HEADER GENE REGULATION 30-APR-09 3H95 TITLE CRYSTAL STRUCTURE OF THE NUDIX DOMAIN OF NUDT6 COMPND MOL_ID: 1; COMPND 2 MOLECULE: NUCLEOSIDE DIPHOSPHATE-LINKED MOIETY X MOTIF 6; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: RESIDUES 141-316; COMPND 5 SYNONYM: NUDIX MOTIF 6, PROTEIN GFG, GFG-1, ANTISENSE BASIC COMPND 6 FIBROBLAST GROWTH FACTOR; COMPND 7 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 GENE: FGF2AS, NUDT6; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3) R3 PRARE; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PNIC-BSA4 KEYWDS NUDT6, NUDIX, HYDROLASE, GFG, GFG-1, FGF2AS, STRUCTURAL GENOMICS, KEYWDS 2 STRUCTURAL GENOMICS CONSORTIUM, SGC, SGC STOCKHOLM, ISOPEPTIDE BOND, KEYWDS 3 GENE REGULATION EXPDTA X-RAY DIFFRACTION AUTHOR L.TRESAUGUES,M.MOCHE,C.H.ARROWSMITH,H.BERGLUND,C.BOUNTRA,R.COLLINS, AUTHOR 2 A.M.EDWARDS,S.FLODIN,A.FLORES,S.GRASLUND,M.HAMMARSTROM,A.JOHANSSON, AUTHOR 3 I.JOHANSSON,T.KARLBERG,T.KOTYENOVA,A.KOTZCH,T.K.NIELSEN,T.NYMAN, AUTHOR 4 C.PERSSON,J.SAGEMARK,H.SCHUELER,P.SCHUTZ,M.I.SIPONEN,L.SVENSSON, AUTHOR 5 A.G.THORSELL,S.VAN DEN BERG,J.WEIGELT,M.WELIN,M.WISNIEWSKA, AUTHOR 6 P.NORDLUND,STRUCTURAL GENOMICS CONSORTIUM (SGC) REVDAT 3 06-SEP-23 3H95 1 REMARK SEQADV REVDAT 2 13-JUL-11 3H95 1 VERSN REVDAT 1 07-JUL-09 3H95 0 JRNL AUTH L.TRESAUGUES,M.MOCHE,C.H.ARROWSMITH,H.BERGLUND,C.BOUNTRA, JRNL AUTH 2 R.COLLINS,A.M.EDWARDS,S.FLODIN,A.FLORES,S.GRASLUND, JRNL AUTH 3 M.HAMMARSTROM,A.JOHANSSON,I.JOHANSSON,T.KARLBERG, JRNL AUTH 4 T.KOTYENOVA,A.KOTZCH,T.K.NIELSEN,T.NYMAN,C.PERSSON, JRNL AUTH 5 J.SAGEMARK,H.SCHUELER,P.SCHUTZ,M.I.SIPONEN,L.SVENSSON, JRNL AUTH 6 A.G.THORSELL,S.VAN DEN BERG,J.WEIGELT,M.WELIN,M.WISNIEWSKA, JRNL AUTH 7 P.NORDLUND JRNL TITL CRYSTAL STRUCTURE OF THE NUDIX DOMAIN OF NUDT6 JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 1.70 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) : 1.70 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 19.08 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 3 NUMBER OF REFLECTIONS : 21832 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) : 0.196 REMARK 3 R VALUE (WORKING SET) : 0.194 REMARK 3 FREE R VALUE : 0.221 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 1149 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) : 1.70 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.74 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1572 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 100.0 REMARK 3 BIN R VALUE (WORKING SET) : 0.2520 REMARK 3 BIN FREE R VALUE SET COUNT : 82 REMARK 3 BIN FREE R VALUE : 0.3200 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1319 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 25 REMARK 3 SOLVENT ATOMS : 143 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 24.10 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 24.76 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.00000 REMARK 3 B22 (A**2) : 0.00000 REMARK 3 B33 (A**2) : -0.01000 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): 0.105 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.102 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.069 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 2.081 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.954 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.944 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 1431 ; 0.016 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): 1303 ; 0.014 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 1944 ; 1.836 ; 1.993 REMARK 3 BOND ANGLES OTHERS (DEGREES): 3046 ; 5.516 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 176 ; 6.842 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 69 ;34.003 ;23.913 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 263 ;13.500 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 11 ;14.681 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 214 ; 0.111 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 1578 ; 0.008 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 295 ; 0.007 ; 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): 838 ; 1.152 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 341 ; 0.278 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 1374 ; 2.059 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 593 ; 2.932 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 564 ; 4.909 ; 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 3H95 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 01-MAY-09. REMARK 100 THE DEPOSITION ID IS D_1000052848. