HEADER TRANSFERASE 16-AUG-06 2I2B TITLE CRYSTAL STRUCTURE OF LMNADK1 FROM LISTERIA MONOCYTOGENES 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 KEYWDS CRYSTAL STRUCTURE OF LMNADK1 IN COMPLEX WITH LIGAND ANALOG, KEYWDS 2 TRANSFERASE EXPDTA X-RAY DIFFRACTION AUTHOR G.PONCET-MONTANGE,G.LABESSE REVDAT 7 30-AUG-23 2I2B 1 REMARK REVDAT 6 24-JUN-20 2I2B 1 REMARK SEQADV REVDAT 5 14-FEB-18 2I2B 1 REMARK REVDAT 4 13-JUL-11 2I2B 1 VERSN REVDAT 3 24-FEB-09 2I2B 1 VERSN REVDAT 2 04-NOV-08 2I2B 1 JRNL REVDAT 1 07-AUG-07 2I2B 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) : 30.99 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 3 NUMBER OF REFLECTIONS : 15878 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) : 0.204 REMARK 3 R VALUE (WORKING SET) : 0.203 REMARK 3 FREE R VALUE : 0.231 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 831 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) : 1158 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 100.0 REMARK 3 BIN R VALUE (WORKING SET) : 0.2370 REMARK 3 BIN FREE R VALUE SET COUNT : 53 REMARK 3 BIN FREE R VALUE : 0.3090 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1995 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 53 REMARK 3 SOLVENT ATOMS : 66 REMARK 3 REMARK 3 B VALUES. REMARK 3 B VALUE TYPE : LIKELY RESIDUAL REMARK 3 FROM WILSON PLOT (A**2) : 28.60 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 22.04 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 1.15000 REMARK 3 B22 (A**2) : 2.09000 REMARK 3 B33 (A**2) : -3.24000 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): 0.233 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.180 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.126 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 9.615 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.941 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.927 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 2102 ; 0.009 ; 0.021 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 2852 ; 1.342 ; 1.967 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 255 ; 9.630 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 90 ;32.729 ;23.222 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 323 ;16.278 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 11 ;13.619 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 313 ; 0.090 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 1594 ; 0.004 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 887 ; 0.197 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 1381 ; 0.308 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 117 ; 0.525 ; 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): 45 ; 0.171 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 15 ; 0.203 ; 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): 1316 ; 0.461 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 2045 ; 0.731 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 913 ; 0.980 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 807 ; 1.296 ; 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 : 8 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): 11.6337 23.1709 21.8067 REMARK 3 T TENSOR REMARK 3 T11: -0.0026 T22: -0.0038 REMARK 3 T33: -0.0805 T12: 0.0556 REMARK 3 T13: 0.0227 T23: -0.0806 REMARK 3 L TENSOR REMARK 3 L11: 3.1014 L22: 1.3405 REMARK 3 L33: 3.9833 L12: -0.4315 REMARK 3 