HEADER HYDROLASE 24-MAY-13 4KX3 TITLE STRUCTURE OF MURINE CYTOSOLIC 5'-NUCLEOTIDASE III COMPLEXED WITH TITLE 2 THYMIDINE MONOPHOSPHATE COMPND MOL_ID: 1; COMPND 2 MOLECULE: ISOFORM 1 OF CYTOSOLIC 5'-NUCLEOTIDASE 3A; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: CATALYTICALLY INACTIVE CN-III; COMPND 5 SYNONYM: 7-METHYLGUANOSINE PHOSPHATE-SPECIFIC 5'-NUCLEOTIDASE,7- COMPND 6 METHYLGUANOSINE NUCLEOTIDASE,CYTOSOLIC 5'-NUCLEOTIDASE 3,CYTOSOLIC COMPND 7 5'-NUCLEOTIDASE III,CN-III,LUPIN,PYRIMIDINE 5'-NUCLEOTIDASE 1,P5'N-1, COMPND 8 P5N-1,PN-I; COMPND 9 EC: 3.1.3.5,3.1.3.91; COMPND 10 ENGINEERED: YES; COMPND 11 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: MUS MUSCULUS; SOURCE 3 ORGANISM_COMMON: HOUSE MOUSE; SOURCE 4 ORGANISM_TAXID: 10090; SOURCE 5 GENE: NT5C3A, NT5C3; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: ROSETTA 2; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PVP16-GW KEYWDS SUBSTRATE COMPLEX, HAD SUPERFAMILY, NUCLEOTIDASE, UMPH-1, CYTOSOLIC KEYWDS 2 5'-NUCLEOTIDASE III, P5N-1, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR E.BITTO,C.A.BINGMAN,C.L.GROBOSKY REVDAT 3 12-FEB-25 4KX3 1 COMPND SOURCE REMARK DBREF REVDAT 3 2 1 SEQRES HET HETNAM HETSYN REVDAT 3 3 1 FORMUL LINK SITE ATOM REVDAT 2 20-SEP-23 4KX3 1 REMARK SEQADV LINK REVDAT 1 05-JUN-13 4KX3 0 JRNL AUTH E.BITTO,C.A.BINGMAN,C.L.GROBOSKY JRNL TITL STRUCTURE OF MURINE CYTOSOLIC 5'-NUCLEOTIDASE III COMPLEXED JRNL TITL 2 WITH THYMIDINE MONOPHOSPHATE JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 2.10 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 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) : 2.10 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 46.92 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 3 NUMBER OF REFLECTIONS : 19848 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) : 0.156 REMARK 3 R VALUE (WORKING SET) : 0.153 REMARK 3 FREE R VALUE : 0.217 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 991 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) : 2.10 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.16 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1341 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.93 REMARK 3 BIN R VALUE (WORKING SET) : 0.1730 REMARK 3 BIN FREE R VALUE SET COUNT : 80 REMARK 3 BIN FREE R VALUE : 0.2920 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2334 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 53 REMARK 3 SOLVENT ATOMS : 246 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 20.43 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 28.37 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.32000 REMARK 3 B22 (A**2) : 0.32000 REMARK 3 B33 (A**2) : -0.65000 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): 0.185 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.173 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.104 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 3.885 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.966 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.932 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 2439 ; 0.018 ; 0.019 REMARK 3 BOND LENGTHS OTHERS (A): 2387 ; 0.001 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 3274 ; 1.759 ; 1.974 REMARK 3 BOND ANGLES OTHERS (DEGREES): 5510 ; 0.845 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 