HEADER HYDROLASE 21-DEC-07 2VKQ TITLE CRYSTAL STRUCTURE OF HUMAN CYTOSOLIC 5'-NUCLEOTIDASE III (CN-III, TITLE 2 NT5C3) IN COMPLEX WITH BERYLLIUM TRIFLUORIDE COMPND MOL_ID: 1; COMPND 2 MOLECULE: CYTOSOLIC 5'-NUCLEOTIDASE III; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: RESIDUES 13-285; COMPND 5 SYNONYM: CN-III, PYRIMIDINE 5'-NUCLEOTIDASE 1, P5'N-1, P5N-1, PN-I, COMPND 6 URIDINE 5'-MONOPHOSPHATE HYDROLASE 1, P36; COMPND 7 EC: 3.1.3.5; COMPND 8 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 8 EXPRESSION_SYSTEM_VARIANT: PGRO7; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_VECTOR: P28A-LIC KEYWDS HYDROLASE, NUCLEOTIDASE, DISEASE MUTATION, HEMOLYTIC ANEMIA, KEYWDS 2 PHOSPHOTRANSFERASE, NUCLEOTIDE-BINDING, ENDOPLASMIC RETICULUM, KEYWDS 3 NUCLEOTIDE METABOLISM EXPDTA X-RAY DIFFRACTION AUTHOR K.WALLDEN,M.MOCHE,C.H.ARROWSMITH,H.BERGLUND,R.BUSAM,R.COLLINS, AUTHOR 2 L.G.DAHLGREN,A.EDWARDS,S.FLODIN,A.FLORES,S.GRASLUND,M.HAMMARSTROM, AUTHOR 3 M.D.HERMAN,A.JOHANSSON,I.JOHANSSON,A.KALLAS,T.KARLBERG,T.KOTENYOVA, AUTHOR 4 L.LEHTIO,M.E.NILSSON,T.NYMAN,C.PERSSON,J.SAGEMARK,A.G.THORSELL, AUTHOR 5 L.TRESAUGUES,S.VAN DEN BERG,J.WEIGELT,M.WELIN,P.NORDLUND,STRUCTURAL AUTHOR 6 GENOMICS CONSORTIUM (SGC) REVDAT 5 13-DEC-23 2VKQ 1 REMARK LINK REVDAT 4 22-APR-15 2VKQ 1 SOURCE AUTHOR REVDAT 3 13-JUL-11 2VKQ 1 VERSN REVDAT 2 24-FEB-09 2VKQ 1 VERSN REVDAT 1 08-JAN-08 2VKQ 0 JRNL AUTH K.WALLDEN,P.STENMARK,S.FLODIN,T.NYMAN,M.MOCHE,M.EHN, JRNL AUTH 2 M.HAMMARSTROM,P.NILSSON-EHLE,P.NORDLUND JRNL TITL CRYSTAL STRUCTURE OF HUMAN CYTOSOLIC 5'- NUCLEOTIDASE III JRNL REF TO BE PUBLISHED JRNL REFN REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH K.WALLDEN,P.STENMARK,T.NYMAN,S.FLODIN,S.GRASLUND,P.LOPPNAU, REMARK 1 AUTH 2 V.BIANCHI,P.NORDLUND REMARK 1 TITL CRYSTAL STRUCTURE OF HUMAN CYTOSOLIC 5'- NUCLEOTIDASE II: REMARK 1 TITL 2 INSIGHTS INTO ALLOSTERIC REGULATION AND SUBSTRATE REMARK 1 TITL 3 RECOGNITION REMARK 1 REF J.BIOL.CHEM. V. 282 17828 2007 REMARK 1 REFN ISSN 0021-9258 REMARK 1 PMID 17405878 REMARK 1 DOI 10.1074/JBC.M700917200 REMARK 2 REMARK 2 RESOLUTION. 2.50 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.2.0019 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) : 2.50 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 30.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 99.5 REMARK 3 NUMBER OF REFLECTIONS : 11573 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) : 0.211 REMARK 3 R VALUE (WORKING SET) : 0.210 REMARK 3 FREE R VALUE : 0.242 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.700 REMARK 3 FREE R VALUE TEST SET COUNT : 570 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) : 2.50 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.56 REMARK 3 REFLECTION IN BIN (WORKING SET) : 866 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 BIN R VALUE (WORKING SET) : 0.3530 REMARK 3 BIN FREE R VALUE SET COUNT : 34 REMARK 3 BIN FREE R VALUE : 0.4900 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2188 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 5 REMARK 3 SOLVENT ATOMS : 36 REMARK 3 REMARK 3 B VALUES. REMARK 3 B VALUE TYPE : LIKELY RESIDUAL REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 46.09 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -1.22000 REMARK 3 B22 (A**2) : 1.61000 REMARK 3 B33 (A**2) : -0.38000 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): 0.488 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.270 