L13: -1.6709 L23: 0.8996 REMARK 3 S TENSOR REMARK 3 S11: -0.1087 S12: -0.1534 S13: 0.1253 REMARK 3 S21: 0.1510 S22: 0.0358 S23: 0.1596 REMARK 3 S31: -0.2639 S32: -0.2906 S33: 0.0729 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): 22.3932 26.8697 25.0476 REMARK 3 T TENSOR REMARK 3 T11: 0.1646 T22: 0.1398 REMARK 3 T33: 0.1190 T12: 0.0236 REMARK 3 T13: -0.0177 T23: -0.1348 REMARK 3 L TENSOR REMARK 3 L11: 2.7557 L22: 0.6128 REMARK 3 L33: 2.2264 L12: -0.2776 REMARK 3 L13: -1.2465 L23: 1.1116 REMARK 3 S TENSOR REMARK 3 S11: 0.0475 S12: -0.6295 S13: 0.5625 REMARK 3 S21: 0.2471 S22: 0.2837 S23: -0.2514 REMARK 3 S31: -0.4656 S32: 0.0765 S33: -0.3312 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): 31.6553 13.6564 16.5455 REMARK 3 T TENSOR REMARK 3 T11: -0.1058 T22: -0.0887 REMARK 3 T33: -0.2219 T12: -0.0193 REMARK 3 T13: -0.0107 T23: -0.0499 REMARK 3 L TENSOR REMARK 3 L11: 8.9442 L22: 5.6893 REMARK 3 L33: 6.5155 L12: -2.4817 REMARK 3 L13: -0.5877 L23: 3.1072 REMARK 3 S TENSOR REMARK 3 S11: 0.0041 S12: -0.4884 S13: 0.1049 REMARK 3 S21: 0.7708 S22: -0.0451 S23: 0.0652 REMARK 3 S31: -0.1398 S32: -0.0356 S33: 0.0410 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): 17.8593 13.5316 -4.1198 REMARK 3 T TENSOR REMARK 3 T11: -0.1578 T22: -0.0758 REMARK 3 T33: -0.1127 T12: 0.0426 REMARK 3 T13: -0.0024 T23: -0.0111 REMARK 3 L TENSOR REMARK 3 L11: 1.5913 L22: 2.2048 REMARK 3 L33: 3.9139 L12: -0.3901 REMARK 3 L13: -0.0386 L23: 0.1601 REMARK 3 S TENSOR REMARK 3 S11: 0.0272 S12: 0.0861 S13: 0.0213 REMARK 3 S21: -0.1767 S22: -0.1069 S23: 0.3960 REMARK 3 S31: -0.0719 S32: -0.4701 S33: 0.0797 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): 17.3329 7.1558 8.1491 REMARK 3 T TENSOR REMARK 3 T11: -0.0168 T22: -0.0054 REMARK 3 T33: -0.0331 T12: -0.0583 REMARK 3 T13: 0.0640 T23: 0.0365 REMARK 3 L TENSOR REMARK 3 L11: 16.5147 L22: 31.5503 REMARK 3 L33: 11.8564 L12: -7.7155 REMARK 3 L13: -4.1368 L23: -15.4564 REMARK 3 S TENSOR REMARK 3 S11: -0.5478 S12: -0.7645 S13: -1.2517 REMARK 3 S21: 3.6939 S22: -1.4357 S23: 0.4288 REMARK 3 S31: 0.0763 S32: 0.2706 S33: 1.9835 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): 19.5191 10.5393 13.2831 REMARK 3 T TENSOR REMARK 3 T11: 0.2357 T22: -0.1217 REMARK 3 T33: -0.0179 T12: -0.0495 REMARK 3 T13: 0.0540 T23: -0.0188 REMARK 3 L TENSOR REMARK 3 L11: 9.8761 L22: 0.2263 REMARK 3 L33: 39.7405 L12: 1.4949 REMARK 3 L13: 19.8111 L23: 2.9987 REMARK 3 S TENSOR REMARK 3 S11: -0.8339 S12: -0.8020 S13: 0.1680 REMARK 3 S21: 2.7682 S22: 2.3703 S23: -1.9519 REMARK 3 S31: 1.7482 S32: -3.9732 S33: -1.5365 REMARK 3 REMARK 3 TLS GROUP : 7 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): 30.0836 24.7192 14.9272 REMARK 3 T TENSOR REMARK 3 T11: 0.0947 T22: 0.0341 REMARK 3 T33: -0.0207 T12: 0.0305 REMARK 3 T13: -0.0588 T23: -0.0601 REMARK 3 L TENSOR REMARK 3 L11: 82.8034 L22: 110.1849 REMARK 3 L33: 5.6494 L12: -31.2770 REMARK 3 L13: 0.5035 L23: -23.7579 REMARK 3 S TENSOR REMARK 3 S11: -0.5039 S12: -0.7351 S13: 2.7920 REMARK 3 S21: 1.6683 S22: 0.4663 S23: 1.0244 REMARK 3 S31: 1.2466 S32: -1.1401 S33: 0.0377 REMARK 3 REMARK 3 TLS GROUP : 8 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 401 A 401 REMARK 3 ORIGIN FOR THE GROUP (A): 37.2856 16.6052 17.0267 REMARK 3 T TENSOR REMARK 3 T11: -0.0157 T22: 0.0180 REMARK 3 T33: -0.0003 T12: -0.1098 REMARK 3 T13: 0.0315 T23: 0.0332 REMARK 3 L TENSOR REMARK 3 L11: 83.7139 L22: 116.7281 REMARK 3 L33: 50.9418 L12: 83.7456 REMARK 3 L13: -13.9117 L23: -53.9468 REMARK 3 S TENSOR REMARK 3 S11: 2.6031 S12: 0.6616 S13: 0.4338 REMARK 3 S21: -0.3008 S22: 0.7530 S23: -1.9557 REMARK 3 S31: 1.9759 S32: 2.7155 S33: -3.3561 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 2I2B 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_1000039047. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 22-JUN-05 REMARK 200 TEMPERATURE (KELVIN) : 100.0 REMARK 200 PH : 5.40 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ESRF REMARK 200 BEAMLINE : ID29 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.978 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 : 15878 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.100 REMARK 200 RESOLUTION RANGE LOW (A) : 30.990 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 200 DATA REDUNDANCY : 5.500 REMARK 200 R MERGE (I) : 0.08200 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 18.1000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.10 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.21 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 5.70 REMARK 200 R MERGE FOR SHELL (I) : 0.48800 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.900 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 2I2A REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 47.11 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.33 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, PH 5.40 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 31.62150 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 37.28250 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 59.14500 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 31.62150 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 37.28250 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 59.14500 REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 31.62150 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 37.28250 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 59.14500 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 31.62150 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 37.28250 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 59.14500 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 63.24300 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 63.24300 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 110 REMARK 465 ILE A 111 REMARK 465 GLY A 112 REMARK 465 LYS A 113 REMARK 465 ARG A 190 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 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 HIS A 71 CG ND1 CD2 CE1 NE2 REMARK 470 ASP A 84 CG OD1 OD2 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 GLU A 94 CG CD OE1 OE2 REMARK 470 GLN A 96 CG CD OE1 NE2 REMARK 470 LYS A 108 CG CD CE NZ REMARK 470 LYS A 114 CG CD CE NZ REMARK 470 VAL A 191 CG1 CG2 REMARK 470 LYS A 215 CG CD CE NZ 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 PRO A 132 O HOH A 463 2.15 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 10 CB - CG - OD2 ANGL. DEV. = 6.2 DEGREES REMARK 500 ASP A 222 CB - CG - OD2 ANGL. DEV. = 6.1 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 ASP A 77 -18.65 -175.09 REMARK 500 ASN A 122 -63.02 -96.30 REMARK 500 PHE A 133 91.50 86.94 REMARK 500 ASP A 141 -7.60 80.20 REMARK 500 ALA A 162 -125.32 -101.74 REMARK 500 HIS A 204 -5.58 79.25 REMARK 500 ASN A 