HEADER TRANSFERASE 16-AUG-06 2I2E OBSLTE 07-MAR-12 2I2E 4DY6 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 GENE: PPNK1; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 7 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 8 EXPRESSION_SYSTEM_PLASMID: PET22B KEYWDS CRYSTAL STRUCTURE OF LMNADK1 BOUND TO A NAD ANALOG, TRANSFERASE EXPDTA X-RAY DIFFRACTION AUTHOR G.PONCET-MONTANGE,L.ASSAIRI,S.AROLD,S.POCHET,G.LABESSE REVDAT 5 07-MAR-12 2I2E 1 OBSLTE REVDAT 4 13-JUL-11 2I2E 1 VERSN REVDAT 3 24-FEB-09 2I2E 1 VERSN REVDAT 2 04-NOV-08 2I2E 1 JRNL REVDAT 1 07-AUG-07 2I2E 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. 2.20 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) : 2.20 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 35.09 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.8 REMARK 3 NUMBER OF REFLECTIONS : 13914 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) : 0.205 REMARK 3 R VALUE (WORKING SET) : 0.203 REMARK 3 FREE R VALUE : 0.238 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) (%) : 90.52 REMARK 3 BIN R VALUE (WORKING SET) : 0.2590 REMARK 3 BIN FREE R VALUE SET COUNT : 48 REMARK 3 BIN FREE R VALUE : 0.3500 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2018 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 62 REMARK 3 SOLVENT ATOMS : 54 REMARK 3 REMARK 3 B VALUES. REMARK 3 B VALUE TYPE : LIKELY RESIDUAL REMARK 3 FROM WILSON PLOT (A**2) : 38.30 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 40.67 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 1.09000 REMARK 3 B22 (A**2) : 2.76000 REMARK 3 B33 (A**2) : -3.85000 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): 0.290 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.210 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.149 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 11.838 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.953 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.931 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 2147 ; 0.010 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 2913 ; 1.452 ; 1.975 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 253 ; 9.131 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 98 ;34.376 ;23.265 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 347 ;15.608 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 13 ;16.436 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 316 ; 0.125 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 1618 ; 0.004 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 815 ; 0.201 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 1372 ; 0.308 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 92 ; 0.151 ; 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): 39 ; 0.148 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 3 ; 0.293 ; 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): 1319 ; 0.479 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 2039 ; 0.760 ; 2.000 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 973 ; 1.092 ; 3.000 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 874 ; 1.529 ; 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 : 5 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): 10.9107 23.8839 21.9936 REMARK 3 T TENSOR REMARK 3 T11: 0.0061 T22: -0.0050 REMARK 3 T33: -0.0811 T12: 0.0396 REMARK 3 T13: 0.0460 T23: -0.0662 REMARK 3 L TENSOR REMARK 3 L11: 3.6639 L22: 1.1218 REMARK 3 L33: 6.5191 L12: -0.0516 REMARK 3 L13: -1.2088 L23: 1.0237 REMARK 3 S TENSOR REMARK 3 S11: -0.1097 S12: -0.1226 S13: 0.0956 REMARK 3 S21: 0.0397 S22: 0.0181 S23: 0.1173 REMARK 3 S31: -0.1117 S32: -0.2706 S33: 0.0916 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): 22.2308 26.6242 25.7044 REMARK 3 T TENSOR REMARK 3 T11: 0.2074 T22: 0.1532 REMARK 3 T33: 0.1004 T12: 0.0294 REMARK 3 T13: 0.0242 T23: -0.1221 REMARK 3 L TENSOR REMARK 3 L11: 2.5527 L22: 0.1301 REMARK 3 L33: 3.1658 L12: 0.4556 REMARK 3 L13: -0.4232 L23: 0.3129 REMARK 3 S TENSOR REMARK 3 S11: 0.0249 S12: -0.7301 S13: 0.3795 REMARK 3 S21: -0.0145 S22: 0.1295 S23: -0.1440 REMARK 3 S31: -0.2210 S32: 0.3257 S33: -0.1545 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): 31.7071 13.6727 16.8764 REMARK 3 T TENSOR REMARK 3 T11: -0.0861 T22: -0.0305 REMARK 3 T33: -0.1729 T12: -0.0278 REMARK 3 T13: 0.0370 T23: -0.0673 REMARK 3 L TENSOR REMARK 3 L11: 0.3360 L22: 16.7153 REMARK 3 L33: 7.4648 L12: 2.2077 REMARK 3 L13: -0.7096 L23: -1.0327 REMARK 3 S TENSOR REMARK 3 S11: 0.0922 S12: -0.4146 S13: -0.0206 REMARK 3 S21: 1.1148 S22: -0.0304 S23: -0.2166 REMARK 3 S31: -0.0538 S32: -0.1728 S33: -0.0618 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): 17.7099 13.4572 -4.3669 REMARK 3 T TENSOR REMARK 3 T11: -0.1224 T22: -0.0875 REMARK 3 T33: -0.1342 T12: 0.0392 REMARK 3 T13: 0.0009 T23: 0.0079 REMARK 3 L TENSOR REMARK 3 L11: 1.5262 L22: 2.2336 REMARK 3 L33: 3.1144 L12: -0.2637 REMARK 3 L13: 0.0188 L23: 0.1739 REMARK 3 S TENSOR REMARK 3 S11: 0.0368 S12: 0.0918 S13: 0.0998 REMARK 3 S21: -0.1429 S22: -0.0923 S23: 0.3843 REMARK 3 S31: -0.0029 S32: -0.3832 S33: 0.0555 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): 17.5890 8.8507 11.6122 REMARK 3 T TENSOR REMARK 3 T11: 0.2010 T22: -0.0768 REMARK 3 T33: 0.0269 T12: -0.0543 REMARK 3 T13: 0.1274 T23: 0.0605 REMARK 3 L TENSOR REMARK 3 L11: 6.7299 L22: 7.9897 REMARK 3 L33: 10.0712 L12: -5.3018 REMARK 3 L13: -1.6700 L23: 7.3836 REMARK 3 S TENSOR REMARK 3 S11: 0.2418 S12: -0.7448 S13: -0.8667 REMARK 3 S21: 1.7005 S22: -0.9840 S23: 1.0793 REMARK 3 S31: 0.3426 S32: -1.6570 S33: 0.7423 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 2I2E 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 RCSB ID CODE IS RCSB039050. 