HEADER TRANSFERASE 28-FEB-12 4DY6
TITLE CRYSTAL STRUCTURE OF NAD KINASE 1 FROM LISTERIA MONOCYTOGENES IN
TITLE 2 COMPLEX WITH 2'-PHOSPHATE BIS(ADENOSINE)-5'-DIPHOSPHATE
COMPND MOL_ID: 1;
COMPND 2 MOLECULE: INORGANIC POLYPHOSPHATE/ATP-NAD KINASE 1;
COMPND 3 CHAIN: A;
COMPND 4 SYNONYM: POLY(P)/ATP NAD KINASE 1;
COMPND 5 EC: 2.7.1.23;
COMPND 6 ENGINEERED: YES
SOURCE MOL_ID: 1;
SOURCE 2 ORGANISM_SCIENTIFIC: LISTERIA MONOCYTOGENES;
SOURCE 3 ORGANISM_TAXID: 1639;
SOURCE 4 GENE: LMO0968, PPNK1;
SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI;
SOURCE 6 EXPRESSION_SYSTEM_TAXID: 469008;
SOURCE 7 EXPRESSION_SYSTEM_STRAIN: BL21(DE3);
SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID;
SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PET22B
KEYWDS LMNADK1, NAD ANALOG, INORGANIC POLYPHOSPHATES, TRANSFERASE
EXPDTA X-RAY DIFFRACTION
AUTHOR G.PONCET-MONTANGE,L.ASSAIRI,S.AROLD,S.POCHET,G.LABESSE
REVDAT 2 13-SEP-23 4DY6 1 REMARK SEQADV
REVDAT 1 07-MAR-12 4DY6 0
SPRSDE 07-MAR-12 4DY6 2I2E
JRNL AUTH G.PONCET-MONTANGE,L.ASSAIRI,S.AROLD,S.POCHET,G.LABESSE
JRNL TITL NAD KINASES USE SUBSTRATE-ASSISTED CATALYSIS FOR SPECIFIC
JRNL TITL 2 RECOGNITION OF NAD.
JRNL REF J.BIOL.CHEM. V. 282 33925 2007
JRNL REFN ISSN 0021-9258
JRNL PMID 17686780
JRNL DOI 10.1074/JBC.M701394200
REMARK 2
REMARK 2 RESOLUTION. 2.20 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) : 2.20
REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 33.55
REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000
REMARK 3 COMPLETENESS FOR RANGE (%) : 98.8
REMARK 3 NUMBER OF REFLECTIONS : 14651
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) : 0.209
REMARK 3 R VALUE (WORKING SET) : 0.206
REMARK 3 FREE R VALUE : 0.250
REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000
REMARK 3 FREE R VALUE TEST SET COUNT : 737
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) : 2.20
REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.26
REMARK 3 REFLECTION IN BIN (WORKING SET) : 916
REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 90.35
REMARK 3 BIN R VALUE (WORKING SET) : 0.3260
REMARK 3 BIN FREE R VALUE SET COUNT : 48
REMARK 3 BIN FREE R VALUE : 0.4460
REMARK 3
REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT.
REMARK 3 PROTEIN ATOMS : 2058
REMARK 3 NUCLEIC ACID ATOMS : 0
REMARK 3 HETEROGEN ATOMS : 62
REMARK 3 SOLVENT ATOMS : 100
REMARK 3
REMARK 3 B VALUES.
REMARK 3 FROM WILSON PLOT (A**2) : NULL
REMARK 3 MEAN B VALUE (OVERALL, A**2) : 48.09
REMARK 3 OVERALL ANISOTROPIC B VALUE.
REMARK 3 B11 (A**2) : -0.32000
REMARK 3 B22 (A**2) : 0.89000
REMARK 3 B33 (A**2) : -0.57000
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): 0.316
REMARK 3 ESU BASED ON FREE R VALUE (A): 0.227
REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.158
REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 14.244
REMARK 3
REMARK 3 CORRELATION COEFFICIENTS.
REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.950
REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.929
REMARK 3
REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT
REMARK 3 BOND LENGTHS REFINED ATOMS (A): 2221 ; 0.010 ; 0.021
REMARK 3 BOND LENGTHS OTHERS (A): 1493 ; 0.001 ; 0.020
REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 3014 ; 1.293 ; 1.982
REMARK 3 BOND ANGLES OTHERS (DEGREES): 3627 ; 1.378 ; 3.000
REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 259 ; 6.301 ; 5.000
REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 105 ;32.992 ;23.333
REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 372 ;15.595 ;15.000
REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 14 ;20.062 ;15.000
REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 323 ; 0.074 ; 0.200
REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2426 ; 0.005 ; 0.020
REMARK 3 GENERAL PLANES OTHERS (A): 476 ; 0.002 ; 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): 1294 ; 0.878 ; 1.500
REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 527 ; 0.108 ; 1.500
REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 2095 ; 1.594 ; 2.000
REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL
REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 927 ; 1.252 ; 3.000
REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL
REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 919 ; 1.955 ; 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 : 6
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 76
REMARK 3 ORIGIN FOR THE GROUP (A): 11.1210 23.6080 21.8060
REMARK 3 T TENSOR
REMARK 3 T11: 0.2377 T22: 0.2110
REMARK 3 T33: 0.1271 T12: 0.0411
REMARK 3 T13: 0.0511 T23: -0.0573
REMARK 3 L TENSOR
REMARK 3 L11: 1.5106 L22: 0.2303
REMARK 3 L33: 3.3740 L12: -0.5072
REMARK 3 L13: -1.2330 L23: 0.8313
REMARK 3 S TENSOR
REMARK 3 S11: -0.0409 S12: -0.0698 S13: -0.0030
REMARK 3 S21: -0.0154 S22: -0.0048 S23: -0.0413
REMARK 3 S31: 0.0707 S32: -0.2293 S33: 0.0458
REMARK 3
REMARK 3 TLS GROUP : 2
REMARK 3 NUMBER OF COMPONENTS GROUP : 2
REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI
REMARK 3 RESIDUE RANGE : A 77 A 97
REMARK 3 RESIDUE RANGE : A 245 A 251
REMARK 3 ORIGIN FOR THE GROUP (A): 22.4430 26.5750 25.6480
REMARK 3 T TENSOR
REMARK 3 T11: 0.4769 T22: 0.3527
REMARK 3 T33: 0.2169 T12: -0.0188
REMARK 3 T13: 0.2759 T23: -0.2062
REMARK 3 L TENSOR
REMARK 3 L11: 6.2814 L22: -0.3768
REMARK 3 L33: 0.7002 L12: -0.5664
REMARK 3 L13: -4.5740 L23: 0.8053
REMARK 3 S TENSOR
REMARK 3 S11: 0.2843 S12: -1.4375 S13: 0.6391
REMARK 3 S21: -0.4601 S22: 0.1535 S23: -0.4011
REMARK 3 S31: -0.0943 S32: 1.0377 S33: -0.4378
REMARK 3
REMARK 3 TLS GROUP : 3
REMARK 3 NUMBER OF COMPONENTS GROUP : 1
REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI
REMARK 3 RESIDUE RANGE : A 252 A 263
