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 <I/SIGMA(I)> 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 <I/SIGMA(I)> 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