294 ; 5.938 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 111 ;38.081 ;25.405 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 454 ;14.336 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 9 ;17.827 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 365 ; 0.104 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2699 ; 0.009 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 526 ; 0.001 ; 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): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 RIGID-BOND RESTRAINTS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; FREE ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; BONDED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 NCS RESTRAINTS STATISTICS REMARK 3 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 : 1.20 REMARK 3 ION PROBE RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: HYDROGENS HAVE BEEN ADDED IN THE RIDING REMARK 3 POSITIONS U VALUES : REFINED INDIVIDUALLY REMARK 4 REMARK 4 4KX3 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 28-MAY-13. REMARK 100 THE DEPOSITION ID IS D_1000079903. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 23-MAR-13 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 21-ID-G REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97856 REMARK 200 MONOCHROMATOR : DIAMOND [111] REMARK 200 OPTICS : BERYLLIUM LENSES REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : RAYONIX MX-300 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 19922 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.100 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 2.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 200 DATA REDUNDANCY : 13.80 REMARK 200 R MERGE (I) : 0.11800 REMARK 200 R SYM (I) : 0.08600 REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 6.9000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.10 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.14 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 14.30 REMARK 200 R MERGE FOR SHELL (I) : 0.58600 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> 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: 4FE3 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 46.99 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.32 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 20% PEG 3350, 0.10 M HEPES, 0.050 M REMARK 280 AMMONIUM ACETATE, VAPOR DIFFUSION, TEMPERATURE 283K, PH 8.0 REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 43 2 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,X,Z+3/4 REMARK 290 4555 Y,-X,Z+1/4 REMARK 290 5555 -X,Y,-Z REMARK 290 6555 X,-Y,-Z+1/2 REMARK 290 7555 Y,X,-Z+1/4 REMARK 290 8555 -Y,-X,-Z+3/4 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 142.93650 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 214.40475 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 71.46825 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 142.93650 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 71.46825 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 214.40475 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: PISA 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 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 425 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 SER A 1 REMARK 465 THR A 2 REMARK 465 ASN A 3 REMARK 465 