REMARK 3 ORIGIN FOR THE GROUP (A): 31.6500 14.1140 16.8780
REMARK 3 T TENSOR
REMARK 3 T11: 0.2401 T22: 0.2228
REMARK 3 T33: 0.1433 T12: -0.0051
REMARK 3 T13: 0.0218 T23: -0.0388
REMARK 3 L TENSOR
REMARK 3 L11: 0.0431 L22: 8.9350
REMARK 3 L33: 3.7801 L12: 1.6885
REMARK 3 L13: -0.5213 L23: 1.4093
REMARK 3 S TENSOR
REMARK 3 S11: 0.0650 S12: -0.0143 S13: 0.0435
REMARK 3 S21: 0.5072 S22: 0.0033 S23: 0.1531
REMARK 3 S31: 0.0606 S32: 0.0131 S33: -0.0683
REMARK 3
REMARK 3 TLS GROUP : 4
REMARK 3 NUMBER OF COMPONENTS GROUP : 1
REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI
REMARK 3 RESIDUE RANGE : A 98 A 244
REMARK 3 ORIGIN FOR THE GROUP (A): 17.7750 13.4470 -4.3980
REMARK 3 T TENSOR
REMARK 3 T11: 0.2245 T22: 0.1914
REMARK 3 T33: 0.1978 T12: 0.0287
REMARK 3 T13: 0.0196 T23: -0.0097
REMARK 3 L TENSOR
REMARK 3 L11: 0.1405 L22: 0.3745
REMARK 3 L33: 1.6330 L12: -0.2111
REMARK 3 L13: -0.0533 L23: 0.1825
REMARK 3 S TENSOR
REMARK 3 S11: 0.0737 S12: 0.0364 S13: 0.0365
REMARK 3 S21: -0.0246 S22: -0.0884 S23: 0.0182
REMARK 3 S31: 0.0086 S32: -0.1411 S33: 0.0146
REMARK 3
REMARK 3 TLS GROUP : 5
REMARK 3 NUMBER OF COMPONENTS GROUP : 1
REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI
REMARK 3 RESIDUE RANGE : A 301 A 302
REMARK 3 ORIGIN FOR THE GROUP (A): 19.9300 11.8700 12.1460
REMARK 3 T TENSOR
REMARK 3 T11: 0.8782 T22: 0.7934
REMARK 3 T33: 0.1738 T12: -0.2387
REMARK 3 T13: 0.0945 T23: -0.2674
REMARK 3 L TENSOR
REMARK 3 L11: 0.7272 L22: -8.2956
REMARK 3 L33: 0.3465 L12: -4.0958
REMARK 3 L13: -0.7029 L23: 0.0837
REMARK 3 S TENSOR
REMARK 3 S11: -0.8408 S12: -0.7523 S13: 0.4973
REMARK 3 S21: 0.8606 S22: 0.7182 S23: -0.2840
REMARK 3 S31: 0.4262 S32: -0.3682 S33: 0.1226
REMARK 3
REMARK 3 TLS GROUP : 6
REMARK 3 NUMBER OF COMPONENTS GROUP : 1
REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI
REMARK 3 RESIDUE RANGE : A 401 A 494
REMARK 3 ORIGIN FOR THE GROUP (A): 19.0039 15.6509 2.9232
REMARK 3 T TENSOR
REMARK 3 T11: 0.2148 T22: 0.1764
REMARK 3 T33: 0.2010 T12: 0.0080
REMARK 3 T13: 0.0036 T23: -0.0015
REMARK 3 L TENSOR
REMARK 3 L11: 0.0262 L22: 0.0949
REMARK 3 L33: 0.4365 L12: 0.0642
REMARK 3 L13: 0.0544 L23: 0.1280
REMARK 3 S TENSOR
REMARK 3 S11: 0.0153 S12: -0.0003 S13: 0.0144
REMARK 3 S21: -0.0102 S22: -0.0021 S23: 0.0279
REMARK 3 S31: -0.0051 S32: -0.0274 S33: -0.0133
REMARK 3
REMARK 3 BULK SOLVENT MODELLING.
REMARK 3 METHOD USED : MASK
REMARK 3 PARAMETERS FOR MASK CALCULATION
REMARK 3 VDW PROBE RADIUS : 1.40
REMARK 3 ION PROBE RADIUS : 0.80
REMARK 3 SHRINKAGE RADIUS : 0.80
REMARK 3
REMARK 3 OTHER REFINEMENT REMARKS:
REMARK 3 HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
REMARK 3 U VALUES : WITH TLS ADDED
REMARK 4
REMARK 4 4DY6 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11
REMARK 100
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 29-FEB-12.
