HEADER HYDROLASE 04-JUL-10 2XJF TITLE CRYSTAL STRUCTURE OF THE D52N VARIANT OF CYTOSOLIC 5'-NUCLEOTIDASE II TITLE 2 WITH A COVALENTLY MODIFIED ASN52 COMPND MOL_ID: 1; COMPND 2 MOLECULE: CYTOSOLIC PURINE 5'-NUCLEOTIDASE; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: RESIDUES 1-536; COMPND 5 SYNONYM: CYTOSOLIC 5'-NUCLEOTIDASE II; COMPND 6 EC: 3.1.3.5; COMPND 7 ENGINEERED: YES; COMPND 8 MUTATION: 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: R3 PRARE2; SOURCE 9 EXPRESSION_SYSTEM_VECTOR: P28A-LIC KEYWDS ALLOSTERIC ENZYME, CN-II, GMP-IMP SPECIFIC NUCLEOTIDASE, HIGH KM 5- KEYWDS 2 PRIME NUCLEOTIDASE, HYDROLASE, METAL-BINDING, NT5C2, NUCLEOTIDE KEYWDS 3 METABOLISM, NUCLEOTIDE-BINDING, PHOSPHOPROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR K.WALLDEN,P.NORDLUND REVDAT 5 23-OCT-24 2XJF 1 REMARK REVDAT 4 20-DEC-23 2XJF 1 REMARK LINK REVDAT 3 20-JUL-16 2XJF 1 HETNAM HETSYN REVDAT 2 27-APR-11 2XJF 1 JRNL REMARK REVDAT 1 16-MAR-11 2XJF 0 JRNL AUTH K.WALLDEN,P.NORDLUND JRNL TITL STRUCTURAL BASIS FOR THE ALLOSTERIC REGULATION AND SUBSTRATE JRNL TITL 2 RECOGNITION OF HUMAN CYTOSOLIC 5'-NUCLEOTIDASE II JRNL REF J.MOL.BIOL. V. 408 684 2011 JRNL REFN ISSN 0022-2836 JRNL PMID 21396942 JRNL DOI 10.1016/J.JMB.2011.02.059 REMARK 2 REMARK 2 RESOLUTION. 2.10 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) : 2.10 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 65.23 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 96.0 REMARK 3 NUMBER OF REFLECTIONS : 41334 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) : 0.178 REMARK 3 FREE R VALUE : 0.225 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 2224 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) : 2.15 REMARK 3 REFLECTION IN BIN (WORKING SET) : 3053 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 98.03 REMARK 3 BIN R VALUE (WORKING SET) : 0.2210 REMARK 3 BIN FREE R VALUE SET COUNT : 179 REMARK 3 BIN FREE R VALUE : 0.2940 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 3764 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 33 REMARK 3 SOLVENT ATOMS : 250 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 25.41 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.13000 REMARK 3 B22 (A**2) : -0.04000 REMARK 3 B33 (A**2) : -0.09000 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): 0.157 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.154 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.104 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 7.573 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.952 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.933 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 3963 ; 0.018 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 5352 ; 1.625 ; 1.968 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 471 ; 6.326 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 188 ;32.111 ;22.872 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 683 ;15.721 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 28 ;12.763 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 