HEADER TRANSFERASE 16-AUG-06 2I2A 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; SOURCE 7 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 8 EXPRESSION_SYSTEM_PLASMID: PET22B KEYWDS NADP BOUND CRYSTAL STRUCTURE OF LMNADK1, TRANSFERASE EXPDTA X-RAY DIFFRACTION AUTHOR G.LABESSE REVDAT 6 21-FEB-24 2I2A 1 REMARK SEQADV REVDAT 5 14-FEB-18 2I2A 1 REMARK REVDAT 4 13-JUL-11 2I2A 1 VERSN REVDAT 3 24-FEB-09 2I2A 1 VERSN REVDAT 2 04-NOV-08 2I2A 1 JRNL REVDAT 1 07-AUG-07 2I2A 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) : 37.37 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 95.7 REMARK 3 NUMBER OF REFLECTIONS : 15714 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) : 0.201 REMARK 3 R VALUE (WORKING SET) : 0.199 REMARK 3 FREE R VALUE : 0.261 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 2.900 REMARK 3 FREE R VALUE TEST SET COUNT : 477 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) : 1183 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 97.92 REMARK 3 BIN R VALUE (WORKING SET) : 0.2510 REMARK 3 BIN FREE R VALUE SET COUNT : 41 REMARK 3 BIN FREE R VALUE : 0.2420 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2059 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 54 REMARK 3 SOLVENT ATOMS : 123 REMARK 3 REMARK 3 B VALUES. REMARK 3 B VALUE TYPE : LIKELY RESIDUAL REMARK 3 FROM WILSON PLOT (A**2) : 25.10 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 22.29 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.17000 REMARK 3 B22 (A**2) : 2.33000 REMARK 3 B33 (A**2) : -2.15000 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): 0.247 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.212 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.165 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 12.447 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.947 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.920 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 2177 ; 0.010 ; 0.021 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 2957 ; 1.538 ; 1.967 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 265 ; 9.576 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 97 ;35.689 ;23.608 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 346 ;15.993 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 11 ;17.050 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 321 ; 0.140 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 1643 ; 0.004 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 933 ; 0.213 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 1431 ; 0.309 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 144 ; 0.277 ; 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): 52 ; 0.218 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 14 ; 0.152 ; 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): 1357 ; 0.463 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 2105 ; 0.767 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 943 ; 1.111 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 851 ; 1.600 ; 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): 10.6960 23.9369 21.6522 REMARK 3 T TENSOR REMARK 3 T11: -0.0499 T22: -0.0310 REMARK 3 T33: -0.0498 T12: 0.0349 REMARK 3 T13: 0.0300 T23: -0.0472 REMARK 3 L TENSOR REMARK 3 L11: 3.2378 L22: 0.9080 REMARK 3 L33: 6.1532 L12: -0.5895 REMARK 3 L13: -1.1267 L23: 1.8889 REMARK 3 S TENSOR REMARK 3 S11: -0.0965 S12: -0.2978 S13: 0.0424 REMARK 3 S21: 0.0264 S22: 0.0657 S23: 0.0026 REMARK 3 S31: -0.1944 S32: -0.2450 S33: 0.0309 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): 21.4222 27.1307 25.2361 REMARK 3 T TENSOR REMARK 3 T11: 0.2619 T22: 0.2432 REMARK 3 T33: 0.1683 T12: 0.0678 REMARK 3 T13: 0.0456 T23: -0.1531 REMARK 3 L TENSOR REMARK 3 L11: 3.0058 L22: 0.0353 REMARK 3 L33: 0.7209 L12: 0.3257 REMARK 3 L13: -1.4721 L23: -0.1595 REMARK 3 S TENSOR REMARK 3 S11: 0.0721 S12: -0.6893 S13: 0.4712 REMARK 3 S21: 0.0872 S22: 0.2210 S23: -0.3700 REMARK 3 S31: -0.4177 S32: 0.3700 S33: -0.2931 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): 30.8134 13.4567 16.8111 REMARK 3 T TENSOR REMARK 3 T11: -0.0869 T22: -0.0233 REMARK 3 T33: -0.1736 T12: 0.0027 REMARK 3 T13: -0.0130 T23: -0.0603 REMARK 3 L TENSOR REMARK 3 L11: 7.6901 L22: 11.5189 REMARK 3 L33: 7.3265 L12: 3.8542 REMARK 3 L13: -2.4301 L23: -1.0011 REMARK 3 S TENSOR REMARK 3 S11: -0.1210 S12: -0.2383 S13: 0.0994 REMARK 3 S21: 1.0916 S22: 0.1226 S23: -0.0627 REMARK 3 S31: -0.2533 S32: -0.4743 S33: -0.0016 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): 16.8601 13.4824 -4.6474 REMARK 3 T TENSOR REMARK 3 T11: -0.1325 T22: -0.0975 REMARK 3 T33: -0.1273 T12: 0.0350 REMARK 3 T13: 0.0058 T23: 0.0264 REMARK 3 L TENSOR REMARK 3 L11: 1.8079 L22: 1.8802 REMARK 3 L33: 2.3037 L12: -0.1507 REMARK 3 L13: 0.0255 L23: 0.2718 REMARK 3 S TENSOR REMARK 3 S11: 0.0601 S12: 0.1767 S13: 0.1901 