REMARK 100 THE DEPOSITION ID IS D_1000070930.
REMARK 200
REMARK 200 EXPERIMENTAL DETAILS
REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION
REMARK 200 DATE OF DATA COLLECTION : 11-APR-06
REMARK 200 TEMPERATURE (KELVIN) : 100
REMARK 200 PH : 5.4
REMARK 200 NUMBER OF CRYSTALS USED : 1
REMARK 200
REMARK 200 SYNCHROTRON (Y/N) : Y
REMARK 200 RADIATION SOURCE : ESRF
REMARK 200 BEAMLINE : ID23-1
REMARK 200 X-RAY GENERATOR MODEL : NULL
REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M
REMARK 200 WAVELENGTH OR RANGE (A) : 0.933
REMARK 200 MONOCHROMATOR : SI(111)
REMARK 200 OPTICS : NULL
REMARK 200
REMARK 200 DETECTOR TYPE : CCD
REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315R
REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM
REMARK 200 DATA SCALING SOFTWARE : SCALA 3.2.5
REMARK 200
REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 14651
REMARK 200 RESOLUTION RANGE HIGH (A) : 2.200
REMARK 200 RESOLUTION RANGE LOW (A) : 63.888
REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL
REMARK 200
REMARK 200 OVERALL.
REMARK 200 COMPLETENESS FOR RANGE (%) : 99.1
REMARK 200 DATA REDUNDANCY : 3.200
REMARK 200 R MERGE (I) : 0.04800
REMARK 200 R SYM (I) : 0.04800
REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 18.6000
REMARK 200
REMARK 200 IN THE HIGHEST RESOLUTION SHELL.
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.20
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.32
REMARK 200 COMPLETENESS FOR SHELL (%) : 94.5
REMARK 200 DATA REDUNDANCY IN SHELL : 2.10
REMARK 200 R MERGE FOR SHELL (I) : 0.46000
REMARK 200 R SYM FOR SHELL (I) : 0.46000
REMARK 200 <I/SIGMA(I)> FOR SHELL : 1.600
REMARK 200
REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH
REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT
REMARK 200 SOFTWARE USED: AMORE
REMARK 200 STARTING MODEL: PDB ENTRY 2I2C
REMARK 200
REMARK 200 REMARK: NULL
REMARK 280
REMARK 280 CRYSTAL
REMARK 280 SOLVENT CONTENT, VS (%): 46.21
REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.29
REMARK 280
REMARK 280 CRYSTALLIZATION CONDITIONS: 0.3 M POTASSIUM CHLORIDE, 50 MM TRI
REMARK 280 -SODIUM CITRATE DIHYDRATE, 15-20% W/V PEG400, PH 5.4, VAPOR
REMARK 280 DIFFUSION, HANGING DROP, TEMPERATURE 291K
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 31.55000
REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 37.86500
REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 59.42500
REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 31.55000
REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 37.86500
REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 59.42500
REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 31.55000
REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 37.86500
REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 59.42500
REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 31.55000
REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 37.86500
REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 59.42500
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: TETRAMERIC
REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TETRAMERIC
REMARK 350 SOFTWARE USED: PISA
REMARK 350 TOTAL BURIED SURFACE AREA: 14080 ANGSTROM**2
REMARK 350 SURFACE AREA OF THE COMPLEX: 40440 ANGSTROM**2
REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -54.0 KCAL/MOL
REMARK 350 APPLY THE FOLLOWING TO CHAINS: A
REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000
REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000
REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000
REMARK 350 BIOMT1 2 -1.000000 0.000000 0.000000 63.10000
REMARK 350 BIOMT2 2 0.000000 -1.000000 0.000000 0.00000
REMARK 350 BIOMT3 2 0.000000 0.000000 1.000000 0.00000
REMARK 350 BIOMT1 3 -1.000000 0.000000 0.000000 63.10000
REMARK 350 BIOMT2 3 0.000000 1.000000 0.000000 0.00000
REMARK 350 BIOMT3 3 0.000000 0.000000 -1.000000 0.00000
REMARK 350 BIOMT1 4 1.000000 0.000000 0.000000 0.00000
REMARK 350 BIOMT2 4 0.000000 -1.000000 0.000000 0.00000
REMARK 350 BIOMT3 4 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 GLY A 110
REMARK 465 ILE A 111
REMARK 465 GLY A 112
REMARK 465 LYS A 113
REMARK 465 LYS A 114
REMARK 465 ASP A 264
REMARK 465 LEU A 265
REMARK 465 GLU A 266
REMARK 465 HIS A 267
REMARK 465 HIS A 268
REMARK 465 HIS A 269
REMARK 465 HIS A 270
REMARK 465 HIS A 271
REMARK 465 HIS A 272
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 ALA A 91 CB
REMARK 470 ARG A 193 CG CD NE CZ NH1 NH2
REMARK 470 GLN A 232 CG CD OE1 NE2
REMARK 500
REMARK 500 GEOMETRY AND STEREOCHEMISTRY
REMARK 500 SUBTOPIC: CLOSE CONTACTS
REMARK 500
REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC
REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15
REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A
REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375
REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE
REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS.
REMARK 500
REMARK 500 DISTANCE CUTOFF:
REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS
REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS
REMARK 500
REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE
REMARK 500 NE ARG A 190 O HOH A 499 4555 1.78
REMARK 500
REMARK 500 REMARK: NULL
REMARK 500
REMARK 500 GEOMETRY AND STEREOCHEMISTRY
REMARK 500 SUBTOPIC: TORSION ANGLES
REMARK 500