562 ; 0.121 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 3013 ; 0.007 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 1713 ; 0.214 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 2668 ; 0.307 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 247 ; 0.142 ; 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): 58 ; 0.198 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 14 ; 0.155 ; 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): 2418 ; 1.012 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 3766 ; 1.577 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1794 ; 2.689 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1586 ; 3.740 ; 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 : 1.20 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 2XJF COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 04-JUL-10. REMARK 100 THE DEPOSITION ID IS D_1290044484. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 02-NOV-07 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 : ID23-2 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.87260 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARMOSAIC 225 MM CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 43556 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.100 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 96.4 REMARK 200 DATA REDUNDANCY : 5.000 REMARK 200 R MERGE (I) : 0.11000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 11.7000 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) : 2.21 REMARK 200 COMPLETENESS FOR SHELL (%) : 98.1 REMARK 200 DATA REDUNDANCY IN SHELL : 5.00 REMARK 200 R MERGE FOR SHELL (I) : 0.44000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.900 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 2JC9 REMARK 200 REMARK 200 REMARK: NONE REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 61.50 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.19 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M BICINE PH 9.0, 10% PEG 6000. 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 46.04750 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 64.11100 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 65.21950 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 46.04750 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 64.11100 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 65.21950 REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 46.04750 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 64.11100 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 65.21950 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 46.04750 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 64.11100 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 65.21950 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: 6870 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 38470 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -1.9 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 -1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 