HEADER HYDROLASE 25-JAN-18 6FL4 TITLE A. THALIANA NUDT1 IN COMPLEX WITH 8-OXO-DGTP COMPND MOL_ID: 1; COMPND 2 MOLECULE: NUDIX HYDROLASE 1; COMPND 3 CHAIN: A, B; COMPND 4 SYNONYM: ATNUDT1,7,8-DIHYDRO-8-OXOGUANINE-TRIPHOSPHATASE,8-OXO-DGTP COMPND 5 DIPHOSPHATASE,8-OXO-DGTPASE,DIHYDRONEOPTERIN TRIPHOSPHATE COMPND 6 DIPHOSPHATASE,DIHYDRONEOPTERIN TRIPHOSPHATE PYROPHOSPHOHYDROLASE, COMPND 7 DHNTP PYROPHOSPHOHYDROLASE,NADH PYROPHOSPHATASE; COMPND 8 EC: 3.6.1.55,3.6.1.67,3.6.1.22; COMPND 9 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ARABIDOPSIS THALIANA; SOURCE 3 ORGANISM_COMMON: MOUSE-EAR CRESS; SOURCE 4 ORGANISM_TAXID: 3702; SOURCE 5 GENE: NUDT1, NUDX1, AT1G68760, F14K14.13; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS 8-OXO-DGTP, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR A.S.JEMTH,E.SCALETTI-HUTCHINSON,M.CARTER,T.HELLEDAY,P.STENMARK REVDAT 3 08-MAY-24 6FL4 1 LINK REVDAT 2 21-AUG-19 6FL4 1 JRNL REVDAT 1 06-FEB-19 6FL4 0 JRNL AUTH A.S.JEMTH,E.SCALETTI,M.CARTER,T.HELLEDAY,P.STENMARK JRNL TITL CRYSTAL STRUCTURE AND SUBSTRATE SPECIFICITY OF THE JRNL TITL 2 8-OXO-DGTP HYDROLASE NUDT1 FROM ARABIDOPSIS THALIANA. JRNL REF BIOCHEMISTRY V. 58 887 2019 JRNL REFN ISSN 0006-2960 JRNL PMID 30614695 JRNL DOI 10.1021/ACS.BIOCHEM.8B00950 REMARK 2 REMARK 2 RESOLUTION. 1.60 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0158 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.60 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 38.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 99.5 REMARK 3 NUMBER OF REFLECTIONS : 38947 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) : 0.181 REMARK 3 R VALUE (WORKING SET) : 0.179 REMARK 3 FREE R VALUE : 0.214 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 2085 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) : 1.60 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.64 REMARK 3 REFLECTION IN BIN (WORKING SET) : 2762 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 96.90 REMARK 3 BIN R VALUE (WORKING SET) : 0.3110 REMARK 3 BIN FREE R VALUE SET COUNT : 147 REMARK 3 BIN FREE R VALUE : 0.2910 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2196 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 68 REMARK 3 SOLVENT ATOMS : 249 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 17.87 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.51000 REMARK 3 B22 (A**2) : 1.55000 REMARK 3 B33 (A**2) : -1.04000 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): 0.087 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.089 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.063 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 1.869 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.963 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.939 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 2368 ; 0.011 ; 0.019 REMARK 3 BOND LENGTHS OTHERS (A): 2129 ; 0.002 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 3237 ; 1.689 ; 1.990 REMARK 3 BOND ANGLES OTHERS (DEGREES): 4969 ; 0.884 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 284 ; 5.751 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 103 ;32.495 ;24.175 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 382 ;10.903 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 12 ;18.273 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 339 ; 0.083 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2586 ; 0.007 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): 488 ; 0.002 ; 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): 1127 ; 1.185 ; 1.579 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 1126 ; 1.181 ; 1.577 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 1414 ; 1.918 ; 2.360 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): 1415 ; 1.918 ; 2.362 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1240 ; 1.943 ; 1.890 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): 1228 ; 1.909 ; 1.868 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): 1804 ; 2.991 ; 2.721 REMARK 3 LONG RANGE B REFINED ATOMS (A**2): 2632 ; 4.753 ;19.850 REMARK 3 LONG RANGE B OTHER ATOMS (A**2): 2629 ; 4.753 ;19.784 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 : NULL REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.20 REMARK 3 ION PROBE RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: HYDROGENS HAVE BEEN ADDED IN THE RIDING REMARK 3 POSITIONS REMARK 4 REMARK 4 6FL4 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 25-JAN-18. REMARK 100 THE DEPOSITION ID IS D_1200008516. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 31-OCT-15 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ESRF REMARK 200 BEAMLINE : ID29 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.07 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS3 S 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XDS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 47078 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.600 REMARK 200 RESOLUTION RANGE LOW (A) : 38.700 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.4 REMARK 200 DATA REDUNDANCY : 5.600 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 1.9000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.60 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.69 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL 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: MOLREP REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 47.61 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.35 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 40 % (V/V) PEG300, 0.1 M SODIUM REMARK 280 ACETATE/ACETIC ACID (PH 4.5), 0.2 M NACL, VAPOR DIFFUSION, REMARK 280 SITTING DROP, TEMPERATURE 291K 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 32.44900 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 38.70600 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 61.21000 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 32.44900 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 38.70600 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 61.21000 REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 32.44900 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 38.70600 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 61.21000 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 32.44900 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 38.70600 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 61.21000 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: 4120 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 12810 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -53.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, 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 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 1 REMARK 465 SER A 2 REMARK 465 THR A 3 REMARK 465 GLY A 4 REMARK 465 GLU A 5 REMARK 465 GLY A 144 REMARK 465 GLY A 145 REMARK 465 GLY A 146 REMARK 465 ASP A 147 REMARK 465 MET B 1 REMARK 465 SER B 2 REMARK 465 THR B 3 REMARK 465 GLY B 4 REMARK 465 GLU B 5 REMARK 465 GLY B 144 REMARK 465 GLY B 145 REMARK 465 GLY B 146 REMARK 465 ASP B 147 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 B 28 NE - CZ - NH1 ANGL. DEV. = 4.8 DEGREES REMARK 500 ARG B 28 NE - CZ - NH2 ANGL. DEV. = -4.6 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 LEU A 71 -69.45 -100.69 REMARK 500 ASN A 121 54.72 -140.19 REMARK 500 LEU B 71 -66.04 -102.47 REMARK 500 ASN B 121 57.05 -150.11 REMARK 500 REMARK 500 REMARK: NULL REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A 201 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLY A 40 O REMARK 620 2 GLU A 60 OE2 78.4 REMARK 620 3 8DG A 203 O1B 90.2 88.2 REMARK 620 4 8DG A 203 O1A 95.4 173.8 90.8 REMARK 620 5 HOH A 333 O 88.1 90.9 178.2 89.9 REMARK 620 6 HOH A 387 O 172.9 94.5 89.4 91.7 92.3 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A 202 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU A 56 OE1 REMARK 620 2 GLU A 60 OE2 89.0 REMARK 620 3 8DG A 203 O1G 83.7 160.9 REMARK 620 4 8DG A 203 O1B 103.1 80.6 83.9 REMARK 620 5 HOH A 304 O 99.0 114.3 84.4 153.6 REMARK 620 6 HOH A 305 O 162.4 79.9 110.9 88.6 73.7 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG B 202 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLY B 40 O REMARK 620 2 GLU B 60 OE2 76.8 REMARK 620 3 8DG B 203 O1B 88.9 90.6 REMARK 620 4 8DG B 203 O2A 103.5 178.1 87.5 REMARK 620 5 HOH B 357 O 95.3 93.0 175.0 88.9 REMARK 620 6 HOH B 376 O 173.6 97.1 89.2 82.5 86.9 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG B 201 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU B 56 OE1 REMARK 620 2 GLU B 60 OE2 88.9 REMARK 620 3 8DG B 203 O1B 101.8 81.1 REMARK 620 4 8DG B 203 O2G 81.8 155.0 78.2 REMARK 620 5 HOH B 322 O 96.6 112.5 157.3 91.7 REMARK 620 6 HOH B 325 O 168.5 79.9 78.7 109.4 85.9 REMARK 620 N 1 2 3 4 5 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 201 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MG A 202 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue 8DG A 203 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MG B 201 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MG B 202 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue 8DG B 203 DBREF 6FL4 A 1 147 UNP Q9CA40 NUDT1_ARATH 1 147 DBREF 6FL4 B 1 147 UNP Q9CA40 NUDT1_ARATH 1 147 SEQRES 1 A 147 MET SER THR GLY GLU ALA ILE PRO ARG VAL ALA VAL VAL SEQRES 2 A 147 VAL PHE ILE LEU ASN GLY ASN SER ILE LEU LEU GLY ARG SEQRES 3 A 147 ARG ARG SER SER ILE GLY ASN SER THR PHE ALA LEU PRO SEQRES 4 A 147 GLY GLY HIS LEU GLU PHE GLY GLU SER PHE GLU GLU CYS SEQRES 5 A 147 ALA ALA ARG GLU VAL MET GLU GLU THR GLY LEU LYS ILE SEQRES 6 A 147 GLU LYS MET LYS LEU LEU THR VAL THR ASN ASN VAL PHE SEQRES 7 A 147 LYS GLU ALA PRO THR PRO SER HIS TYR VAL SER VAL SER SEQRES 8 A 147 ILE ARG ALA VAL LEU VAL ASP PRO SER GLN GLU PRO LYS SEQRES 9 A 147 ASN MET GLU PRO GLU LYS CYS GLU GLY TRP ASP TRP TYR SEQRES 10 A 147 ASP TRP GLU ASN LEU PRO LYS PRO LEU PHE TRP PRO LEU SEQRES 11 A 147 GLU LYS LEU PHE GLY SER GLY PHE ASN PRO PHE THR HIS SEQRES 12 A 147 GLY GLY GLY ASP SEQRES 1 B 147 MET SER THR GLY GLU ALA ILE PRO ARG VAL ALA VAL VAL SEQRES 2 B 147 VAL PHE ILE LEU ASN GLY ASN SER ILE LEU LEU GLY ARG SEQRES 3 B 147 ARG ARG SER SER ILE GLY ASN SER THR PHE ALA LEU PRO SEQRES 4 B 147 GLY GLY HIS LEU GLU PHE GLY GLU SER PHE GLU GLU CYS SEQRES 5 B 147 ALA ALA ARG GLU VAL MET GLU GLU THR GLY LEU LYS ILE SEQRES 6 B 147 GLU LYS MET LYS LEU LEU THR VAL THR ASN ASN VAL PHE SEQRES 7 B 147 LYS GLU ALA PRO THR PRO SER HIS TYR VAL SER VAL SER SEQRES 8 B 147 ILE ARG ALA VAL LEU VAL ASP PRO SER GLN GLU PRO LYS SEQRES 9 B 147 ASN MET GLU PRO GLU LYS CYS GLU GLY TRP ASP TRP TYR SEQRES 10 B 147 ASP TRP GLU ASN LEU PRO LYS PRO LEU PHE TRP PRO LEU SEQRES 11 B 147 GLU LYS LEU PHE GLY SER GLY PHE ASN PRO PHE THR HIS SEQRES 12 B 147 GLY GLY GLY ASP HET MG A 201 1 HET MG A 202 1 HET 8DG