REMARK 500 TORSION ANGLES OUTSIDE THE EXPECTED RAMACHANDRAN REGIONS:
REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER;
REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE).
REMARK 500
REMARK 500 STANDARD TABLE:
REMARK 500 FORMAT:(10X,I3,1X,A3,1X,A1,I4,A1,4X,F7.2,3X,F7.2)
REMARK 500
REMARK 500 EXPECTED VALUES: GJ KLEYWEGT AND TA JONES (1996). PHI/PSI-
REMARK 500 CHOLOGY: RAMACHANDRAN REVISITED. STRUCTURE 4, 1395 - 1400
REMARK 500
REMARK 500 M RES CSSEQI PSI PHI
REMARK 500 GLU A 94 38.97 -92.96
REMARK 500 ASN A 122 -74.20 -97.73
REMARK 500 ASP A 141 -1.77 72.97
REMARK 500 ALA A 162 -135.86 -104.70
REMARK 500 HIS A 204 -4.98 80.53
REMARK 500 ASN A 213 -73.88 -126.78
REMARK 500 ASP A 222 -125.62 51.69
REMARK 500
REMARK 500 REMARK: NULL
REMARK 800
REMARK 800 SITE
REMARK 800 SITE_IDENTIFIER: AC1
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE A22 A 301
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC2
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CIT A 302
DBREF 4DY6 A 1 264 UNP Q8Y8D7 PPNK1_LISMO 1 264
SEQADV 4DY6 LEU A 265 UNP Q8Y8D7 EXPRESSION TAG
SEQADV 4DY6 GLU A 266 UNP Q8Y8D7 EXPRESSION TAG
SEQADV 4DY6 HIS A 267 UNP Q8Y8D7 EXPRESSION TAG
SEQADV 4DY6 HIS A 268 UNP Q8Y8D7 EXPRESSION TAG
SEQADV 4DY6 HIS A 269 UNP Q8Y8D7 EXPRESSION TAG
SEQADV 4DY6 HIS A 270 UNP Q8Y8D7 EXPRESSION TAG
SEQADV 4DY6 HIS A 271 UNP Q8Y8D7 EXPRESSION TAG
SEQADV 4DY6 HIS A 272 UNP Q8Y8D7 EXPRESSION TAG
SEQRES 1 A 272 MET LYS TYR MET ILE THR SER LYS GLY ASP GLU LYS SER
SEQRES 2 A 272 ASP LEU LEU ARG LEU ASN MET ILE ALA GLY PHE GLY GLU
SEQRES 3 A 272 TYR ASP MET GLU TYR ASP ASP VAL GLU PRO GLU ILE VAL
SEQRES 4 A 272 ILE SER ILE GLY GLY ASP GLY THR PHE LEU SER ALA PHE
SEQRES 5 A 272 HIS GLN TYR GLU GLU ARG LEU ASP GLU ILE ALA PHE ILE
SEQRES 6 A 272 GLY ILE HIS THR GLY HIS LEU GLY PHE TYR ALA ASP TRP
SEQRES 7 A 272 ARG PRO ALA GLU ALA ASP LYS LEU VAL LYS LEU LEU ALA
SEQRES 8 A 272 LYS GLY GLU TYR GLN LYS VAL SER TYR PRO LEU LEU LYS
SEQRES 9 A 272 THR THR VAL LYS TYR GLY ILE GLY LYS LYS GLU ALA THR
SEQRES 10 A 272 TYR LEU ALA LEU ASN GLU SER THR VAL LYS SER SER GLY
SEQRES 11 A 272 GLY PRO PHE VAL VAL ASP VAL VAL ILE ASN ASP ILE HIS
SEQRES 12 A 272 PHE GLU ARG PHE ARG GLY ASP GLY LEU CYS MET SER THR
SEQRES 13 A 272 PRO SER GLY THR THR ALA TYR ASN LYS SER LEU GLY GLY
SEQRES 14 A 272 ALA LEU MET HIS PRO SER ILE GLU ALA MET GLN LEU THR
SEQRES 15 A 272 GLU MET ALA SER ILE ASN ASN ARG VAL TYR ARG THR ILE
SEQRES 16 A 272 GLY SER PRO LEU VAL PHE PRO LYS HIS HIS VAL VAL SER
SEQRES 17 A 272 LEU GLN PRO VAL ASN ASP LYS ASP PHE GLN ILE SER VAL
SEQRES 18 A 272 ASP HIS LEU SER ILE LEU HIS ARG ASP VAL GLN GLU ILE
