HEADER TRANSFERASE 16-AUG-06 2I2D
TITLE CRYSTAL STRUCTURE OF LMNADK1
COMPND MOL_ID: 1;
COMPND 2 MOLECULE: PROBABLE INORGANIC POLYPHOSPHATE/ATP-NAD KINASE 1;
COMPND 3 CHAIN: A;
COMPND 4 SYNONYM: POLYP, /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 STRAIN: BACTERIA;
SOURCE 5 GENE: PPNK1;
SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI;
SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562;
SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID;
SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PET22B
KEYWDS CRYSTAL STRUCTURE OF LMNADK1 BOUND TO A NAD ANALOG, TRANSFERASE
EXPDTA X-RAY DIFFRACTION
AUTHOR G.PONCET-MONTANGE,G.LABESSE
REVDAT 6 30-AUG-23 2I2D 1 REMARK SEQADV
REVDAT 5 14-FEB-18 2I2D 1 REMARK
REVDAT 4 13-JUL-11 2I2D 1 VERSN
REVDAT 3 24-FEB-09 2I2D 1 VERSN
REVDAT 2 04-NOV-08 2I2D 1 JRNL
REVDAT 1 07-AUG-07 2I2D 0
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. 2.22 ANGSTROMS.
REMARK 3
REMARK 3 REFINEMENT.
REMARK 3 PROGRAM : REFMAC 5.2.0005
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) : 2.22
REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 37.93
REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000
REMARK 3 COMPLETENESS FOR RANGE (%) : 96.6
REMARK 3 NUMBER OF REFLECTIONS : 13383
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) : 0.208
REMARK 3 R VALUE (WORKING SET) : 0.207
REMARK 3 FREE R VALUE : 0.252
REMARK 3 FREE R VALUE TEST SET SIZE (%) : 2.900
REMARK 3 FREE R VALUE TEST SET COUNT : 405
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) : 2.22
REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.28
REMARK 3 REFLECTION IN BIN (WORKING SET) : 760
REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 75.79
REMARK 3 BIN R VALUE (WORKING SET) : 0.2310
REMARK 3 BIN FREE R VALUE SET COUNT : 29
REMARK 3 BIN FREE R VALUE : 0.3660
REMARK 3
REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT.
REMARK 3 PROTEIN ATOMS : 1979
REMARK 3 NUCLEIC ACID ATOMS : 0
REMARK 3 HETEROGEN ATOMS : 58
REMARK 3 SOLVENT ATOMS : 59
REMARK 3
REMARK 3 B VALUES.
REMARK 3 B VALUE TYPE : LIKELY RESIDUAL
REMARK 3 FROM WILSON PLOT (A**2) : 38.50
REMARK 3 MEAN B VALUE (OVERALL, A**2) : 34.88
REMARK 3 OVERALL ANISOTROPIC B VALUE.
REMARK 3 B11 (A**2) : 0.68000
REMARK 3 B22 (A**2) : 1.85000
REMARK 3 B33 (A**2) : -2.54000
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): 0.306
REMARK 3 ESU BASED ON FREE R VALUE (A): 0.227
REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.159
REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 12.595
REMARK 3
REMARK 3 CORRELATION COEFFICIENTS.
REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.942
REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.923
REMARK 3
REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT
REMARK 3 BOND LENGTHS REFINED ATOMS (A): 2101 ; 0.012 ; 0.021
REMARK 3 BOND LENGTHS OTHERS (A): 5 ; 0.004 ; 0.020
REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 2854 ; 2.257 ; 1.966
REMARK 3 BOND ANGLES OTHERS (DEGREES): 11 ; 0.958 ; 3.000
REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 254 ; 9.347 ; 5.000
REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 93 ;34.036 ;23.548
REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 324 ;15.103 ;15.000
REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 10 ;15.371 ;15.000
REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 310 ; 0.339 ; 0.200
REMARK 3 GENERAL PLANES REFINED ATOMS (A): 1595 ; 0.004 ; 0.020
REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL
REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 892 ; 0.218 ; 0.200
REMARK 3 NON-BONDED CONTACTS OTHERS (A): 6 ; 0.063 ; 0.200
REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 1373 ; 0.316 ; 0.200
REMARK 3 NON-BONDED TORSION OTHERS (A): 5 ; 0.116 ; 0.200
REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 92 ; 0.194 ; 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): 47 ; 0.293 ; 0.200
REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL
REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 5 ; 0.335 ; 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): 1306 ; 0.472 ; 1.500
REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL
REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 2026 ; 0.778 ; 2.000
REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL
REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 929 ; 1.116 ; 3.000
REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL
REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 827 ; 1.502 ; 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): 10.7138 23.8751 21.5719
REMARK 3 T TENSOR
REMARK 3 T11: 0.0056 T22: 0.0009
REMARK 3 T33: -0.0624 T12: 0.0472
REMARK 3 T13: 0.0315 T23: -0.0569
REMARK 3 L TENSOR
REMARK 3 L11: 3.0554 L22: 1.2393
REMARK 3 L33: 5.4419 L12: -0.2742
REMARK 3 L13: -1.4667 L23: 1.0291
REMARK 3 S TENSOR
REMARK 3 S11: -0.1057 S12: -0.0612 S13: 0.0333
REMARK 3 S21: 0.0520 S22: 0.0316 S23: 0.1618
REMARK 3 S31: -0.0978 S32: -0.2403 S33: 0.0741
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): 21.6088 26.3227 25.7091
REMARK 3 T TENSOR
REMARK 3 T11: 0.1314 T22: 0.2044
REMARK 3 T33: 0.0969 T12: 0.0383
REMARK 3 T13: 0.0119 T23: -0.1121
REMARK 3 L TENSOR
REMARK 3 L11: 2.2342 L22: 0.3888
REMARK 3 L33: 5.0879 L12: 0.4488
REMARK 3 L13: -1.7126 L23: 0.7178
REMARK 3 S TENSOR
REMARK 3 S11: 0.0017 S12: -0.7559 S13: 0.2871
REMARK 3 S21: 0.0793 S22: 0.2158 S23: -0.1461
REMARK 3 S31: -0.2109 S32: 0.0805 S33: -0.2176
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): 31.4026 13.5432 16.8324
REMARK 3 T TENSOR
REMARK 3 T11: -0.0921 T22: -0.0697
REMARK 3 T33: -0.1539 T12: -0.0037
REMARK 3 T13: 0.0247 T23: -0.0284
REMARK 3 L TENSOR
REMARK 3 L11: 1.0763 L22: 15.3909
REMARK 3 L33: 10.7429 L12: 3.8210
REMARK 3 L13: -1.9582 L23: -3.3297
REMARK 3 S TENSOR
REMARK 3 S11: 0.0291 S12: -0.3290 S13: -0.0846
REMARK 3 S21: 0.9146 S22: 0.0177 S23: -0.3357
REMARK 3 S31: -0.1428 S32: 0.0750 S33: -0.0468
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): 17.4806 13.3998 -4.3418
REMARK 3 T TENSOR
REMARK 3 T11: -0.1050 T22: -0.0789
REMARK 3 T33: -0.1260 T12: 0.0232
REMARK 3 T13: 0.0014 T23: 0.0144
REMARK 3 L TENSOR
REMARK 3 L11: 1.5218 L22: 1.9878
REMARK 3 L33: 2.5476 L12: -0.2951
REMARK 3 L13: -0.1023 L23: 0.2098
REMARK 3 S TENSOR
REMARK 3 S11: 0.0380 S12: 0.1108 S13: 0.0637
REMARK 3 S21: -0.1294 S22: -0.0546 S23: 0.3533
REMARK 3 S31: 0.0113 S32: -0.3540 S33: 0.0166
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 273 A 273
REMARK 3 ORIGIN FOR THE GROUP (A): 18.3769 9.8304 13.3409