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 : NULL REMARK 200 DATA SCALING SOFTWARE : NULL REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 13914 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.200 REMARK 200 RESOLUTION RANGE LOW (A) : 35.100 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 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) : NULL REMARK 200 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 (%) : 94.0 REMARK 200 DATA REDUNDANCY IN SHELL : 2.10 REMARK 200 R MERGE FOR SHELL (I) : 0.46000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 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: NULL REMARK 200 STARTING MODEL: PDB ENTRY 2I2D REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 48.05 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.37 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 31.55150 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 37.86400 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 59.42400 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 31.55150 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 37.86400 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 59.42400 REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 31.55150 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 37.86400 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 59.42400 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 31.55150 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 37.86400 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 59.42400 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 63.10300 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 63.10300 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 317 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 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 ASP A 28 CB CG OD1 OD2 REMARK 470 LYS A 85 CG CD CE NZ REMARK 470 ALA A 91 CB REMARK 470 LYS A 92 CG CD CE NZ REMARK 470 GLU A 94 CG CD OE1 OE2 REMARK 470 ARG A 190 CG CD NE CZ NH1 NH2 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: 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 10 CB - CG - OD2 ANGL. DEV. = 5.7 DEGREES REMARK 500 ASP A 32 CB - CG - OD2 ANGL. DEV. = 6.0 DEGREES REMARK 500 ASP A 222 CB - CG - OD2 ANGL. DEV. = 6.5 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 MET A 29 108.08 73.91 REMARK 500 ASP A 77 -59.93 87.99 REMARK 500 GLU A 94 48.11 -95.58 REMARK 500 ASN A 122 -73.28 -94.81 REMARK 500 ASP A 141 -1.32 74.95 REMARK 500 ALA A 162 -129.17 -99.10 REMARK 500 ALA A 185 67.14 38.62 REMARK 500 HIS A 204 -9.66 87.74 REMARK 500 ASN A 213 -115.42 -106.06 REMARK 500 ASP A 214 94.03 43.77 REMARK 500 ASP A 222 -120.24 54.85 REMARK 500 PHE A 248 -62.38 156.13 REMARK 500 ILE A 262 -62.17 -101.52 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 37.72 REMARK 500 ASN A 213 ASP A 214 73.99 REMARK 500 ARG A 247 PHE A 248 -61.46 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 23.5 L L OUTSIDE RANGE REMARK 500 ASP A 77 19.1 L L OUTSIDE RANGE REMARK 500 ASN A 213 21.8 L L OUTSIDE RANGE REMARK 500 ASP A 214 18.4 L L OUTSIDE RANGE REMARK 500 REMARK 500 REMARK: NULL REMARK 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH A 317 DISTANCE = 6.22 ANGSTROMS 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 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 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: 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: 2I2F RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF LMNADK1 DBREF 2I2E A 1 264 UNP Q8Y8D7 PPNK1_LISMO 1 264 SEQADV 2I2E LEU A 265 UNP Q8Y8D7 CLONING ARTIFACT SEQADV 2I2E GLU A 266 UNP Q8Y8D7 CLONING ARTIFACT SEQADV 2I2E HIS A 267 UNP Q8Y8D7 EXPRESSION TAG SEQADV 2I2E HIS A 268 UNP Q8Y8D7 EXPRESSION TAG SEQADV 2I2E HIS A 269 UNP Q8Y8D7 EXPRESSION TAG SEQADV 2I2E HIS A 270 UNP Q8Y8D7 EXPRESSION TAG SEQADV 2I2E HIS A 271 UNP Q8Y8D7 EXPRESSION TAG SEQADV 2I2E 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 273 49 HET CIT A 274 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 *54(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 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 ARG A 247 N GLN A 96 SHEET 4 B 8 VAL A 207 PRO A 211 -1 N VAL A 207 O TYR A 236 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 ARG A 247 N GLN A 96 SHEET 4 C 9 VAL A 207 PRO A 211 -1 N VAL A 207 O TYR A 236 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 SER A 220 N THR A 125 SHEET 9 C 9 LEU A 224 HIS A 228 -1 O ILE A 226 N ILE A 219 CISPEP 1 ASP A 28 MET A 29 0 -4.40 CISPEP 2 GLY A 130 GLY A 131 0 -9.51 SITE 1 AC1 20 GLY A 44 ASP A 45 GLY A 46 PHE A 74 SITE 2 AC1 20 ASN A 122 GLU A 123 GLY A 149 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 313 HOH A 318 HOH A 320 HOH A 325 SITE 1 AC2 10 VAL A 98 TYR A 100 HIS A 173 ARG A 247 SITE 2 AC2 10 PHE A 251 PRO A 252 PHE A 253 ARG A 256 SITE 3 AC2 10 HOH A 321 HOH A 328 CRYST1 63.103 75.728 118.848 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 0.015847 0.000000 0.000000 0.00000 SCALE2 0.000000 0.013205 0.000000 0.00000 SCALE3 0.000000 0.000000 0.008414 0.00000