A 203 32 HET MG B 201 1 HET MG B 202 1 HET 8DG B 203 32 HETNAM MG MAGNESIUM ION HETNAM 8DG 8-OXO-2'-DEOXYGUANOSINE-5'-TRIPHOSPHATE FORMUL 3 MG 4(MG 2+) FORMUL 5 8DG 2(C10 H16 N5 O14 P3) FORMUL 9 HOH *249(H2 O) HELIX 1 AA1 SER A 48 GLY A 62 1 15 HELIX 2 AA2 GLU A 120 LEU A 122 5 3 HELIX 3 AA3 PHE A 127 SER A 136 1 10 HELIX 4 AA4 SER B 48 GLY B 62 1 15 HELIX 5 AA5 PHE B 127 SER B 136 1 10 SHEET 1 AA1 5 PHE A 36 ALA A 37 0 SHEET 2 AA1 5 SER A 21 ARG A 27 -1 N GLY A 25 O ALA A 37 SHEET 3 AA1 5 ARG A 9 ASN A 18 -1 N ASN A 18 O SER A 21 SHEET 4 AA1 5 HIS A 86 LEU A 96 1 O VAL A 90 N ALA A 11 SHEET 5 AA1 5 ILE A 65 VAL A 77 -1 N ASN A 76 O TYR A 87 SHEET 1 AA2 4 GLY A 40 HIS A 42 0 SHEET 2 AA2 4 ARG A 9 ASN A 18 -1 N VAL A 12 O GLY A 41 SHEET 3 AA2 4 SER A 21 ARG A 27 -1 O SER A 21 N ASN A 18 SHEET 4 AA2 4 CYS A 111 ASP A 118 -1 O GLU A 112 N ARG A 26 SHEET 1 AA3 5 PHE B 36 ALA B 37 0 SHEET 2 AA3 5 SER B 21 ARG B 27 -1 N GLY B 25 O ALA B 37 SHEET 3 AA3 5 ARG B 9 ASN B 18 -1 N ASN B 18 O SER B 21 SHEET 4 AA3 5 SER B 85 LEU B 96 1 O ILE B 92 N PHE B 15 SHEET 5 AA3 5 ILE B 65 PHE B 78 -1 N PHE B 78 O SER B 85 SHEET 1 AA4 4 GLY B 40 HIS B 42 0 SHEET 2 AA4 4 ARG B 9 ASN B 18 -1 N VAL B 12 O GLY B 41 SHEET 3 AA4 4 SER B 21 ARG B 27 -1 O SER B 21 N ASN B 18 SHEET 4 AA4 4 CYS B 111 ASP B 118 -1 O GLU B 112 N ARG B 26 LINK O GLY A 40 MG MG A 201 1555 1555 2.16 LINK OE1 GLU A 56 MG MG A 202 1555 1555 2.37 LINK OE2 GLU A 60 MG MG A 201 1555 1555 2.15 LINK OE2 GLU A 60 MG MG A 202 1555 1555 2.38 LINK MG MG A 201 O1B 8DG A 203 1555 1555 2.10 LINK MG MG A 201 O1A 8DG A 203 1555 1555 2.00 LINK MG MG A 201 O HOH A 333 1555 1555 2.09 LINK MG MG A 201 O HOH A 387 1555 1555 2.18 LINK MG MG A 202 O1G 8DG A 203 1555 1555 1.96 LINK MG MG A 202 O1B 8DG A 203 1555 1555 2.19 LINK MG MG A 202 O HOH A 304 1555 1555 2.36 LINK MG MG A 202 O HOH A 305 1555 1555 2.38 LINK O GLY B 40 MG MG B 202 1555 1555 2.18 LINK OE1 GLU B 56 MG MG B 201 1555 1555 2.36 LINK OE2 GLU B 60 MG MG B 201 1555 1555 2.44 LINK OE2 GLU B 60 MG MG B 202 1555 1555 2.20 LINK MG MG B 201 O1B 8DG B 203 1555 1555 2.31 LINK MG MG B 201 O2G 8DG B 203 1555 1555 2.29 LINK MG MG B 201 O HOH B 322 1555 1555 2.25 LINK MG MG B 201 O HOH B 325 1555 1555 2.42 LINK MG MG B 202 O1B 8DG B 203 1555 1555 2.15 LINK MG MG B 202 O2A 8DG B 203 1555 1555 2.08 LINK MG MG B 202 O HOH B 357 1555 1555 2.09 LINK MG MG B 202 O HOH B 376 1555 1555 2.28 CISPEP 1 LYS A 124 PRO A 125 0 -2.55 CISPEP 2 LYS B 124 PRO B 125 0 -3.01 SITE 1 AC1 6 GLY A 40 GLU A 60 MG A 202 8DG A 203 SITE 2 AC1 6 HOH A 333 HOH A 387 SITE 1 AC2 6 GLU A 56 GLU A 60 MG A 201 8DG A 203 SITE 2 AC2 6 HOH A 304 HOH A 305 SITE 1 AC3 24 ALA A 11 VAL A 13 ARG A 27 LEU A 38 SITE 2 AC3 24 GLY A 40 GLY A 41 HIS A 42 GLU A 56 SITE 3 AC3 24 GLU A 60 ASN A 76 PHE A 78 SER A 89 SITE 4 AC3 24 LYS A 110 PHE A 127 MG A 201 MG A 202 SITE 5 AC3 24 HOH A 304 HOH A 327 HOH A 333 HOH A 351 SITE 6 AC3 24 HOH A 357 HOH A 360 HOH A 387 GLU B 120 SITE 1 AC4 6 GLU B 56 GLU B 60 MG B 202 8DG B 203 SITE 2 AC4 6 HOH B 322 HOH B 325 SITE 1 AC5 6 GLY B 40 GLU B 60 MG B 201 8DG B 203 SITE 2 AC5 6 HOH B 357 HOH B 376 SITE 1 AC6 24 ALA B 11 VAL B 13 ARG B 27 ALA B 37 SITE 2 AC6 24 LEU B 38 GLY B 40 GLY B 41 HIS B 42 SITE 3 AC6 24 GLU B 56 GLU B 60 ASN B 76 SER B 89 SITE 4 AC6 24 LYS B 110 PHE B 127 PRO B 129 MG B 201 SITE 5 AC6 24 MG B 202 HOH B 301 HOH B 314 HOH B 325 SITE 6 AC6 24 HOH B 350 HOH B 357 HOH B 376 HOH B 392 CRYST1 64.898 77.412 122.420 90.00 90.00 90.00 I 2 2 2 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 0.015409 0.000000 0.000000 0.00000 SCALE2 0.000000 0.012918 0.000000 0.00000 SCALE3 0.000000 0.000000 0.008169 0.00000