REMARK 3 T TENSOR
REMARK 3 T11: 0.1742 T22: 0.1774
REMARK 3 T33: -0.0317 T12: -0.0380
REMARK 3 T13: 0.1139 T23: 0.0554
REMARK 3 L TENSOR
REMARK 3 L11: 47.0430 L22: 92.8698
REMARK 3 L33: 22.9484 L12: -0.3686
REMARK 3 L13: 31.6295 L23: 12.2512
REMARK 3 S TENSOR
REMARK 3 S11: -0.4663 S12: -1.1696 S13: -2.5904
REMARK 3 S21: 0.5661 S22: 1.4288 S23: 1.3755
REMARK 3 S31: 0.4782 S32: -2.1383 S33: -0.9624
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 274 A 274
REMARK 3 ORIGIN FOR THE GROUP (A): 29.8399 24.5099 14.3665
REMARK 3 T TENSOR
REMARK 3 T11: 0.2683 T22: 0.1989
REMARK 3 T33: -0.0028 T12: -0.2128
REMARK 3 T13: 0.0099 T23: 0.0478
REMARK 3 L TENSOR
REMARK 3 L11: 267.9790 L22: 164.4969
REMARK 3 L33: 68.0229 L12:-165.0771
REMARK 3 L13: -21.1956 L23: 77.6097
REMARK 3 S TENSOR
REMARK 3 S11: -0.8604 S12: -2.8908 S13: 3.0349
REMARK 3 S21: -6.3000 S22: -0.6377 S23: -1.6610
REMARK 3 S31: -4.4099 S32: 3.6353 S33: 1.4981
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 2I2D COMPLIES WITH FORMAT V. 3.30, 13-JUL-11
REMARK 100
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 18-AUG-06.
REMARK 100 THE DEPOSITION ID IS D_1000039049.
REMARK 200
REMARK 200 EXPERIMENTAL DETAILS
REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION
REMARK 200 DATE OF DATA COLLECTION : NULL
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 : NULL
REMARK 200 OPTICS : NULL
REMARK 200
REMARK 200 DETECTOR TYPE : CCD
REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315
REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM
REMARK 200 DATA SCALING SOFTWARE : SCALA
REMARK 200
REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 13383
REMARK 200 RESOLUTION RANGE HIGH (A) : 2.220
REMARK 200 RESOLUTION RANGE LOW (A) : 37.900
REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000
REMARK 200
REMARK 200 OVERALL.
REMARK 200 COMPLETENESS FOR RANGE (%) : 96.8
REMARK 200 DATA REDUNDANCY : 4.900
REMARK 200 R MERGE (I) : 0.05400
REMARK 200 R SYM (I) : NULL
REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 22.9000
REMARK 200
REMARK 200 IN THE HIGHEST RESOLUTION SHELL.
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.22
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.34
REMARK 200 COMPLETENESS FOR SHELL (%) : 81.2
REMARK 200 DATA REDUNDANCY IN SHELL : 4.00
REMARK 200 R MERGE FOR SHELL (I) : 0.41100
REMARK 200 R SYM FOR SHELL (I) : NULL
REMARK 200 <I/SIGMA(I)> FOR SHELL : 3.500
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 2I2B
REMARK 200
REMARK 200 REMARK: NULL
REMARK 280
REMARK 280 CRYSTAL
REMARK 280 SOLVENT CONTENT, VS (%): 47.40
REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.34
REMARK 280
REMARK 280 CRYSTALLIZATION CONDITIONS: 0.3 M POTASSIUM CHLORIDE, 50 MM TRI
REMARK 280 -SODIUM CITRATE DIHYDRATE, 15-20% W/V POLYETHYLENE GLYCOL 400,
REMARK 280 PH 5.4, VAPOR DIFFUSION, HANGING DROP
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 31.24050
REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 37.92550
REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 59.17500
REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 31.24050
REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 37.92550
REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 59.17500
REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 31.24050
REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 37.92550
REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 59.17500
REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 31.24050
REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 37.92550
REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 59.17500
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 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 62.48100
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 62.48100
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 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 302 LIES ON A SPECIAL POSITION.