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.207 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 19.036 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.949 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.917 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 2229 ; 0.009 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): 1506 ; 0.001 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 3006 ; 1.039 ; 1.973 REMARK 3 BOND ANGLES OTHERS (DEGREES): 3705 ; 0.820 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 272 ; 5.407 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 106 ;40.976 ;25.566 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 421 ;13.990 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 8 ;21.309 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 341 ; 0.057 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2444 ; 0.003 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 419 ; 0.001 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 445 ; 0.204 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): 1486 ; 0.167 ; 0.200 REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 1076 ; 0.173 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): 1133 ; 0.080 ; 0.200 REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 61 ; 0.390 ; 0.200 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): 5 ; 0.183 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): 10 ; 0.246 ; 0.200 REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 5 ; 0.096 ; 0.200 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): 1778 ; 0.399 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 2193 ; 0.466 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1023 ; 0.869 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 813 ; 1.292 ; 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 : 1 REMARK 3 REMARK 3 TLS GROUP : 1 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 1 A 999 REMARK 3 ORIGIN FOR THE GROUP (A): 26.9798 15.3807 15.4157 REMARK 3 T TENSOR REMARK 3 T11: -0.1459 T22: -0.0476 REMARK 3 T33: -0.0054 T12: 0.0437 REMARK 3 T13: -0.0789 T23: 0.0258 REMARK 3 L TENSOR REMARK 3 L11: 4.5685 L22: 2.2646 REMARK 3 L33: 3.4450 L12: 0.5448 REMARK 3 L13: -1.4996 L23: -0.7919 REMARK 3 S TENSOR REMARK 3 S11: 0.0623 S12: 0.6507 S13: 0.7142 REMARK 3 S21: -0.0912 S22: 0.0774 S23: 0.1945 REMARK 3 S31: -0.1494 S32: -0.3705 S33: -0.1397 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. REMARK 4 REMARK 4 2VKQ COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 21-DEC-07. REMARK 100 THE DEPOSITION ID IS D_1290034832. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 25-FEB-06 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 : ID14-4 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.94 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : NULL REMARK 200 DETECTOR MANUFACTURER : NULL REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 12172 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.500 REMARK 200 RESOLUTION RANGE LOW (A) : 78.090 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.7 REMARK 200 DATA REDUNDANCY : 5.900 REMARK 200 R MERGE (I) : 0.09000 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 15.0000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.50 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.64 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 6.20 REMARK 200 R MERGE FOR SHELL (I) : 