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 30-JAN-09 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 : ID23-1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.979300 REMARK 200 MONOCHROMATOR : SI 111 REMARK 200 OPTICS : TIROIDAL MIRROR REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315R REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 23294 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.690 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 200 DATA REDUNDANCY : 10.30 REMARK 200 R MERGE (I) : 0.05900 REMARK 200 R SYM (I) : 0.05600 REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 22.2000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.69 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.79 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.8 REMARK 200 DATA REDUNDANCY IN SHELL : 10.30 REMARK 200 R MERGE FOR SHELL (I) : 0.57400 REMARK 200 R SYM FOR SHELL (I) : 0.54500 REMARK 200 <I/SIGMA(I)> FOR SHELL : 4.100 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: MRBUMP REMARK 200 STARTING MODEL: PDB ENTRY 1VCD REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 43.10 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.16 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 30% PEG 3350, 0.4M TRI-AMMONIUM REMARK 280 CITRATE, 5MM MAGNESIUM CHLORIDE, VAPOR DIFFUSION, HANGING DROP, REMARK 280 TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 41 21 2 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 -Y+1/2,X+1/2,Z+1/4 REMARK 290 4555 Y+1/2,-X+1/2,Z+3/4 REMARK 290 5555 -X+1/2,Y+1/2,-Z+1/4 REMARK 290 6555 X+1/2,-Y+1/2,-Z+3/4 REMARK 290 7555 Y,X,-Z REMARK 290 8555 -Y,-X,-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 66.85500 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 27.26500 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 27.26500 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 33.42750 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 27.26500 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 27.26500 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 100.28250 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 27.26500 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 27.26500 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 33.42750 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 27.26500 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 27.26500 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 100.28250 REMARK 290 SMTRY1 7 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 7 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 66.85500 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: 6610 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 14950 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -32.0 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 1.000000 0.000000 0.00000 REMARK 350 BIOMT2 2 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 133.71000 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 A1131 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 118 REMARK 465 HIS A 119 REMARK 465 HIS A 120 REMARK 465 HIS A 121 REMARK 465 HIS A 122 REMARK 465 HIS A 123 REMARK 465 HIS A 124 REMARK 465 SER A 125 REMARK 465 SER A 126 REMARK 465 GLY A 127 REMARK 465 VAL A 128 REMARK 465 ASP A 129 REMARK 465 LEU A 130 REMARK 465 GLY A 131 REMARK 465 THR A 132 REMARK 465 GLU A 133 REMARK 465 ASN A 134 REMARK 465 LEU A 135 REMARK 465 TYR A 136 REMARK 465 PHE A 137 REMARK 465 GLN A 138 REMARK 465 SER A 139 REMARK 465 MET A 140 REMARK 465 SER A 141 REMARK 465 HIS A 142 REMARK 465 THR A 213 REMARK 465 ASN A 214 REMARK 465 PRO A 215 REMARK 465 GLY A 216 REMARK 465 ALA A 217 REMARK 465 PHE A 218 REMARK 465 GLY A 219 REMARK 465 LYS A 220 REMARK 465 SER A 221 REMARK 465 LYS A 313 REMARK 465 GLY A 314 REMARK 465 ILE A 315 REMARK 465 ASP A 316 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 O HOH A 1152 O HOH A 1153 2.03 REMARK 500 OG2 FLC A 1 O HOH A 1129 2.05 REMARK 500 OD1 ASP A 280 O HOH A 1121 2.09 REMARK 500 O HOH A 1112 O HOH A 1145 2.10 