HEADER TRANSFERASE 16-AUG-06 2I2C
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 EGD-E;
SOURCE 3 ORGANISM_TAXID: 169963;
SOURCE 4 STRAIN: EGD-E;
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 NADP BOUND CRYSTAL STRUCTURE OF LMNADK1, TRANSFERASE
EXPDTA X-RAY DIFFRACTION
AUTHOR PONCET-MONTANGE G.,LABESSE G.
REVDAT 4 13-JUL-11 2I2C 1 VERSN
REVDAT 3 24-FEB-09 2I2C 1 VERSN
REVDAT 2 04-NOV-08 2I2C 1 JRNL
REVDAT 1 07-AUG-07 2I2C 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. 1.85 ANGSTROMS.
REMARK 3
REMARK 3 REFINEMENT.
REMARK 3 PROGRAM : REFMAC 5.2.0005
REMARK 3 AUTHORS : MURSHUDOV,VAGIN,DODSON
REMARK 3
REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD
REMARK 3
REMARK 3 DATA USED IN REFINEMENT.
REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.85
REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 23.29
REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000
REMARK 3 COMPLETENESS FOR RANGE (%) : 98.7
REMARK 3 NUMBER OF REFLECTIONS : 22941
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) : 0.192
REMARK 3 R VALUE (WORKING SET) : 0.191
REMARK 3 FREE R VALUE : 0.210
REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100
REMARK 3 FREE R VALUE TEST SET COUNT : 1240
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) : 1.85
REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.90
REMARK 3 REFLECTION IN BIN (WORKING SET) : 1501
REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 90.06
REMARK 3 BIN R VALUE (WORKING SET) : 0.2980
REMARK 3 BIN FREE R VALUE SET COUNT : 93
REMARK 3 BIN FREE R VALUE : 0.4150
REMARK 3
REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT.
REMARK 3 PROTEIN ATOMS : 2073
REMARK 3 NUCLEIC ACID ATOMS : 0
REMARK 3 HETEROGEN ATOMS : 51
REMARK 3 SOLVENT ATOMS : 133
REMARK 3
REMARK 3 B VALUES.
REMARK 3 B VALUE TYPE : LIKELY RESIDUAL
REMARK 3 FROM WILSON PLOT (A**2) : 27.70
REMARK 3 MEAN B VALUE (OVERALL, A**2) : 32.27
REMARK 3 OVERALL ANISOTROPIC B VALUE.
REMARK 3 B11 (A**2) : 0.55000
REMARK 3 B22 (A**2) : 1.88000
REMARK 3 B33 (A**2) : -2.44000
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): 0.149
REMARK 3 ESU BASED ON FREE R VALUE (A): 0.127
REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.094
REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 6.300
REMARK 3
REMARK 3 CORRELATION COEFFICIENTS.
REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.958
REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.953
REMARK 3
REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT
REMARK 3 BOND LENGTHS REFINED ATOMS (A): 2251 ; 0.010 ; 0.021
REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL
REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 3045 ; 1.451 ; 1.964
REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL
REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 268 ;10.268 ; 5.000
REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 104 ;31.946 ;22.692
REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 382 ;14.977 ;15.000
REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 17 ;15.501 ;15.000
REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 330 ; 0.152 ; 0.200
REMARK 3 GENERAL PLANES REFINED ATOMS (A): 1690 ; 0.005 ; 0.020
REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL
REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 997 ; 0.197 ; 0.200
REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL
REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 1470 ; 0.313 ; 0.200
REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL
REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 150 ; 0.255 ; 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): 57 ; 0.175 ; 0.200
REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL
REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 20 ; 0.107 ; 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): 1382 ; 0.424 ; 1.500
REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL
REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 2137 ; 0.683 ; 2.000
REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1021 ; 0.883 ; 3.000
REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 905 ; 1.195 ; 4.500
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): 11.1525 23.3901 21.9517
REMARK 3 T TENSOR
REMARK 3 T11: -0.0339 T22: 0.0087
REMARK 3 T33: -0.0616 T12: 0.0586
REMARK 3 T13: 0.0327 T23: -0.0569
REMARK 3 L TENSOR
REMARK 3 L11: 3.0575 L22: 1.1959
REMARK 3 L33: 6.7993 L12: 0.2503
REMARK 3 L13: -1.6518 L23: 1.1608
REMARK 3 S TENSOR
REMARK 3 S11: -0.1134 S12: -0.1709 S13: 0.0489
REMARK 3 S21: 0.0398 S22: 0.0395 S23: -0.0018
REMARK 3 S31: -0.0871 S32: -0.1992 S33: 0.0739
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): 21.9379 26.5496 26.0052
REMARK 3 T TENSOR
REMARK 3 T11: 0.2154 T22: 0.1747
REMARK 3 T33: 0.0769 T12: 0.0948
REMARK 3 T13: 0.0548 T23: -0.0883
REMARK 3 L TENSOR
REMARK 3 L11: 2.6167 L22: 0.2609
REMARK 3 L33: 1.6186 L12: 0.6692
REMARK 3 L13: -0.8354 L23: 0.1347
REMARK 3 S TENSOR
REMARK 3 S11: -0.0244 S12: -0.4906 S13: 0.2080
REMARK 3 S21: 0.0208 S22: 0.1680 S23: -0.0704
REMARK 3 S31: -0.3417 S32: 0.3116 S33: -0.1436
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): 31.4916 13.9246 16.7602
REMARK 3 T TENSOR
REMARK 3 T11: -0.1129 T22: -0.0415
REMARK 3 T33: -0.1797 T12: -0.0244
REMARK 3 T13: 0.0047 T23: -0.0642
REMARK 3 L TENSOR
REMARK 3 L11: 3.6791 L22: 13.7055
REMARK 3 L33: 5.4500 L12: 1.4798
REMARK 3 L13: 0.1622 L23: 0.8356
REMARK 3 S TENSOR
REMARK 3 S11: 0.0695 S12: -0.5257 S13: 0.0841
REMARK 3 S21: 0.5646 S22: -0.1822 S23: 0.1085
REMARK 3 S31: -0.0792 S32: -0.1161 S33: 0.1127
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): 17.4363 13.4379 -4.5821
REMARK 3 T TENSOR
REMARK 3 T11: -0.1414 T22: -0.1021
REMARK 3 T33: -0.1216 T12: 0.0329
REMARK 3 T13: -0.0085 T23: 0.0033
REMARK 3 L TENSOR
REMARK 3 L11: 1.4395 L22: 1.9808
REMARK 3 L33: 2.4841 L12: -0.1313
REMARK 3 L13: -0.0476 L23: 0.3500
REMARK 3 S TENSOR
REMARK 3 S11: 0.0382 S12: 0.0842 S13: 0.0948
REMARK 3 S21: -0.1590 S22: -0.0725 S23: 0.2802
REMARK 3 S31: -0.1094 S32: -0.3761 S33: 0.0343
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): 18.0841 8.8833 10.9013
REMARK 3 T TENSOR
REMARK 3 T11: 0.0340 T22: 0.0227
REMARK 3 T33: 0.0385 T12: -0.0135
REMARK 3 T13: 0.0428 T23: 0.0585
REMARK 3 L TENSOR
REMARK 3 L11: 5.3316 L22: 15.8103
REMARK 3 L33: 7.8670 L12: -1.9743
REMARK 3 L13: -4.3921 L23: 9.6307
REMARK 3 S TENSOR
REMARK 3 S11: 0.0661 S12: -1.8393 S13: -1.2217
REMARK 3 S21: 1.2789 S22: -0.5445 S23: 0.0596
REMARK 3 S31: 0.4259 S32: -0.8567 S33: 0.4784
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 301 A 301
REMARK 3 ORIGIN FOR THE GROUP (A): 17.9202 35.3688 15.6165
REMARK 3 T TENSOR
REMARK 3 T11: 0.0073 T22: 0.0023
REMARK 3 T33: 0.0115 T12: -0.0039
REMARK 3 T13: -0.0047 T23: 0.0159
REMARK 3 L TENSOR
REMARK 3 L11: 101.0535 L22: 88.7964
REMARK 3 L33: 9.8195 L12: -9.0239
REMARK 3 L13: -4.2584 L23: -28.7442
REMARK 3 S TENSOR
REMARK 3 S11: 1.9226 S12: -1.5164 S13: -1.3653
REMARK 3 S21: 0.3358 S22: -1.5701 S23: 0.1804
REMARK 3 S31: 2.8660 S32: -0.3855 S33: -0.3525
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 2I2C COMPLIES WITH FORMAT V. 3.30, 13-JUL-11
REMARK 100
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 17-AUG-06.
REMARK 100 THE RCSB ID CODE IS RCSB039048.
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 : ID14-2
REMARK 200 X-RAY GENERATOR MODEL : NULL
REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M
REMARK 200 WAVELENGTH OR RANGE (A) : 0.9793
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 : 22941
REMARK 200 RESOLUTION RANGE HIGH (A) : 1.850
REMARK 200 RESOLUTION RANGE LOW (A) : 25.300
REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000
REMARK 200
REMARK 200 OVERALL.
REMARK 200 COMPLETENESS FOR RANGE (%) : 98.9
REMARK 200 DATA REDUNDANCY : 5.200
REMARK 200 R MERGE (I) : 0.06800
REMARK 200 R SYM (I) : NULL
REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 17.3000
REMARK 200
REMARK 200 IN THE HIGHEST RESOLUTION SHELL.
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.85
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.95
REMARK 200 COMPLETENESS FOR SHELL (%) : 93.5
REMARK 200 DATA REDUNDANCY IN SHELL : 2.90
REMARK 200 R MERGE FOR SHELL (I) : 0.44200
REMARK 200 R SYM FOR SHELL (I) : NULL
REMARK 200 <I/SIGMA(I)> FOR SHELL : 1.900
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 2I2B
REMARK 200
REMARK 200 REMARK: NULL
REMARK 280
REMARK 280 CRYSTAL
REMARK 280 SOLVENT CONTENT, VS (%): 47.64
REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.35
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, PH
REMARK 280 5.4, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 333K
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 31.53500
REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 37.64850
REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 59.32500
REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 31.53500
REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 37.64850
REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 59.32500
REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 31.53500
REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 37.64850
REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 59.32500
REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 31.53500
REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 37.64850
REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 59.32500
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,PQS
REMARK 350 TOTAL BURIED SURFACE AREA: 14050 ANGSTROM**2
REMARK 350 SURFACE AREA OF THE COMPLEX: 39950 ANGSTROM**2
REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -33.0 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 63.07000
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 63.07000
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 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 92 CG CD CE NZ
REMARK 470 GLN A 96 CG CD OE1 NE2
REMARK 470 ILE A 111 CG1 CG2 CD1
REMARK 470 LYS A 113 CB CG CD CE NZ
REMARK 470 LYS A 114 CG CD CE NZ
REMARK 470 ARG A 193 CG CD NE CZ NH1 NH2
REMARK 470 GLN A 232 CG CD OE1 NE2
REMARK 470 GLU A 263 CG CD OE1 OE2
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 GLY A 130 C GLY A 130 O 0.220
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 28 CB - CG - OD2 ANGL. DEV. = 5.7 DEGREES
REMARK 500 ASP A 77 N - CA - C ANGL. DEV. = 25.4 DEGREES
REMARK 500 ASP A 264 CB - CG - OD2 ANGL. DEV. = 5.5 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 TYR A 27 -155.73 -130.22
REMARK 500 MET A 29 75.87 95.09
REMARK 500 HIS A 71 135.63 0.69
REMARK 500 LEU A 72 95.53 75.89
REMARK 500 ASP A 77 -52.02 13.69
REMARK 500 ILE A 111 -98.89 42.85
REMARK 500 LYS A 113 105.40 68.13
REMARK 500 LYS A 114 142.74 59.38
REMARK 500 GLU A 115 68.62 74.00
REMARK 500 ASN A 122 -69.01 -98.56
REMARK 500 ALA A 162 -127.54 -101.57
REMARK 500 HIS A 204 -12.27 81.56
REMARK 500 ASN A 213 -107.97 -111.83
REMARK 500 ASP A 214 87.32 32.86
REMARK 500 ASP A 222 -125.12 52.48
REMARK 500 PHE A 248 -64.01 137.28
REMARK 500 ILE A 262 -60.75 -99.10
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 75.94
REMARK 500 GLY A 130 GLY A 131 -34.35
REMARK 500 ASN A 213 ASP A 214 84.65
REMARK 500 ARG A 247 PHE A 248 -34.27
REMARK 500
REMARK 500 REMARK: NULL
REMARK 500
REMARK 500 GEOMETRY AND STEREOCHEMISTRY
REMARK 500 SUBTOPIC: MAIN CHAIN PLANARITY
REMARK 500
REMARK 500 THE FOLLOWING RESIDUES HAVE A PSEUDO PLANARITY
REMARK 500 TORSION ANGLE, C(I) - CA(I) - N(I+1) - O(I), GREATER
REMARK 500 10.0 DEGREES. (M=MODEL NUMBER; RES=RESIDUE NAME;
REMARK 500 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER;
REMARK 500 I=INSERTION CODE).
