGNESIUM ION HETNAM POP PYROPHOSPHATE 2- FORMUL 2 MG 4(MG 2+) FORMUL 6 POP H2 O7 P2 2- FORMUL 7 HOH *72(H2 O) HELIX 1 1 SER A 4 SER A 14 1 11 HELIX 2 2 ASN A 23 VAL A 27 5 5 HELIX 3 3 THR A 75 ASN A 87 1 13 HELIX 4 4 ARG A 117 ARG A 122 1 6 HELIX 5 5 GLY A 176 ARG A 180 5 5 HELIX 6 6 LEU A 195 ASP A 199 5 5 SHEET 1 A 4 ILE A 18 LYS A 20 0 SHEET 2 A 4 VAL A 96 GLU A 105 -1 O TYR A 103 N LYS A 20 SHEET 3 A 4 LYS A 139 ALA A 148 -1 O ILE A 146 N VAL A 96 SHEET 4 A 4 LEU A 125 THR A 126 -1 N THR A 126 O VAL A 147 SHEET 1 B 4 TYR A 32 THR A 35 0 SHEET 2 B 4 ARG A 160 LYS A 168 -1 O GLY A 162 N VAL A 34 SHEET 3 B 4 ILE A 110 GLY A 116 -1 N SER A 111 O SER A 167 SHEET 4 B 4 TRP A 133 ILE A 134 -1 O ILE A 134 N ALA A 112 SHEET 1 C 2 GLU A 39 TYR A 43 0 SHEET 2 C 2 TYR A 56 LYS A 60 -1 O ILE A 59 N PHE A 40 SHEET 1 D 3 TYR A 90 GLU A 93 0 SHEET 2 D 3 SER A 64 CYS A 68 1 N CYS A 68 O VAL A 92 SHEET 3 D 3 VAL A 153 TYR A 156 -1 O VAL A 153 N VAL A 67 CISPEP 1 LYS A 20 PRO A 21 0 -3.93 SITE 1 AC1 1 POP A 277 SITE 1 AC2 3 GLU A 93 GLY A 95 ASP A 150 SITE 1 AC3 2 HIS A 128 THR A 130 SITE 1 AC4 6 GLN A 115 GLY A 116 HIS A 128 THR A 130 SITE 2 AC4 6 ALA A 131 HOH A 348 SITE 1 AC5 9 ARG A 117 SER A 118 SER A 119 TYR A 177 SITE 2 AC5 9 SER A 183 LYS A 184 TYR A 185 MG A 205 SITE 3 AC5 9 HOH A 307 CRYST1 171.569 171.569 171.569 90.00 90.00 90.00 I 4 3 2 48 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 0.005829 0.000000 0.000000 0.00000 SCALE2 0.000000 0.005829 0.000000 0.00000 SCALE3 0.000000 0.000000 0.005829 0.00000 MASTER 545 0 5 6 13 0 8 6 0 0 0 16 END