GLN A 4 REMARK 465 GLU A 5 REMARK 465 SER A 6 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 147 CD GLU A 147 OE1 0.080 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 MET A 52 CG - SD - CE ANGL. DEV. = 10.1 DEGREES REMARK 500 ASP A 72 CB - CG - OD2 ANGL. DEV. = -6.6 DEGREES REMARK 500 ARG A 264 NE - CZ - NH1 ANGL. DEV. = -3.1 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 PHE A 50 -75.82 -106.01 REMARK 500 ASP A 195 -163.21 -78.03 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 302 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 49 OD2 REMARK 620 2 ASN A 51 O 85.0 REMARK 620 3 ASP A 238 OD1 72.7 88.3 REMARK 620 4 TMP A 301 O1P 103.4 98.5 171.9 REMARK 620 5 HOH A 401 O 84.4 167.0 81.5 91.2 REMARK 620 6 HOH A 402 O 162.8 87.8 91.5 93.2 100.4 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 TMP A 301 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG A 302 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO A 303 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO A 304 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO A 305 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EPE A 308 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO A 309 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4FE3 RELATED DB: PDB REMARK 900 CYTOSOLIC 5'-NUCLEOTIDASE III COMPLEXED WITH URIDINE MONOPHOSPHATE REMARK 900 RELATED ID: 2G06 RELATED DB: PDB REMARK 900 CYTOSOLIC 5'-NUCLEOTIDASE III WITH BOUND MAGNESIUM(II) IN AN OPEN REMARK 900 FORM REMARK 900 RELATED ID: 2G09 RELATED DB: PDB REMARK 900 CYTOSOLIC 5'-NUCLEOTIDASE III COMPLEX WITH PHOSPHATE IN THE ACTIVE REMARK 900 SITE REMARK 900 RELATED ID: 4KX5 RELATED DB: PDB REMARK 999 REMARK 999 SEQUENCE REMARK 999 THE CRYSTALLIZED SEQUENCE REFERS TO Q9D020-1|5NT3_MOUSE ISOFORM 1 REMARK 999 OF CYTOSOLIC 5'-NUCLEOTIDASE DBREF 4KX3 A 1 297 UNP Q9D020 5NT3A_MOUSE 1 297 SEQADV 4KX3 SER A 1 UNP Q9D020 MET 1 ENGINEERED MUTATION SEQADV 4KX3 ASN A 51 UNP Q9D020 ASP 51 ENGINEERED MUTATION SEQRES 1 A 297 SER THR ASN GLN GLU SER ALA VAL HIS LEU LYS MET MET SEQRES 2 A 297 PRO GLU PHE GLN LYS SER SER VAL ARG ILE LYS ASN PRO SEQRES 3 A 297 THR ARG VAL GLU GLU ILE ILE CME GLY LEU ILE LYS GLY SEQRES 4 A 297 GLY ALA ALA LYS LEU GLN ILE ILE THR ASP PHE ASN MET SEQRES 5 A 297 THR LEU SER ARG PHE SER TYR ASN GLY LYS ARG CME PRO SEQRES 6 A 297 THR CYS HIS ASN ILE ILE ASP ASN CYS LYS LEU VAL THR SEQRES 7 A 297 ASP GLU CYS ARG ARG LYS LEU LEU GLN LEU LYS GLU GLN SEQRES 8 A 297 TYR TYR ALA ILE GLU VAL ASP PRO VAL LEU THR VAL GLU SEQRES 9 A 297 GLU LYS PHE PRO TYR MET VAL GLU TRP TYR THR LYS SER SEQRES 10 A 297 HIS GLY LEU LEU ILE GLU GLN GLY ILE PRO LYS ALA LYS SEQRES 11 A 297 LEU LYS GLU ILE VAL ALA ASP SER ASP VAL MET LEU LYS SEQRES 12 A 297 GLU GLY TYR GLU ASN PHE PHE GLY LYS LEU GLN GLN HIS SEQRES 13 A 297 GLY ILE PRO VAL PHE ILE PHE SER ALA GLY ILE GLY ASP SEQRES 14 A 297 VAL LEU GLU GLU VAL ILE ARG GLN ALA GLY VAL TYR HIS SEQRES 15 A 297 SER ASN VAL LYS VAL VAL SER ASN PHE MET ASP PHE ASP SEQRES 16 A 297 GLU ASN GLY VAL LEU LYS GLY PHE LYS GLY GLU LEU ILE SEQRES 17 A 297 HIS VAL PHE ASN LYS HIS ASP GLY ALA LEU LYS ASN THR SEQRES 18 A 297 ASP TYR PHE SER GLN LEU LYS ASP ASN SER ASN ILE ILE SEQRES 19 A 297 LEU LEU GLY ASP SER GLN GLY ASP LEU ARG MET ALA ASP SEQRES 20 A 297 GLY VAL ALA ASN VAL GLU HIS ILE LEU LYS ILE GLY TYR SEQRES 21 A 297 LEU