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 NZ LYS A 172 OG2 FLC A 1 7556 2.19 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 156 NE - CZ - NH1 ANGL. DEV. = 3.6 DEGREES REMARK 500 ARG A 156 NE - CZ - NH2 ANGL. DEV. = -4.1 DEGREES REMARK 500 ARG A 266 NE - CZ - NH2 ANGL. DEV. = -3.6 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 GLU A 181 -5.67 79.49 REMARK 500 GLN A 211 -159.61 -125.25 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 FLC A 1 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 2 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 3 DBREF 3H95 A 141 316 UNP P53370 NUDT6_HUMAN 141 316 SEQADV 3H95 MET A 118 UNP P53370 EXPRESSION TAG SEQADV 3H95 HIS A 119 UNP P53370 EXPRESSION TAG SEQADV 3H95 HIS A 120 UNP P53370 EXPRESSION TAG SEQADV 3H95 HIS A 121 UNP P53370 EXPRESSION TAG SEQADV 3H95 HIS A 122 UNP P53370 EXPRESSION TAG SEQADV 3H95 HIS A 123 UNP P53370 EXPRESSION TAG SEQADV 3H95 HIS A 124 UNP P53370 EXPRESSION TAG SEQADV 3H95 SER A 125 UNP P53370 EXPRESSION TAG SEQADV 3H95 SER A 126 UNP P53370 EXPRESSION TAG SEQADV 3H95 GLY A 127 UNP P53370 EXPRESSION TAG SEQADV 3H95 VAL A 128 UNP P53370 EXPRESSION TAG SEQADV 3H95 ASP A 129 UNP P53370 EXPRESSION TAG SEQADV 3H95 LEU A 130 UNP P53370 EXPRESSION TAG SEQADV 3H95 GLY A 131 UNP P53370 EXPRESSION TAG SEQADV 3H95 THR A 132 UNP P53370 EXPRESSION TAG SEQADV 3H95 GLU A 133 UNP P53370 EXPRESSION TAG SEQADV 3H95 ASN A 134 UNP P53370 EXPRESSION TAG SEQADV 3H95 LEU A 135 UNP P53370 EXPRESSION TAG SEQADV 3H95 TYR A 136 UNP P53370 EXPRESSION TAG SEQADV 3H95 PHE A 137 UNP P53370 EXPRESSION TAG SEQADV 3H95 GLN A 138 UNP P53370 EXPRESSION TAG SEQADV 3H95 SER A 139 UNP P53370 EXPRESSION TAG SEQADV 3H95 MET A 140 UNP P53370 EXPRESSION TAG SEQRES 1 A 199 MET HIS HIS HIS HIS HIS HIS SER SER GLY VAL ASP LEU SEQRES 2 A 199 GLY THR GLU ASN LEU TYR PHE GLN SER MET SER HIS GLN SEQRES 3 A 199 VAL GLY VAL ALA GLY ALA VAL PHE ASP GLU SER THR ARG SEQRES 4 A 199 LYS ILE LEU VAL VAL GLN ASP ARG ASN LYS LEU LYS ASN SEQRES 5 A 199 MET TRP LYS PHE PRO GLY GLY LEU SER GLU PRO GLU GLU SEQRES 6 A 199 ASP ILE GLY ASP THR ALA VAL ARG GLU VAL PHE GLU GLU SEQRES 7 A 199 THR GLY ILE LYS SER GLU PHE ARG SER VAL LEU SER ILE SEQRES 8 A 199 ARG GLN GLN HIS THR ASN PRO GLY ALA PHE GLY LYS SER SEQRES 9 A 199 ASP MET TYR ILE ILE CYS ARG LEU LYS PRO TYR SER PHE SEQRES 10 A 199 THR ILE ASN PHE CYS GLN GLU GLU CYS LEU ARG CYS GLU SEQRES 11 A 199 TRP MET ASP LEU ASN ASP LEU ALA LYS THR GLU ASN THR SEQRES 12 A 199 THR PRO ILE THR SER ARG VAL ALA ARG LEU LEU LEU TYR SEQRES 13 A 199 GLY TYR ARG GLU GLY PHE ASP LYS ILE ASP LEU THR VAL SEQRES 14 A 199 GLU GLU LEU PRO ALA VAL TYR THR GLY LEU PHE TYR LYS SEQRES 15 A 199 LEU TYR HIS LYS GLU LEU PRO GLU ASN TYR LYS THR MET SEQRES 16 A 199 LYS GLY ILE ASP HET FLC A 1 17 HET GOL A 2 6 HET GOL A 3 6 HETNAM FLC CITRATE ANION HETNAM GOL GLYCEROL HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 2 FLC C6 H5 O7 3- FORMUL 3 GOL 2(C3 H8 O3) FORMUL 5 HOH *143(H2 O) HELIX 1 1 ASP A 183 GLY A 197 1 15 HELIX 2 2 LEU A 251 THR A 257 1 7 HELIX 3 3 THR A 261 GLY A 278 1 18 HELIX 4 4 PHE A 279 ILE A 282 5 4 HELIX 5 5 PRO A 306 THR A 311 1 6 SHEET 1 A 4 GLY A 175 LEU A 177 0 SHEET 2 A 4 GLY A 145 ASP A 152 -1 N VAL A 146 O GLY A 176 SHEET 3 A 4 MET A 223 PRO A 231 1 O CYS A 227 N ALA A 149 SHEET 4 A 4 SER A 200 GLN A 210 -1 N LEU A 206 O ILE A 226 SHEET 1 B 4 GLY A 175 LEU A 177 0 SHEET 2 B 4 GLY A 145 ASP A 152 -1 N VAL A 146 O GLY A 176 SHEET 3 B 4 LYS A 157 ASP A 163 -1 O LYS A 157 N ASP A 152 SHEET 4 B 4 CYS A 243 ASP A 250 -1 O LEU A 244 N GLN A 162 SHEET 1 C 2 LEU A 284 PRO A 290 0 SHEET 2 C 2 PHE A 297 LYS A 303 -1 O HIS A 302 N THR A 285 SITE 1 AC1 13 GOL A 2 LYS A 166 LYS A 172 ARG A 209 SITE 2 AC1 13 THR A 261 ALA A 291 VAL A 292 TYR A 293 SITE 3 AC1 13 TYR A 298 HOH A1003 HOH A1038 HOH A1120 SITE 4 AC1 13 HOH A1129 SITE 1 AC2 8 FLC A 1 ALA A 147 LYS A 172 PHE A 173 SITE 2 AC2 8 ARG A 209 TYR A 224 ILE A 263 THR A 264 SITE 1 AC3 9 GLU A 153 SER A 154 THR A 257 GLU A 258 SITE 2 AC3 9 THR A 260 PRO A 262 SER A 265 TYR A 275 SITE 3 AC3 9 HOH A1034 CRYST1 54.530 54.530 133.710 90.00 90.00 90.00 P 41 21 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 0.018339 0.000000 0.000000 0.00000 SCALE2 0.000000 0.018339 0.000000 0.00000 SCALE3 0.000000 0.000000 0.007479 0.00000