REMARK 500
REMARK 500 M RES CSSEQI ANGLE
REMARK 500 GLY A 130 13.59
REMARK 500
REMARK 500 REMARK: NULL
REMARK 500
REMARK 500 GEOMETRY AND STEREOCHEMISTRY
REMARK 500 SUBTOPIC: CHIRAL CENTERS
REMARK 500
REMARK 500 UNEXPECTED CONFIGURATION OF THE FOLLOWING CHIRAL
REMARK 500 CENTER(S) USING IMPROPER CA--C--CB--N CHIRALITY
REMARK 500 FOR AMINO ACIDS AND C1'--O4'--N1(N9)--C2' FOR
REMARK 500 NUCLEIC ACIDS OR EQUIVALENT ANGLE
REMARK 500 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,A1,6X,F5.1,6X,A1,10X,A1,3X,A16)
REMARK 500
REMARK 500 M RES CSSEQI IMPROPER EXPECTED FOUND DETAILS
REMARK 500 MET A 29 21.2 L L OUTSIDE RANGE
REMARK 500 HIS A 71 19.0 L L OUTSIDE RANGE
REMARK 500 ASP A 77 13.3 L L OUTSIDE RANGE
REMARK 500 ASN A 213 19.0 L L OUTSIDE RANGE
REMARK 500 ASP A 214 15.9 L L OUTSIDE RANGE
REMARK 500 PHE A 248 24.8 L L OUTSIDE RANGE
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 DTA A 273
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC2
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PG4 A 301
REMARK 900
REMARK 900 RELATED ENTRIES
REMARK 900 RELATED ID: 2I1W RELATED DB: PDB
REMARK 900 CRYSTAL STRUCTURE OF NAD KINASE 1 FROM LISTERIA
REMARK 900 MONOCYTOGENES
REMARK 900 RELATED ID: 2I29 RELATED DB: PDB
REMARK 900 CRYSTAL STRUCTURE OF NAD KINASE 1 FROM LISTERIA
REMARK 900 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: 2I2D 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 2I2C A 1 264 UNP Q8Y8D7 PPNK1_LISMO 1 264
SEQADV 2I2C LEU A 265 UNP Q8Y8D7 CLONING ARTIFACT
SEQADV 2I2C GLU A 266 UNP Q8Y8D7 CLONING ARTIFACT
SEQADV 2I2C HIS A 267 UNP Q8Y8D7 EXPRESSION TAG
SEQADV 2I2C HIS A 268 UNP Q8Y8D7 EXPRESSION TAG
SEQADV 2I2C HIS A 269 UNP Q8Y8D7 EXPRESSION TAG
SEQADV 2I2C HIS A 270 UNP Q8Y8D7 EXPRESSION TAG
SEQADV 2I2C HIS A 271 UNP Q8Y8D7 EXPRESSION TAG
SEQADV 2I2C 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 DTA A 273 38
HET PG4 A 301 13
HETNAM DTA (2S,3S,4R,5R,2'S,3'S,4'R,5'R)-2,2'-
HETNAM 2 DTA [DITHIOBIS(METHYLENE)]BIS[5-(6-AMINO-9H-PURIN-9-YL)
HETNAM 3 DTA TETRAHYDROFURAN-3,4-DIOL]
HETNAM PG4 TETRAETHYLENE GLYCOL
HETSYN DTA DI-(5'-THIOADENOSINE)
FORMUL 2 DTA C20 H24 N10 O6 S2
FORMUL 3 PG4 C8 H18 O5
FORMUL 4 HOH *133(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 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 MET A 4
SHEET 4 A 4 ALA A 63 HIS A 68 1 O ILE A 67 N SER A 41
SHEET 1 B 6 GLU A 115 ALA A 120 0
SHEET 2 B 6 GLN A 96 TYR A 109 -1 N VAL A 107 O ALA A 116
SHEET 3 B 6 VAL A 231 ARG A 247 -1 O PHE A 245 N VAL A 98
SHEET 4 B 6 VAL A 207 PRO A 211 -1 N LEU A 209 O ILE A 234
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 GLN A 218 N LYS A 127
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 -28.25
CISPEP 2 GLY A 70 HIS A 71 0 25.27
CISPEP 3 GLY A 112 LYS A 113 0 -2.31
CISPEP 4 LYS A 113 LYS A 114 0 27.83
CISPEP 5 LYS A 114 GLU A 115 0 -15.30
SITE 1 AC1 17 ASP A 45 LEU A 72 PHE A 74 TYR A 75
SITE 2 AC1 17 ASN A 122 GLU A 123 ASP A 150 SER A 158
SITE 3 AC1 17 THR A 161 ALA A 162 TYR A 163 SER A 166
SITE 4 AC1 17 ALA A 185 ILE A 187 HOH A 410 HOH A 418
SITE 5 AC1 17 HOH A 431
SITE 1 AC2 6 MET A 1 ASP A 60 ALA A 63 TYR A 95
SITE 2 AC2 6 LYS A 97 HIS A 244
CRYST1 63.070 75.297 118.650 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 0.015855 0.000000 0.000000 0.00000
SCALE2 0.000000 0.013281 0.000000 0.00000
SCALE3 0.000000 0.000000 0.008428 0.00000
(ATOM LINES ARE NOT SHOWN.)
END