REMARK 375 HOH A 314 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 GLY A 70
REMARK 465 HIS A 71
REMARK 465 LEU A 72
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 GLU A 11 CG CD OE1 OE2
REMARK 470 LYS A 12 CG CD CE NZ
REMARK 470 LEU A 15 CG CD1 CD2
REMARK 470 ASP A 28 CB CG OD1 OD2
REMARK 470 GLU A 35 CG CD OE1 OE2
REMARK 470 LYS A 85 CG CD CE NZ
REMARK 470 LYS A 88 CG CD CE NZ
REMARK 470 ALA A 91 CB
REMARK 470 LYS A 92 CG CD CE NZ
REMARK 470 GLN A 96 CG CD OE1 NE2
REMARK 470 ARG A 190 CG CD NE CZ NH1 NH2
REMARK 470 VAL A 191 CB CG1 CG2
REMARK 470 ARG A 193 CG CD NE CZ NH1 NH2
REMARK 470 GLN A 232 CG CD OE1 NE2
REMARK 470 ARG A 247 CB CG CD NE CZ NH1 NH2
REMARK 470 ARG A 249 CG CD NE CZ NH1 NH2
REMARK 500
REMARK 500 GEOMETRY AND STEREOCHEMISTRY
REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT
REMARK 500
REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT.
REMARK 500
REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE
REMARK 500 O ALA A 185 O HOH A 297 1.91
REMARK 500 N PHE A 253 O2 CIT A 274 2.07
REMARK 500 OE1 GLU A 123 O2E A2D A 273 2.17
REMARK 500
REMARK 500 REMARK: NULL
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 N6B A2D A 273 O HOH A 297 4555 1.56
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 ASP A 32 CB - CG - OD2 ANGL. DEV. = 6.6 DEGREES
REMARK 500 ASP A 222 CB - CG - OD2 ANGL. DEV. = 6.7 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 MET A 29 71.65 97.03
REMARK 500 ASP A 77 -51.87 144.49
REMARK 500 GLU A 94 53.09 -92.58
REMARK 500 ASN A 122 -69.24 -98.23
REMARK 500 ASP A 141 -11.30 74.61
REMARK 500 ALA A 162 -129.92 -103.80
REMARK 500 ALA A 185 69.06 38.09
REMARK 500 HIS A 204 -14.47 84.89
REMARK 500 ASN A 213 -110.37 -103.93
REMARK 500 ASP A 214 89.26 54.43
REMARK 500 ASP A 222 -121.66 51.03
REMARK 500 PHE A 248 -53.29 147.60
REMARK 500 ILE A 262 -62.63 -99.33
REMARK 500
REMARK 500 REMARK: NULL
REMARK 500
REMARK 500 GEOMETRY AND STEREOCHEMISTRY
REMARK 500 SUBTOPIC: NON-CIS, NON-TRANS
REMARK 500
REMARK 500 THE FOLLOWING PEPTIDE BONDS DEVIATE SIGNIFICANTLY FROM BOTH
REMARK 500 CIS AND TRANS CONFORMATION. CIS BONDS, IF ANY, ARE LISTED
REMARK 500 ON CISPEP RECORDS. TRANS IS DEFINED AS 180 +/- 30 AND
REMARK 500 CIS IS DEFINED AS 0 +/- 30 DEGREES.
REMARK 500 MODEL OMEGA
REMARK 500 ALA A 76 ASP A 77 -69.79
REMARK 500 ASN A 213 ASP A 214 62.37
REMARK 500 ARG A 247 PHE A 248 -36.63
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 A2D A 273
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC2
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CIT A 274
REMARK 900
REMARK 900 RELATED ENTRIES
REMARK 900 RELATED ID: 2I1W RELATED DB: PDB
REMARK 900 CRYSTAL STRUCTURE OF NAD KINASE 1 FROM LISTERIA MONOCYTOGENES
REMARK 900 RELATED ID: 2I29 RELATED DB: PDB
