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 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 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