ASN ASP ARG VAL ASP GLU LEU LEU GLU LYS TYR MET SEQRES 22 A 297 ASP SER TYR ASP ILE VAL LEU VAL LYS GLU GLU SER LEU SEQRES 23 A 297 GLU VAL VAL ASN SER ILE LEU GLN LYS THR LEU MODRES 4KX3 CME A 34 CYS MODIFIED RESIDUE MODRES 4KX3 CME A 64 CYS MODIFIED RESIDUE HET CME A 34 10 HET CME A 64 10 HET TMP A 301 21 HET MG A 302 1 HET EDO A 303 4 HET EDO A 304 4 HET EDO A 305 4 HET EPE A 308 15 HET EDO A 309 4 HETNAM CME S,S-(2-HYDROXYETHYL)THIOCYSTEINE HETNAM TMP THYMIDINE-5'-PHOSPHATE HETNAM MG MAGNESIUM ION HETNAM EDO 1,2-ETHANEDIOL HETNAM EPE 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID HETSYN EDO ETHYLENE GLYCOL HETSYN EPE HEPES FORMUL 1 CME 2(C5 H11 N O3 S2) FORMUL 2 TMP C10 H15 N2 O8 P FORMUL 3 MG MG 2+ FORMUL 4 EDO 4(C2 H6 O2) FORMUL 7 EPE C8 H18 N2 O4 S FORMUL 9 HOH *246(H2 O) HELIX 1 1 HIS A 9 MET A 12 5 4 HELIX 2 2 MET A 13 LYS A 18 1 6 HELIX 3 3 ASN A 25 GLY A 40 1 16 HELIX 4 4 THR A 66 ASN A 73 1 8 HELIX 5 5 THR A 78 ASP A 98 1 21 HELIX 6 6 THR A 102 GLN A 124 1 23 HELIX 7 7 PRO A 127 ALA A 129 5 3 HELIX 8 8 LYS A 130 SER A 138 1 9 HELIX 9 9 GLY A 145 HIS A 156 1 12 HELIX 10 10 GLY A 168 ALA A 178 1 11 HELIX 11 11 ASN A 212 LYS A 219 1 8 HELIX 12 12 ASN A 220 GLN A 226 1 7 HELIX 13 13 SER A 239 MET A 245 5 7 HELIX 14 14 ARG A 264 TYR A 276 1 13 HELIX 15 15 LEU A 286 LEU A 297 1 12 SHEET 1 A 7 VAL A 21 ARG A 22 0 SHEET 2 A 7 ILE A 278 VAL A 281 -1 O VAL A 279 N ARG A 22 SHEET 3 A 7 HIS A 254 LEU A 261 1 N GLY A 259 O ILE A 278 SHEET 4 A 7 ASN A 232 GLY A 237 1 N GLY A 237 O TYR A 260 SHEET 5 A 7 LEU A 44 THR A 48 1 N ILE A 47 O ILE A 234 SHEET 6 A 7 VAL A 160 ILE A 167 1 O PHE A 161 N THR A 48 SHEET 7 A 7 VAL A 185 ASN A 190 1 O LYS A 186 N ILE A 162 SHEET 1 B 2 SER A 58 TYR A 59 0 SHEET 2 B 2 LYS A 62 ARG A 63 -1 O LYS A 62 N TYR A 59 SHEET 1 C 2 MET A 192 PHE A 194 0 SHEET 2 C 2 LEU A 200 PHE A 203 -1 O GLY A 202 N ASP A 193 LINK C ILE A 33 N CME A 34 1555 1555 1.32 LINK C CME A 34 N GLY A 35 1555 1555 1.32 LINK C ARG A 63 N CME A 64 1555 1555 1.32 LINK C CME A 64 N PRO A 65 1555 1555 1.32 LINK OD2 ASP A 49 MG MG A 302 1555 1555 2.21 LINK O ASN A 51 MG MG A 302 1555 1555 2.16 LINK OD1 ASP A 238 MG MG A 302 1555 1555 2.15 LINK O1P TMP A 301 MG MG A 302 1555 1555 2.00 LINK MG MG A 302 O HOH A 401 1555 1555 2.18 LINK MG MG A 302 O HOH A 402 1555 1555 2.08 SITE 1 AC1 25 ASP A 49 PHE A 50 ASN A 51 THR A 66 SITE 2 AC1 25 HIS A 68 ASN A 69 GLU A 96 TRP A 113 SITE 3 AC1 25 TYR A 114 SER A 117 SER A 164 ALA A 165 SITE 4 AC1 25 GLY A 166 LYS A 213 MG A 302 EDO A 304 SITE 5 AC1 25 HOH A 401 HOH A 402 HOH A 417 HOH A 441 SITE 6 AC1 25 HOH A 501 HOH A 504 HOH A 520 HOH A 551 SITE 7 AC1 25 HOH A 557 SITE 1 AC2 6 ASP A 49 ASN A 51 ASP A 238 TMP A 301 SITE 2 AC2 6 HOH A 401 HOH A 402 SITE 1 AC3 5 LYS A 24 PRO A 26 THR A 27 ARG A 28 SITE 2 AC3 5 GLU A 31 SITE 1 AC4 6 ARG A 63 ASN A 69 LYS A 89 TMP A 301 SITE 2 AC4 6 HOH A 551 HOH A 573 SITE 1 AC5 6 GLN A 154 GLY A 157 ARG A 176 SER A 183 SITE 2 AC5 6 ASN A 184 HOH A 531 SITE 1 AC8 6 GLU A 206 GLN A 294 LYS A 295 LEU A 297 SITE 2 AC8 6 HOH A 625 HOH A 626 SITE 1 AC9 6 ALA A 41 ALA A 42 HIS A 156 GLY A 157 SITE 2 AC9 6 ASN A 230 HOH A 565 CRYST1 46.872 46.872 285.873 90.00 90.00 90.00 P 43 2 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 0.021335 0.000000 0.000000 0.00000 SCALE2 0.000000 0.021335 0.000000 0.00000 SCALE3 0.000000 0.000000 0.003498 0.00000