2 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 130.43900 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 -18 REMARK 465 GLY A -17 REMARK 465 SER A -16 REMARK 465 SER A -15 REMARK 465 HIS A -14 REMARK 465 HIS A -13 REMARK 465 HIS A -12 REMARK 465 HIS A -11 REMARK 465 HIS A -10 REMARK 465 HIS A -9 REMARK 465 SER A -8 REMARK 465 SER A -7 REMARK 465 GLY A -6 REMARK 465 LEU A -5 REMARK 465 VAL A -4 REMARK 465 PRO A -3 REMARK 465 ARG A -2 REMARK 465 GLY A -1 REMARK 465 SER A 0 REMARK 465 MET A 1 REMARK 465 SER A 2 REMARK 465 ILE A 397 REMARK 465 PHE A 398 REMARK 465 LEU A 399 REMARK 465 ALA A 400 REMARK 465 GLU A 401 REMARK 465 LEU A 402 REMARK 465 TYR A 403 REMARK 465 LYS A 404 REMARK 465 HIS A 405 REMARK 465 LEU A 406 REMARK 465 ASP A 407 REMARK 465 SER A 408 REMARK 465 SER A 409 REMARK 465 SER A 410 REMARK 465 ASN A 411 REMARK 465 GLU A 412 REMARK 465 ARG A 413 REMARK 465 PRO A 414 REMARK 465 ASP A 415 REMARK 465 ILE A 416 REMARK 465 SER A 417 REMARK 465 SER A 418 REMARK 465 ILE A 419 REMARK 465 GLN A 420 REMARK 465 THR A 489 REMARK 465 VAL A 490 REMARK 465 GLU A 491 REMARK 465 HIS A 492 REMARK 465 THR A 493 REMARK 465 HIS A 494 REMARK 465 VAL A 495 REMARK 465 ASP A 496 REMARK 465 ILE A 497 REMARK 465 ASN A 498 REMARK 465 GLU A 499 REMARK 465 MET A 500 REMARK 465 GLU A 501 REMARK 465 SER A 502 REMARK 465 PRO A 503 REMARK 465 LEU A 504 REMARK 465 ALA A 505 REMARK 465 THR A 506 REMARK 465 ARG A 507 REMARK 465 ASN A 508 REMARK 465 ARG A 509 REMARK 465 THR A 510 REMARK 465 SER A 511 REMARK 465 VAL A 512 REMARK 465 ASP A 513 REMARK 465 PHE A 514 REMARK 465 LYS A 515 REMARK 465 ASP A 516 REMARK 465 THR A 517 REMARK 465 ASP A 518 REMARK 465 TYR A 519 REMARK 465 LYS A 520 REMARK 465 ARG A 521 REMARK 465 HIS A 522 REMARK 465 GLN A 523 REMARK 465 LEU A 524 REMARK 465 THR A 525 REMARK 465 ARG A 526 REMARK 465 SER A 527 REMARK 465 ILE A 528 REMARK 465 SER A 529 REMARK 465 GLU A 530 REMARK 465 ILE A 531 REMARK 465 LYS A 532 REMARK 465 PRO A 533 REMARK 465 PRO A 534 REMARK 465 ASN A 535 REMARK 465 LEU A 536 REMARK 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 ARG A 421 CG CD NE CZ NH1 NH2 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 PHE A 51 C A5N A 52 N 0.146 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 277 NE - CZ - NH1 ANGL. DEV. = 3.8 DEGREES REMARK 500 ARG A 277 NE - CZ - NH2 ANGL. DEV. = -4.3 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 THR A 56 -68.24 -127.78 REMARK 500 PRO A 267 35.88 -82.54 REMARK 500 PHE A 354 -70.76 -103.72 REMARK 500 ASP A 356 -70.54 -85.76 REMARK 500 REMARK 500 REMARK: NULL REMARK 600 REMARK 600 HETEROGEN REMARK 600 REMARK 600 THE IDENTITY OF THE CARBOXY GROUP OF ASN52 (A5N) IS UNCERTAIN REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE DG2 A 1489 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 1490 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 1491 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 1492 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2JC9 RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF HUMAN CYTOSOLIC 