REMARK 900 CRYSTAL STRUCTURE OF NAD KINASE 1 FROM LISTERIA MONOCYTOGENES
REMARK 900 RELATED ID: 2I2A RELATED DB: PDB
REMARK 900 CRYSTAL STRUCTURE OF LMNADK1 FROM LISTERIA MONOCYTOGENES
REMARK 900 RELATED ID: 2I2B RELATED DB: PDB
REMARK 900 CRYSTAL STRUCTURE OF LMNADK1 FROM LISTERIA MONOCYTOGENES
REMARK 900 RELATED ID: 2I2C RELATED DB: PDB
REMARK 900 CRYSTAL STRUCTURE OF LMNADK1
REMARK 900 RELATED ID: 2I2E RELATED DB: PDB
REMARK 900 CRYSTAL STRUCTURE OF LMNADK1
REMARK 900 RELATED ID: 2I2F RELATED DB: PDB
REMARK 900 CRYSTAL STRUCTURE OF LMNADK1
DBREF 2I2D A 1 264 UNP Q8Y8D7 PPNK1_LISMO 1 264
SEQADV 2I2D LEU A 265 UNP Q8Y8D7 CLONING ARTIFACT
SEQADV 2I2D GLU A 266 UNP Q8Y8D7 CLONING ARTIFACT
SEQADV 2I2D HIS A 267 UNP Q8Y8D7 EXPRESSION TAG
SEQADV 2I2D HIS A 268 UNP Q8Y8D7 EXPRESSION TAG
SEQADV 2I2D HIS A 269 UNP Q8Y8D7 EXPRESSION TAG
SEQADV 2I2D HIS A 270 UNP Q8Y8D7 EXPRESSION TAG
SEQADV 2I2D HIS A 271 UNP Q8Y8D7 EXPRESSION TAG
SEQADV 2I2D 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 A2D A 273 45
HET CIT A 274 13
HETNAM A2D BIS{[(2R,3S,4R,5R)-5-(6-AMINO-9H-PURIN-9-YL)-3,4-
HETNAM 2 A2D DIHYDROXYTETRAHYDROFURAN-2-YL]METHYL} DIHYDROGEN
HETNAM 3 A2D DIPHOSPHATE
HETNAM CIT CITRIC ACID
HETSYN A2D BIS(ADENOSINE)-5'-DIPHOSPHATE
FORMUL 2 A2D C20 H26 N10 O13 P2
FORMUL 3 CIT C6 H8 O7
FORMUL 4 HOH *59(H2 O)
HELIX 1 1 ASP A 10 GLU A 26 1 17
HELIX 2 2 GLY A 44 TYR A 55 1 12
HELIX 3 3 GLU A 56 LEU A 59 5 4
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 6 ALA A 116 ALA A 120 0
SHEET 2 B 6 GLN A 96 LYS A 108 -1 N VAL A 107 O ALA A 116
SHEET 3 B 6 GLU A 233 ARG A 247 -1 O PHE A 245 N VAL A 98
SHEET 4 B 6 VAL A 207 PRO A 211 -1 N VAL A 207 O TYR A 236
SHEET 5 B 6 PHE A 133 ILE A 139 -1 N VAL A 138 O SER A 208
SHEET 6 B 6 ILE A 142 GLY A 149 -1 O GLU A 145 N VAL A 137
SHEET 1 C 6 LEU A 199 PRO A 202 0
SHEET 2 C 6 ALA A 178 MET A 184 -1 N LEU A 181 O LEU A 199
SHEET 3 C 6 GLY A 151 SER A 155 -1 N SER A 155 O GLN A 180
SHEET 4 C 6 GLU A 123 SER A 128 -1 N SER A 124 O MET A 154
SHEET 5 C 6 PHE A 217 VAL A 221 -1 O SER A 220 N THR A 125
SHEET 6 C 6 LEU A 224 HIS A 228 -1 O HIS A 228 N PHE A 217
CISPEP 1 ASP A 28 MET A 29 0 -26.84
CISPEP 2 GLY A 130 GLY A 131 0 -7.96
SITE 1 AC1 18 ASP A 45 GLY A 46 PHE A 74 TYR A 75
SITE 2 AC1 18 ASN A 122 GLU A 123 GLY A 149 ASP A 150
SITE 3 AC1 18 SER A 158 THR A 161 ALA A 162 TYR A 163
SITE 4 AC1 18 SER A 166 ALA A 185 ILE A 187 HIS A 223
SITE 5 AC1 18 HOH A 297 HOH A 333
SITE 1 AC2 7 VAL A 98 TYR A 100 HIS A 173 PHE A 251
SITE 2 AC2 7 PRO A 252 PHE A 253 ARG A 256
CRYST1 62.481 75.851 118.350 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 0.016005 0.000000 0.000000 0.00000
SCALE2 0.000000 0.013184 0.000000 0.00000
SCALE3 0.000000 0.000000 0.008450 0.00000
(ATOM LINES ARE NOT SHOWN.)
END