213 -78.37 -121.58 REMARK 500 ASP A 222 -120.26 53.34 REMARK 500 SER A 225 127.32 -179.68 REMARK 500 ILE A 226 63.87 121.78 REMARK 500 PHE A 248 -86.93 133.77 REMARK 500 ILE A 262 -62.93 -99.56 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 -88.57 REMARK 500 VAL A 191 TYR A 192 -67.74 REMARK 500 ARG A 247 PHE A 248 -30.37 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 CC5 A 273 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CC5 A 274 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CIT A 301 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 401 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: 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 2I2B A 1 264 UNP Q8Y8D7 PPNK1_LISMO 1 264 SEQADV 2I2B LEU A 265 UNP Q8Y8D7 CLONING ARTIFACT SEQADV 2I2B GLU A 266 UNP Q8Y8D7 CLONING ARTIFACT SEQADV 2I2B HIS A 267 UNP Q8Y8D7 EXPRESSION TAG SEQADV 2I2B HIS A 268 UNP Q8Y8D7 EXPRESSION TAG SEQADV 2I2B HIS A 269 UNP Q8Y8D7 EXPRESSION TAG SEQADV 2I2B HIS A 270 UNP Q8Y8D7 EXPRESSION TAG SEQADV 2I2B HIS A 271 UNP Q8Y8D7 EXPRESSION TAG SEQADV 2I2B 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 CC5 A 273 17 HET CC5 A 274 17 HET CIT A 301 13 HET GOL A 401 6 HETNAM CC5 BETA-D-ERYTHROFURANOSYL-ADENOSINE HETNAM CIT CITRIC ACID HETNAM GOL GLYCEROL HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 2 CC5 2(C9 H11 N5 O3) FORMUL 4 CIT C6 H8 O7 FORMUL 5 GOL C3 H8 O3 FORMUL 6 HOH *66(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 GLU A 61 5 6 HELIX 4 4 ARG A 79 ALA A 81 5 3 HELIX 5 5 GLU A 82 GLY A 93 1 12 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 A10 GLU A 30 TYR A 31 0 SHEET 2 A10 LYS A 2 SER A 7 1 N TYR A 3 O GLU A 30 SHEET 3 A10 ILE A 38 GLY A 43 1 O ILE A 40 N THR A 6 SHEET 4 A10 ALA A 63 HIS A 68 1 O ILE A 67 N SER A 41 SHEET 5 A10 GLU A 233 ARG A 247 1 O HIS A 244 N PHE A 64 SHEET 6 A10 VAL A 207 PRO A 211 -1 N VAL A 207 O TYR A 236 SHEET 7 A10 VAL A 134 ILE A 139 -1 N VAL A 138 O SER A 208 SHEET 8 A10 ILE A 142 SER A 155 -1 O GLU A 145 N VAL A 137 SHEET 9 A10 ALA A 178 SER A 186 -1 O THR A 182 N CYS A 153 SHEET 10 A10 LEU A 199 PRO A 202 -1 O LEU A 199 N LEU A 181 SHEET 1 B 9 ALA A 116 ALA A 120 0 SHEET 2 B 9 GLN A 96 LYS A 108 -1 N VAL A 107 O ALA A 116 SHEET 3 B 9 GLU A 233 ARG A 247 -1 O ARG A 247 N GLN A 96 SHEET 4 B 9 VAL A 207 PRO A 211 -1 N VAL A 207 O TYR A 236 SHEET 5 B 9 VAL A 134 ILE A 139 -1 N VAL A 138 O SER A 208 SHEET 6 B 9 ILE A 142 SER A 155 -1 O GLU A 145 N VAL A 137 SHEET 7 B 9 GLU A 123 LYS A 127 -1 N SER A 124 O MET A 154 SHEET 8 B 9 PHE A 217 VAL A 221 -1 O GLN A 218 N LYS A 127 SHEET 9 B 9 LEU A 224 HIS A 228 -1 O HIS A 228 N PHE A 217 CISPEP 1 SER A 128 SER A 129 0 25.15 CISPEP 2 PRO A 132 PHE A 133 0 9.97 CISPEP 3 SER A 225 ILE A 226 0 -19.31 SITE 1 AC1 10 ASN A 122 GLU A 123 ASP A 150 ALA A 162 SITE 2 AC1 10 TYR A 163 SER A 166 ALA A 185 ILE A 187 SITE 3 AC1 10 HOH A 437 HOH A 462 SITE 1 AC2 8 ASP A 45 PHE A 74 TYR A 75 ASN A 122 SITE 2 AC2 8 SER A 158 THR A 161 ALA A 162 HOH A 437 SITE 1 AC3 8 TYR A 100 HIS A 173 ARG A 247 PHE A 251 SITE 2 AC3 8 PRO A 252 PHE A 253 ARG A 256 HOH A 442 SITE 1 AC4 7 ILE A 139 ILE A 142 HIS A 143 PHE A 144 SITE 2 AC4 7 TRP A 254 ARG A 255 HIS A 258 CRYST1 63.243 74.565 118.290 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 0.015812 0.000000 0.000000 0.00000 SCALE2 0.000000 0.013411 0.000000 0.00000 SCALE3 0.000000 0.000000 0.008454 0.00000