5'- NUCLEOTIDASE II IN COMPLEX REMARK 900 WITH ADENOSINE REMARK 900 RELATED ID: 2XCV RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF THE D52N VARIANT OF CYTOSOLIC 5'-NUCLEOTIDASE REMARK 900 II IN COMPLEX WITH INOSINE MONOPHOSPHATE AND 2,3- REMARK 900 BISPHOSPHOGLYCERATE REMARK 900 RELATED ID: 2XJD RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF THE D52N VARIANT OF CYTOSOLIC 5'-NUCLEOTIDASE REMARK 900 II IN COMPLEX WITH INORGANIC PHOSPHATE AND DEOXYADENOSINE REMARK 900 TRIPHOSPHATE REMARK 900 RELATED ID: 2J2C RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF HUMAN CYTOSOLIC 5'- NUCLEOTIDASE II (NT5C2, CN- REMARK 900 II) REMARK 900 RELATED ID: 2JCM RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF HUMAN CYTOSOLIC 5'- NUCLEOTIDASE II IN COMPLEX REMARK 900 WITH BERYLLIUM TRIFLUORIDE REMARK 900 RELATED ID: 2XCX RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF THE APOFORM OF THE D52N VARIANT OF CYTOSOLIC 5' REMARK 900 -NUCLEOTIDASE II REMARK 900 RELATED ID: 2XJE RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF THE D52N VARIANT OF CYTOSOLIC 5'-NUCLEOTIDASE REMARK 900 II IN COMPLEX WITH URIDINE 5'-MONOPHOSPHATE AND ADENOSINE REMARK 900 TRIPHOSPHATE REMARK 900 RELATED ID: 2XCW RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF THE D52N VARIANT OF CYTOSOLIC 5 '-NUCLEOTIDASE REMARK 900 II IN COMPLEX WITH INOSINE MONOPHOSPHATE AND AT REMARK 900 RELATED ID: 2XJB RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF THE D52N VARIANT OF CYTOSOLIC 5'-NUCLEOTIDASE REMARK 900 II IN COMPLEX WITH DEOXYGUANOSINE MONOPHOSPHATE AND DEOXYADENOSINE REMARK 900 TRIPHOSPHATE REMARK 900 RELATED ID: 2XJC RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF THE D52N VARIANT OF CYTOSOLIC 5'-NUCLEOTIDASE REMARK 900 II IN COMPLEX WITH GUANOSINE MONOPHOSPHATE AND DIADENOSINE REMARK 900 TETRAPHOSPHATE REMARK 999 REMARK 999 SEQUENCE REMARK 999 ASP52 MUTATED TO AN ASPARAGINE WHICH WAS SUBSEQUENTLY REMARK 999 MODIFIED TO CARBOXY ASPARAGINE (A5N) DBREF 2XJF A 1 536 UNP P49902 5NTC_HUMAN 1 536 SEQADV 2XJF MET A -18 UNP P49902 EXPRESSION TAG SEQADV 2XJF GLY A -17 UNP P49902 EXPRESSION TAG SEQADV 2XJF SER A -16 UNP P49902 EXPRESSION TAG SEQADV 2XJF SER A -15 UNP P49902 EXPRESSION TAG SEQADV 2XJF HIS A -14 UNP P49902 EXPRESSION TAG SEQADV 2XJF HIS A -13 UNP P49902 EXPRESSION TAG SEQADV 2XJF HIS A -12 UNP P49902 EXPRESSION TAG SEQADV 2XJF HIS A -11 UNP P49902 EXPRESSION TAG SEQADV 2XJF HIS A -10 UNP P49902 EXPRESSION TAG SEQADV 2XJF HIS A -9 UNP P49902 EXPRESSION TAG SEQADV 2XJF SER A -8 UNP P49902 EXPRESSION TAG SEQADV 2XJF SER A -7 UNP P49902 EXPRESSION TAG SEQADV 2XJF GLY A -6 UNP P49902 EXPRESSION TAG SEQADV 2XJF LEU A -5 UNP P49902 EXPRESSION TAG SEQADV 2XJF VAL A -4 UNP P49902 EXPRESSION TAG SEQADV 2XJF PRO A -3 UNP P49902 EXPRESSION TAG SEQADV 2XJF ARG A -2 UNP P49902 EXPRESSION TAG SEQADV 2XJF GLY A -1 UNP P49902 EXPRESSION TAG SEQADV 2XJF SER A 0 UNP P49902 EXPRESSION TAG SEQADV 2XJF A5N A 52 UNP P49902 ASP 52 ENGINEERED MUTATION SEQRES 1 A 555 MET GLY SER SER HIS HIS HIS HIS HIS HIS SER SER GLY SEQRES 2 A 555 LEU VAL