0.42000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 2.800 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: PDB ENTRY 2CN1 REMARK 200 REMARK 200 REMARK: NONE REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 52.50 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.60 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 24% PEG1500, 20% GLYCEROL 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 39.02050 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 39.02050 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 44.13250 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 49.69400 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 44.13250 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 49.69400 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 39.02050 REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 44.13250 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 49.69400 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 39.02050 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 44.13250 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 49.69400 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1 REMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN REMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON REMARK 300 BURIED SURFACE AREA. REMARK 350 REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS REMARK 350 GIVEN BELOW. BOTH NON-CRYSTALLOGRAPHIC AND REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN. REMARK 350 REMARK 350 BIOMOLECULE: 1 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PQS 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 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 -5 REMARK 465 GLY A -4 REMARK 465 SER A -3 REMARK 465 SER A -2 REMARK 465 HIS A -1 REMARK 465 HIS A 0 REMARK 465 HIS A 1 REMARK 465 HIS A 2 REMARK 465 HIS A 3 REMARK 465 HIS A 4 REMARK 465 SER A 5 REMARK 465 SER A 6 REMARK 465 GLY A 7 REMARK 465 LEU A 8 REMARK 465 VAL A 9 REMARK 465 PRO A 10 REMARK 465 ARG A 11 REMARK 465 GLY A 12 REMARK 465 SER A 13 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 2009 O HOH A 2010 0.00 REMARK 500 O HOH A 2033 O HOH A 2034 1.83 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 185 CD GLU A 185 OE2 0.097 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 PHE A 39 -72.70 -100.96 REMARK 500 ALA A 114 57.37 71.17 REMARK 500 SER A 264 -40.38 -130.67 REMARK 500 GLN A 271 52.81 38.28 REMARK 500 GLU A 273 39.66 -96.81 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 A2008 DISTANCE = 6.15 ANGSTROMS 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 BEF A1287 BE REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 38 OD1 REMARK 620 2 BEF A1287 F1 108.1 REMARK 620 3 BEF A1287 F2 104.6 111.6 REMARK 620 4 BEF A1287 F3 111.6 110.2 110.6 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A1288 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 38 OD2 REMARK 620 2 ASP A 40 O 87.1 REMARK 620 3 ASP A 227 OD1 69.9 80.5 REMARK 620 4 BEF A1287 F1 80.6 103.9 150.0 REMARK 620 5 HOH A2021 O 76.9 149.6 69.7 98.9 REMARK 620 N 1 2 3 4 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE BEF A 1287 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG A 1288 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2JGA RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF HUMAN CYTOSOLIC 5'- NUCLEOTIDASE III IN REMARK 900 COMPLEX WITH PHOSPHATE AND MAGNESIUM REMARK 900 RELATED ID: 2CN1 RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF HUMAN CYTOSOLIC 5'- NUCLEOTIDASE III (NT5C3) DBREF 2VKQ A -5 13 PDB 2VKQ 2VKQ -5 13 DBREF 2VKQ A 14 286 UNP Q9H0P0 5NT3_HUMAN 13 285 SEQRES 1 A 292 MET GLY SER SER HIS HIS HIS HIS HIS HIS SER SER GLY SEQRES 2 A 292 LEU VAL PRO ARG GLY SER ASN PRO THR ARG VAL GLU GLU SEQRES 3 A 292 ILE ILE CYS GLY LEU ILE LYS GLY GLY ALA ALA LYS LEU SEQRES 4 A 292 GLN ILE ILE THR ASP PHE ASP MET THR LEU SER ARG PHE SEQRES 5 A 292 SER TYR LYS GLY LYS ARG CYS PRO THR CYS HIS ASN ILE SEQRES 6 A 292 ILE ASP ASN CYS LYS LEU VAL THR ASP GLU CYS ARG LYS SEQRES 7 A 292 LYS LEU LEU GLN LEU LYS GLU LYS TYR TYR ALA ILE GLU SEQRES 8 A 292 VAL ASP PRO VAL LEU THR VAL GLU GLU LYS TYR PRO TYR SEQRES 9 A 292 MET VAL GLU TRP TYR THR LYS SER HIS GLY LEU LEU VAL SEQRES 10 A 292 GLN GLN ALA LEU PRO LYS ALA LYS LEU LYS GLU ILE VAL SEQRES 11 A 292 ALA GLU SER ASP VAL MET LEU LYS GLU GLY TYR GLU ASN SEQRES 12 A 292 PHE PHE ASP LYS LEU GLN GLN HIS SER ILE PRO VAL PHE SEQRES 13 A 292 ILE PHE SER ALA GLY ILE GLY ASP VAL LEU GLU GLU VAL SEQRES 14 A 292 ILE ARG GLN ALA GLY VAL TYR HIS PRO ASN VAL LYS VAL SEQRES 15 A 292 VAL SER ASN PHE MET ASP PHE ASP GLU THR GLY VAL LEU SEQRES 16 A 292 LYS GLY PHE LYS GLY GLU LEU ILE HIS VAL PHE ASN LYS SEQRES 17 A 292 HIS ASP GLY ALA LEU ARG ASN THR GLU TYR PHE ASN GLN SEQRES 18 A 292 LEU LYS ASP ASN SER ASN ILE ILE LEU LEU GLY ASP SER SEQRES 19 A 292 GLN GLY ASP LEU ARG MET ALA ASP GLY VAL ALA ASN VAL SEQRES 20 A 292 GLU HIS ILE LEU LYS ILE GLY TYR LEU ASN ASP ARG VAL SEQRES 21 A 292 ASP GLU LEU LEU GLU LYS TYR MET ASP SER TYR ASP ILE SEQRES 22 A 292 VAL LEU VAL GLN ASP GLU SER LEU GLU VAL ALA ASN SER SEQRES 23 A 292 ILE LEU GLN LYS ILE LEU HET BEF A1287 4 HET MG A1288 1 HETNAM BEF BERYLLIUM TRIFLUORIDE ION HETNAM MG MAGNESIUM ION FORMUL 2 BEF BE F3 1- FORMUL 3 MG MG 2+ FORMUL 4 HOH *36(H2 O) HELIX 1 1 ASN A 14 GLY A 29 1 16 HELIX 2 2 THR A 55 ASN A 62 1 8 HELIX 3 3 THR A 67 VAL A 86 1 20 HELIX 4 4 THR A 91 ALA A 114 1 24 HELIX 5 5 LYS A 119 GLU A 126 1 8 HELIX 6 6 GLY A 134 HIS A 145 1 12 HELIX 7 7 GLY A 157 ALA A 167 1 11 HELIX 8 8 ASN A 201 ASN A 209 1 9 HELIX 9 9 ASN A 209 GLN A 215 1 7 HELIX 10 10 GLN A 229 MET A 234 5 6 HELIX 11 11 ARG A 253 ASP A 263 1 11 HELIX 12 12 LEU A 275 LEU A 286 1 12 SHEET 1 AA 6 VAL A 174 ASN A 179 0 SHEET 2 AA 6 VAL A 149 ILE A 156 1 O VAL A 149 N LYS A 175 SHEET 3 AA 6 LEU A 33 THR A 37 1 O ILE A 35 N PHE A 150 SHEET 4 AA 6 ASN A 221 GLY A 226 1 O ASN A 221 N GLN A 34 SHEET 5 AA 6 HIS A 243 LEU A 250 1 O HIS A 243 N ILE A 222 SHEET 6 AA 6 ILE A 267 VAL A 270 1 O ILE A 267 N GLY A 248 SHEET 1 AB 2 SER A 47 TYR A 48 0 SHEET 2 AB 2 LYS A 51 ARG A 52 -1 O LYS A 51 N TYR A 48 SHEET 1 AC 2 MET A 181 PHE A 183 0 SHEET 2 AC 2 LEU A 189 PHE A 192 -1 N LYS A 190 O ASP A 182 LINK OD1 ASP A 38 BE BEF A1287 1555 1555 1.79 LINK OD2 ASP A 38 MG MG A1288 1555 1555 2.18 LINK O ASP A 40 MG MG A1288 1555 1555 2.03 LINK OD1 ASP A 227 MG MG A1288 1555 1555 2.32 LINK F1 BEF A1287 MG MG A1288 1555 1555 1.98 LINK MG MG A1288 O HOH A2021 1555 1555 2.18 SITE 1 AC1 8 ASP A 38 PHE A 39 ASP A 40 SER A 153 SITE 2 AC1 8 ALA A 154 LYS A 202 MG A1288 HOH A2003 SITE 1 AC2 5 ASP A 38 ASP A 40 ASP A 227 BEF A1287 SITE 2 AC2 5 HOH A2021 CRYST1 88.265 99.388 78.041 90.00 90.00 90.00 C 2 2 21 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 0.011330 0.000000 0.000000 0.00000 SCALE2 0.000000 0.010062 0.000000 0.00000 SCALE3 0.000000 0.000000 0.012814 0.00000