HEADER TRANSFERASE 16-AUG-06 2I29 TITLE CRYSTAL STRUCTURE OF NAD KINASE 1 FROM LISTERIA MONOCYTOGENES CAVEAT 2I29 ASP A 77 HAS WRONG CHIRALITY AT ATOM CA 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 NAD-BOUND NAD KINASE IN ORTHORHOMBIC FORM, TRANSFERASE EXPDTA X-RAY DIFFRACTION AUTHOR G.PONCET-MONTANGE,L.ASSAIRI,S.AROLD,S.POCHET,G.LABESSE REVDAT 8 30-AUG-23 2I29 1 REMARK REVDAT 7 24-JUN-20 2I29 1 CAVEAT REMARK SEQADV REVDAT 6 14-FEB-18 2I29 1 REMARK REVDAT 5 24-JAN-18 2I29 1 AUTHOR REVDAT 4 13-JUL-11 2I29 1 VERSN REVDAT 3 24-FEB-09 2I29 1 VERSN REVDAT 2 04-NOV-08 2I29 1 JRNL REVDAT 1 07-AUG-07 2I29 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. 2.10 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) : 2.10 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 34.86 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.5 REMARK 3 NUMBER OF REFLECTIONS : 15633 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) : 0.206 REMARK 3 R VALUE (WORKING SET) : 0.205 REMARK 3 FREE R VALUE : 0.254 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 3.000 REMARK 3 FREE R VALUE TEST SET COUNT : 478 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) : 981 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 85.19 REMARK 3 BIN R VALUE (WORKING SET) : 0.2830 REMARK 3 BIN FREE R VALUE SET COUNT : 31 REMARK 3 BIN FREE R VALUE : 0.2770 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1976 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 57 REMARK 3 SOLVENT ATOMS : 77 REMARK 3 REMARK 3 B VALUES. REMARK 3 B VALUE TYPE : LIKELY RESIDUAL REMARK 3 FROM WILSON PLOT (A**2) : 37.70 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 39.01 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.68000 REMARK 3 B22 (A**2) : 3.79000 REMARK 3 B33 (A**2) : -4.47000 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): 0.241 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.201 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.148 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 11.179 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.948 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.917 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 2122 ; 0.009 ; 0.021 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 2887 ; 1.478 ; 1.964 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 256 ; 9.342 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 96 ;33.082 ;23.438 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 329 ;15.741 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 11 ;19.956 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 314 ; 0.163 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 1617 ; 0.004 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 889 ; 0.212 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 1383 ; 0.309 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 115 ; 0.299 ; 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): 34 ; 0.170 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 10 ; 0.296 ; 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): 1320 ; 0.455 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 2041 ; 0.707 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 930 ; 1.055 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 844 ; 1.244 ; 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): 10.8536 23.2133 21.9260 REMARK 3 T TENSOR REMARK 3 T11: 0.0184 T22: 0.0561 REMARK 3 T33: -0.0448 T12: 0.0465 REMARK 3 T13: 0.0434 T23: -0.0664 REMARK 3 L TENSOR REMARK 3 L11: 3.0171 L22: 0.6746 REMARK 3 L33: 6.7790 L12: -0.3055 REMARK 3 L13: -1.5985 L23: 1.6187 REMARK 3 S TENSOR REMARK 3 S11: -0.0522 S12: -0.1731 S13: 0.1379 REMARK 3 S21: 0.0156 S22: 0.0578 S23: 0.0787 REMARK 3 S31: -0.1871 S32: -0.2483 S33: -0.0056 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): 21.8585 25.6166 25.8639 REMARK 3 T TENSOR REMARK 3 T11: 0.1640 T22: 0.1199 REMARK 3 T33: 0.0591 T12: 0.0351 REMARK 3 T13: 0.0733 T23: -0.1111 REMARK 3 L TENSOR REMARK 3 L11: 1.8804 L22: 0.4556 REMARK 3 L33: 3.9143 L12: 0.8737 REMARK 3 L13: 0.1633 L23: 0.5159 REMARK 3 S TENSOR REMARK 3 S11: -0.0498 S12: -0.5712 S13: 0.3461 REMARK 3 S21: 0.0845 S22: 0.2446 S23: -0.1960 REMARK 3 S31: -0.2550 S32: 0.2500 S33: -0.1949 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): 31.0908 13.7001 16.6672 REMARK 3 T TENSOR REMARK 3 T11: -0.0923 T22: -0.0357 REMARK 3 T33: -0.1711 T12: -0.0169 REMARK 3 T13: -0.0194 T23: -0.0482 REMARK 3 L TENSOR REMARK 3 L11: 3.5343 L22: 13.7830 REMARK 3 L33: 7.1481 L12: 3.9782 REMARK 3 L13: -2.4174 L23: 2.6839 REMARK 3 S TENSOR REMARK 3 S11: 0.1645 S12: -0.5491 S13: 0.1494 REMARK 3 S21: 0.6995 S22: -0.0788 S23: -0.0115 REMARK 3 S31: -0.0402 S32: -0.0301 S33: -0.0857 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): 17.5327 13.3537 -4.2049 REMARK 3 T TENSOR REMARK 3 T11: -0.1271 T22: -0.1202 REMARK 3 T33: -0.1037 T12: 0.0518 REMARK 3 T13: 0.0064 T23: 0.0104 REMARK 3 L TENSOR REMARK 3 L11: 1.4690 L22: 1.8902 REMARK 3 L33: 2.8995 L12: -0.1463 REMARK 3 L13: 0.0957 L23: 0.4699 REMARK 3 S TENSOR REMARK 3 S11: 0.0926 S12: 0.0484 S13: 0.1337 REMARK 3 S21: -0.0799 S22: -0.1318 S23: 0.2879 REMARK 3 S31: -0.1911 S32: -0.3211 S33: 0.0391 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): 17.1313 8.7296 11.1169 REMARK 3 T TENSOR REMARK 3 T11: 0.0463 T22: 0.2020 REMARK 3 T33: 0.0554 T12: 0.0114 REMARK 3 T13: 0.0836 T23: 0.0380 REMARK 3 L TENSOR REMARK 3 L11: 0.0316 L22: 12.9867 REMARK 3 L33: 0.1134 L12: 0.6405 REMARK 3 L13: 0.0599 L23: 1.2135 REMARK 3 S TENSOR REMARK 3 S11: -0.0127 S12: -2.0793 S13: -0.4061 REMARK 3 S21: 0.9707 S22: 0.0526 S23: 0.6092 REMARK 3 S31: 0.1179 S32: -1.4235 S33: -0.0400 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): 30.8602 24.9193 13.5940 REMARK 3 T TENSOR REMARK 3 T11: 0.1035 T22: 0.0434 REMARK 3 T33: 0.0087 T12: 0.0489 REMARK 3 T13: 0.0189 T23: -0.0759 REMARK 3 L TENSOR REMARK 3 L11: 148.7147 L22: 154.4411 REMARK 3 L33: 8.2094 L12: 43.0319 REMARK 3 L13: 33.1290 L23: 20.4373 REMARK 3 S TENSOR REMARK 3 S11: -1.4729 S12: 3.9824 S13: 1.6678 REMARK 3 S21: 0.4382 S22: 3.4690 S23: 0.5662 REMARK 3 S31: 1.1516 S32: -6.1270 S33: -1.9961 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 2I29 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 DEPOSITION ID IS D_1000039045. 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 : ID14-2 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.979 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 : 15633 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.100 REMARK 200 RESOLUTION RANGE LOW (A) : 37.140 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.7 REMARK 200 DATA REDUNDANCY : 6.000 REMARK 200 R MERGE (I) : 0.07100 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 17.2000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : NULL REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : NULL REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : NULL 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 2I1W REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 45.94 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.28 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 31.25150 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 36.76900 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 59.37250 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 31.25150 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 36.76900 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 59.37250 REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 31.25150 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 36.76900 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 59.37250 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 31.25150 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 36.76900 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 59.37250 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: 12670 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 37880 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -70.0 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 62.50300 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 62.50300 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 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 ARG A 58 CG CD NE CZ NH1 NH2 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 249 CG CD NE CZ NH1 NH2 REMARK 470 GLU A 263 CG CD OE1 OE2 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 76 O HOH A 338 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 O HOH A 325 O HOH A 325 4555 2.01 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 77 N - CA - C ANGL. DEV. = 19.5 DEGREES REMARK 500 ASP A 222 CB - CG - OD2 ANGL. DEV. = 7.0 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 -153.12 -103.70 REMARK 500 ASP A 28 103.82 174.57 REMARK 500 MET A 29 58.69 93.14 REMARK 500 ASP A 77 -74.22 74.21 REMARK 500 ASN A 122 -72.62 -100.61 REMARK 500 ASP A 141 -4.86 72.30 REMARK 500 ALA A 162 -126.05 -99.53 REMARK 500 PRO A 174 3.31 -68.75 REMARK 500 ASN A 213 -103.75 -97.30 REMARK 500 ASP A 214 91.29 35.66 REMARK 500 ASP A 222 -116.39 51.49 REMARK 500 PHE A 248 -47.21 163.60 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 35.23 REMARK 500 ASN A 213 ASP A 214 84.40 REMARK 500 ARG A 247 PHE A 248 -67.25 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 NAD 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: 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: 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 2I29 A 1 264 UNP Q8Y8D7 PPNK1_LISMO 1 264 SEQADV 2I29 LEU A 265 UNP Q8Y8D7 CLONING ARTIFACT SEQADV 2I29 GLU A 266 UNP Q8Y8D7 CLONING ARTIFACT SEQADV 2I29 HIS A 267 UNP Q8Y8D7 EXPRESSION TAG SEQADV 2I29 HIS A 268 UNP Q8Y8D7 EXPRESSION TAG SEQADV 2I29 HIS A 269 UNP Q8Y8D7 EXPRESSION TAG SEQADV 2I29 HIS A 270 UNP Q8Y8D7 EXPRESSION TAG SEQADV 2I29 HIS A 271 UNP Q8Y8D7 EXPRESSION TAG SEQADV 2I29 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 NAD A 273 44 HET CIT A 274 13 HETNAM NAD NICOTINAMIDE-ADENINE-DINUCLEOTIDE HETNAM CIT CITRIC ACID FORMUL 2 NAD C21 H27 N7 O14 P2 FORMUL 3 CIT C6 H8 O7 FORMUL 4 HOH *77(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 ARG A 79 ALA A 81 5 3 HELIX 4 4 GLU A 82 GLY A 93 1 12 HELIX 5 5 PRO A 157 THR A 161 5 5 HELIX 6 6 ALA A 162 LEU A 167 1 6 HELIX 7 7 PRO A 252 ILE A 262 1 11 SHEET 1 A 3 TYR A 3 SER A 7 0 SHEET 2 A 3 ILE A 38 GLY A 43 1 O ILE A 40 N THR A 6 SHEET 3 A 3 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 ARG A 247 N GLN A 96 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 MET A 179 O PHE A 201 SHEET 3 C 6 GLY A 151 SER A 155 -1 N CYS A 153 O THR A 182 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 -10.61 CISPEP 2 GLY A 130 GLY A 131 0 -13.37 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 ASP A 150 SER A 158 SITE 3 AC1 18 THR A 161 ALA A 162 TYR A 163 SER A 166 SITE 4 AC1 18 ALA A 185 ILE A 187 TYR A 192 HIS A 223 SITE 5 AC1 18 HOH A 314 HOH A 321 SITE 1 AC2 7 TYR A 100 HIS A 173 HIS A 205 ARG A 247 SITE 2 AC2 7 PHE A 251 PHE A 253 HOH A 302 CRYST1 62.503 73.538 118.745 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 0.015999 0.000000 0.000000 0.00000 SCALE2 0.000000 0.013598 0.000000 0.00000 SCALE3 0.000000 0.000000 0.008421 0.00000