PRO ARG GLY SER MET SER THR SER TRP SER ASP SEQRES 3 A 555 ARG LEU GLN ASN ALA ALA ASP MET PRO ALA ASN MET ASP SEQRES 4 A 555 LYS HIS ALA LEU LYS LYS TYR ARG ARG GLU ALA TYR HIS SEQRES 5 A 555 ARG VAL PHE VAL ASN ARG SER LEU ALA MET GLU LYS ILE SEQRES 6 A 555 LYS CYS PHE GLY PHE A5N MET ASP TYR THR LEU ALA VAL SEQRES 7 A 555 TYR LYS SER PRO GLU TYR GLU SER LEU GLY PHE GLU LEU SEQRES 8 A 555 THR VAL GLU ARG LEU VAL SER ILE GLY TYR PRO GLN GLU SEQRES 9 A 555 LEU LEU SER PHE ALA TYR ASP SER THR PHE PRO THR ARG SEQRES 10 A 555 GLY LEU VAL PHE ASP THR LEU TYR GLY ASN LEU LEU LYS SEQRES 11 A 555 VAL ASP ALA TYR GLY ASN LEU LEU VAL CYS ALA HIS GLY SEQRES 12 A 555 PHE ASN PHE ILE ARG GLY PRO GLU THR ARG GLU GLN TYR SEQRES 13 A 555 PRO ASN LYS PHE ILE GLN ARG ASP ASP THR GLU ARG PHE SEQRES 14 A 555 TYR ILE LEU ASN THR LEU PHE ASN LEU PRO GLU THR TYR SEQRES 15 A 555 LEU LEU ALA CYS LEU VAL ASP PHE PHE THR ASN CYS PRO SEQRES 16 A 555 ARG TYR THR SER CYS GLU THR GLY PHE LYS ASP GLY ASP SEQRES 17 A 555 LEU PHE MET SER TYR ARG SER MET PHE GLN ASP VAL ARG SEQRES 18 A 555 ASP ALA VAL ASP TRP VAL HIS TYR LYS GLY SER LEU LYS SEQRES 19 A 555 GLU LYS THR VAL GLU ASN LEU GLU LYS TYR VAL VAL LYS SEQRES 20 A 555 ASP GLY LYS LEU PRO LEU LEU LEU SER ARG MET LYS GLU SEQRES 21 A 555 VAL GLY LYS VAL PHE LEU ALA THR ASN SER ASP TYR LYS SEQRES 22 A 555 TYR THR ASP LYS ILE MET THR TYR LEU PHE ASP PHE PRO SEQRES 23 A 555 HIS GLY PRO LYS PRO GLY SER SER HIS ARG PRO TRP GLN SEQRES 24 A 555 SER TYR PHE ASP LEU ILE LEU VAL ASP ALA ARG LYS PRO SEQRES 25 A 555 LEU PHE PHE GLY GLU GLY THR VAL LEU ARG GLN VAL ASP SEQRES 26 A 555 THR LYS THR GLY LYS LEU LYS ILE GLY THR TYR THR GLY SEQRES 27 A 555 PRO LEU GLN HIS GLY ILE VAL TYR SER GLY GLY SER SER SEQRES 28 A 555 ASP THR ILE CYS ASP LEU LEU GLY ALA LYS GLY LYS ASP SEQRES 29 A 555 ILE LEU TYR ILE GLY ASP HIS ILE PHE GLY ASP ILE LEU SEQRES 30 A 555 LYS SER LYS LYS ARG GLN GLY TRP ARG THR PHE LEU VAL SEQRES 31 A 555 ILE PRO GLU LEU ALA GLN GLU LEU HIS VAL TRP THR ASP SEQRES 32 A 555 LYS SER SER LEU PHE GLU GLU LEU GLN SER LEU ASP ILE SEQRES 33 A 555 PHE LEU ALA GLU LEU TYR LYS HIS LEU ASP SER SER SER SEQRES 34 A 555 ASN GLU ARG PRO ASP ILE SER SER ILE GLN ARG ARG ILE SEQRES 35 A 555 LYS LYS VAL THR HIS ASP MET ASP MET CYS TYR GLY MET SEQRES 36 A 555 MET GLY SER LEU PHE ARG SER GLY SER ARG GLN THR LEU SEQRES 37 A 555 PHE ALA SER GLN VAL MET ARG TYR ALA ASP LEU TYR ALA SEQRES 38 A 555 ALA SER PHE ILE ASN LEU LEU TYR TYR PRO PHE SER TYR SEQRES 39 A 555 LEU PHE ARG ALA ALA HIS VAL LEU MET PRO HIS GLU SER SEQRES 40 A 555 THR VAL GLU HIS THR HIS VAL ASP ILE ASN GLU MET GLU SEQRES 41 A 555 SER PRO LEU ALA THR ARG ASN ARG THR SER VAL ASP PHE SEQRES 42 A 555 LYS ASP THR ASP TYR LYS ARG HIS GLN LEU THR ARG SER SEQRES 43 A 555 ILE SER GLU ILE LYS PRO PRO ASN LEU MODRES 2XJF A5N A 52 ASN O-CARBOXY-4-IMINO-L-HOMOSERINE HET A5N A 52 11 HET DG2 A1489 15 HET GOL A1490 6 HET GOL A1491 6 HET GOL A1492 6 HETNAM A5N O-CARBOXY-4-IMINO-L-HOMOSERINE HETNAM DG2 (2R)-2,3-DIPHOSPHOGLYCERIC ACID HETNAM GOL GLYCEROL HETSYN DG2 2,3-BISPHOSPHOGLYCERIC