SEQRES 19 A 272 ARG TYR GLU VAL SER ALA LYS LYS ILE HIS PHE ALA ARG
SEQRES 20 A 272 PHE ARG SER PHE PRO PHE TRP ARG ARG VAL HIS ASP SER
SEQRES 21 A 272 PHE ILE GLU ASP LEU GLU HIS HIS HIS HIS HIS HIS
HET A22 A 301 49
HET CIT A 302 13
HETNAM A22 [(2R,3S,4R,5R)-5-(6-AMINO-9H-PURIN-9-YL)-3,4-
HETNAM 2 A22 DIHYDROXYTETRAHYDROFURAN-2-YL]METHYL [(2R,3R,4R,5R)-5-
HETNAM 3 A22 (6-AMINO-9H-PURIN-9-YL)-3-HYDROXY-4-(PHOSPHONOOXY)
HETNAM 4 A22 TETRAHYDROFURAN-2-YL]METHYL DIHYDROGEN DIPHOSPHATE
HETNAM CIT CITRIC ACID
HETSYN A22 2'-PHOSPHATE BIS(ADENOSINE)-5'-DIPHOSPHATE
FORMUL 2 A22 C20 H27 N10 O16 P3
FORMUL 3 CIT C6 H8 O7
FORMUL 4 HOH *100(H2 O)
HELIX 1 1 ASP A 10 GLY A 25 1 16
HELIX 2 2 GLY A 44 TYR A 55 1 12
HELIX 3 3 GLU A 56 ILE A 62 5 7
HELIX 4 4 ARG A 79 ALA A 81 5 3
HELIX 5 5 GLU A 82 LYS A 92 1 11
HELIX 6 6 PRO A 157 THR A 161 5 5
HELIX 7 7 ALA A 162 LEU A 167 1 6
HELIX 8 8 PRO A 252 ILE A 262 1 11
SHEET 1 A 4 GLU A 30 TYR A 31 0
SHEET 2 A 4 LYS A 2 SER A 7 1 N TYR A 3 O GLU A 30
SHEET 3 A 4 ILE A 38 GLY A 43 1 O ILE A 40 N THR A 6
SHEET 4 A 4 ALA A 63 HIS A 68 1 O ILE A 67 N SER A 41
SHEET 1 B 8 ALA A 116 ALA A 120 0
SHEET 2 B 8 GLN A 96 LYS A 108 -1 N VAL A 107 O ALA A 116
SHEET 3 B 8 GLU A 233 ARG A 247 -1 O PHE A 245 N VAL A 98
SHEET 4 B 8 VAL A 207 PRO A 211 -1 N LEU A 209 O ILE A 234
SHEET 5 B 8 PHE A 133 ILE A 139 -1 N VAL A 138 O SER A 208
SHEET 6 B 8 ILE A 142 SER A 155 -1 O GLU A 145 N VAL A 137
SHEET 7 B 8 ALA A 178 SER A 186 -1 O THR A 182 N CYS A 153
SHEET 8 B 8 LEU A 199 PRO A 202 -1 O LEU A 199 N LEU A 181
SHEET 1 C 9 ALA A 116 ALA A 120 0
SHEET 2 C 9 GLN A 96 LYS A 108 -1 N VAL A 107 O ALA A 116
SHEET 3 C 9 GLU A 233 ARG A 247 -1 O PHE A 245 N VAL A 98
SHEET 4 C 9 VAL A 207 PRO A 211 -1 N LEU A 209 O ILE A 234
SHEET 5 C 9 PHE A 133 ILE A 139 -1 N VAL A 138 O SER A 208
SHEET 6 C 9 ILE A 142 SER A 155 -1 O GLU A 145 N VAL A 137
SHEET 7 C 9 GLU A 123 SER A 128 -1 N SER A 124 O MET A 154
SHEET 8 C 9 PHE A 217 VAL A 221 -1 O GLN A 218 N LYS A 127
SHEET 9 C 9 LEU A 224 HIS A 228 -1 O HIS A 228 N PHE A 217
CISPEP 1 GLY A 130 GLY A 131 0 11.08
SITE 1 AC1 20 ASP A 45 GLY A 46 HIS A 71 PHE A 74
SITE 2 AC1 20 TYR A 75 ASN A 122 GLU A 123 ASP A 150
SITE 3 AC1 20 SER A 158 THR A 161 ALA A 162 TYR A 163
SITE 4 AC1 20 SER A 166 ALA A 185 ILE A 187 HIS A 223
SITE 5 AC1 20 HOH A 437 HOH A 442 HOH A 444 HOH A 449
SITE 1 AC2 9 VAL A 98 TYR A 100 HIS A 173 PHE A 251
SITE 2 AC2 9 PRO A 252 PHE A 253 ARG A 256 HOH A 452
SITE 3 AC2 9 HOH A 494
CRYST1 63.100 75.730 118.850 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 0.015848 0.000000 0.000000 0.00000
SCALE2 0.000000 0.013205 0.000000 0.00000
SCALE3 0.000000 0.000000 0.008414 0.00000
(ATOM LINES ARE NOT SHOWN.)
END