ACID; 2,3-BISPHOSPHOGLYCERATE; HETSYN 2 DG2 2,3-BPG; 2,3-DIPHOSPHOGLYCERIC ACID; 2,3- HETSYN 3 DG2 DIPHOSPHOGLYCERATE; 2,3-DPG; (2~{R})-2,3- HETSYN 4 DG2 DIPHOSPHONOOXYPROPANOIC ACID HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 1 A5N C5 H8 N2 O5 FORMUL 2 DG2 C3 H8 O10 P2 FORMUL 3 GOL 3(C3 H8 O3) FORMUL 6 HOH *250(H2 O) HELIX 1 1 SER A 4 ASP A 14 1 11 HELIX 2 2 ASP A 20 ARG A 28 1 9 HELIX 3 3 ARG A 29 ARG A 34 5 6 HELIX 4 4 GLU A 44 ILE A 46 5 3 HELIX 5 5 PRO A 63 ILE A 80 1 18 HELIX 6 6 PRO A 83 PHE A 89 5 7 HELIX 7 7 ARG A 129 TYR A 137 1 9 HELIX 8 8 THR A 155 PHE A 157 5 3 HELIX 9 9 ASN A 158 CYS A 175 1 18 HELIX 10 10 TYR A 194 LYS A 211 1 18 HELIX 11 11 SER A 213 GLU A 220 1 8 HELIX 12 12 ASN A 221 VAL A 226 1 6 HELIX 13 13 GLY A 230 GLY A 243 1 14 HELIX 14 14 ASP A 252 PHE A 264 1 13 HELIX 15 15 PRO A 278 PHE A 283 5 6 HELIX 16 16 PRO A 293 GLY A 297 5 5 HELIX 17 17 SER A 331 GLY A 340 1 10 HELIX 18 18 LYS A 342 LYS A 344 5 3 HELIX 19 19 ASP A 356 GLY A 365 1 10 HELIX 20 20 GLU A 374 LYS A 385 1 12 HELIX 21 21 LYS A 385 LEU A 395 1 11 HELIX 22 22 ARG A 421 CYS A 433 1 13 HELIX 23 23 THR A 448 ALA A 458 1 11 HELIX 24 24 SER A 464 TYR A 471 5 8 HELIX 25 25 MET A 484 SER A 488 5 5 SHEET 1 AA 9 PHE A 36 VAL A 37 0 SHEET 2 AA 9 LEU A 460 ALA A 462 -1 O TYR A 461 N PHE A 36 SHEET 3 AA 9 ARG A 367 VAL A 371 1 O THR A 368 N LEU A 460 SHEET 4 AA 9 ILE A 346 GLY A 350 1 O ILE A 346 N ARG A 367 SHEET 5 AA 9 CYS A 48 PHE A 51 1 O CYS A 48 N LEU A 347 SHEET 6 AA 9 LYS A 244 ALA A 248 1 O LYS A 244 N PHE A 49 SHEET 7 AA 9 LEU A 285 VAL A 288 1 O LEU A 285 N LEU A 247 SHEET 8 AA 9 VAL A 326 GLY A 329 1 O TYR A 327 N VAL A 288 SHEET 9 AA 9 LEU A 302 VAL A 305 -1 O ARG A 303 N SER A 328 SHEET 1 AB 2 LEU A 41 ALA A 42 0 SHEET 2 AB 2 LEU A 476 PHE A 477 -1 O PHE A 477 N LEU A 41 SHEET 1 AC 5 ASN A 126 PHE A 127 0 SHEET 2 AC 5 LEU A 118 HIS A 123 -1 O HIS A 123 N ASN A 126 SHEET 3 AC 5 ASN A 108 VAL A 112 -1 O LEU A 109 N ALA A 122 SHEET 4 AC 5 LEU A 100 ASP A 103 -1 O VAL A 101 N LEU A 110 SHEET 5 AC 5 PHE A 150 LEU A 153 -1 O TYR A 151 N PHE A 102 SHEET 1 AD 3 THR A 179 SER A 180 0 SHEET 2 AD 3 GLY A 184 ASP A 187 -1 O LYS A 186 N THR A 179 SHEET 3 AD 3 LEU A 190 SER A 193 -1 O LEU A 190 N ASP A 187 SHEET 1 AE 2 ARG A 442 SER A 443 0 SHEET 2 AE 2 ARG A 446 GLN A 447 -1 O ARG A 446 N SER A 443 LINK C PHE A 51 N A5N A 52 1555 1555 1.48 LINK C A5N A 52 N MET A 53 1555 1555 1.46 CISPEP 1 SER A 62 PRO A 63 0 -0.25 CISPEP 2 LYS A 292 PRO A 293 0 6.90 SITE 1 AC1 5 ARG A 144 LYS A 362 GLN A 453 ARG A 456 SITE 2 AC1 5 TYR A 457 SITE 1 AC2 9 PHE A 283 ASP A 284 LEU A 285 ILE A 286 SITE 2 AC2 9 GLN A 322 HIS A 323 GLY A 324 ILE A 325 SITE 3 AC2 9 HOH A2250 SITE 1 AC3 6 PHE A 157 ARG A 202 VAL A 205 ASP A 206 SITE 2 AC3 6 TYR A 210 HOH A2103 SITE 1 AC4 5 ASP A 252 TYR A 253 VAL A 288 ASP A 289 SITE 2 AC4 5 GLY A 310 CRYST1 92.095 128.222 130.439 90.00 90.00 90.00 I 2 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 0.010858 0.000000 0.000000 0.00000 SCALE2 0.000000 0.007799 0.000000 0.00000 SCALE3 0.000000 0.000000 0.007666 0.00000