REMARK 3 S21: -0.1291 S22: -0.0845 S23: 0.2451 REMARK 3 S31: -0.0659 S32: -0.2115 S33: 0.0244 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): 16.3579 8.9659 11.2852 REMARK 3 T TENSOR REMARK 3 T11: 0.0964 T22: 0.0696 REMARK 3 T33: 0.0530 T12: -0.0826 REMARK 3 T13: 0.0997 T23: 0.0021 REMARK 3 L TENSOR REMARK 3 L11: 1.0205 L22: 11.0071 REMARK 3 L33: 2.1549 L12: -2.9284 REMARK 3 L13: 1.1459 L23: -1.7844 REMARK 3 S TENSOR REMARK 3 S11: 0.2743 S12: -1.3125 S13: -0.8471 REMARK 3 S21: 0.5872 S22: -0.1992 S23: 0.4602 REMARK 3 S31: 0.5134 S32: -1.9609 S33: -0.0752 REMARK 3 REMARK 3 TLS GROUP : 6 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 301 A 301 REMARK 3 ORIGIN FOR THE GROUP (A): 31.8450 24.8797 13.5849 REMARK 3 T TENSOR REMARK 3 T11: 0.0128 T22: 0.0266 REMARK 3 T33: -0.0026 T12: -0.1322 REMARK 3 T13: 0.0708 T23: 0.0215 REMARK 3 L TENSOR REMARK 3 L11: 132.9807 L22: 283.6825 REMARK 3 L33: 51.5262 L12: 102.8696 REMARK 3 L13: 80.2875 L23: 37.1476 REMARK 3 S TENSOR REMARK 3 S11: 3.3996 S12: 1.5878 S13: 2.8151 REMARK 3 S21: 1.4423 S22: -1.7664 S23: -2.0755 REMARK 3 S31: 0.0152 S32: 3.5250 S33: -1.6332 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 2I2A 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_1000039046. 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 : 15714 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.100 REMARK 200 RESOLUTION RANGE LOW (A) : 37.370 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 96.4 REMARK 200 DATA REDUNDANCY : 5.900 REMARK 200 R MERGE (I) : 0.07700 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 (%) : 91.3 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: MIR REMARK 200 SOFTWARE USED: MOLREP REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 47.74 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.35 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.3 M POTASSIUM CHLORIDE, 50 MM TRI REMARK 280 -SODIUM CITRATE DIHYDRATE, 15-20% W/V POLYETHYLENE GLYCOL 400, 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 30.95100 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 38.71450 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 58.89850 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 30.95100 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 38.71450 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 58.89850 REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 30.95100 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 38.71450 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 58.89850 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 30.95100 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 38.71450 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 58.89850 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1 REMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN REMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON REMARK 300 BURIED SURFACE AREA. REMARK 350 REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS REMARK 350 GIVEN BELOW. BOTH NON-CRYSTALLOGRAPHIC AND REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN. REMARK 350 REMARK 350 BIOMOLECULE: 1 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: TETRAMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TETRAMERIC REMARK 350 SOFTWARE USED: PISA,PQS REMARK 350 TOTAL BURIED SURFACE AREA: 13020 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 40100 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -49.0 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 61.90200 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 61.90200 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 336 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 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 LEU A 15 CG CD1 CD2 REMARK 470 HIS A 71 CG ND1 CD2 CE1 NE2 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 ILE A 111 CG1 CG2 CD1 REMARK 470 LYS A 113 CB CG CD CE NZ REMARK 470 LYS A 114 CG CD CE NZ REMARK 470 ARG A 193 CG CD NE CZ NH1 NH2 REMARK 470 GLN A 232 CG CD OE1 NE2 REMARK 470 ARG A 249 CG CD NE CZ NH1 NH2 REMARK 470 ASP A 264 CG OD1 OD2 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 HOH A 391 O HOH A 397 2.09 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND ANGLES REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 ASP A 28 CB - CG - OD2 ANGL. DEV. = 5.5 DEGREES REMARK 500 ASP A 60 CB - CG - OD2 ANGL. DEV. = 5.5 DEGREES REMARK 500 ASP A 214 CB - CG - OD2 ANGL. DEV. = 6.8 DEGREES REMARK 500 ASP A 222 CB - CG - OD2 ANGL. DEV. = 5.5 DEGREES REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: TORSION ANGLES REMARK 500 REMARK 500 TORSION ANGLES OUTSIDE THE EXPECTED RAMACHANDRAN REGIONS: REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT:(10X,I3,1X,A3,1X,A1,I4,A1,4X,F7.2,3X,F7.2) REMARK 500 REMARK 500 EXPECTED VALUES: GJ KLEYWEGT AND TA JONES (1996). PHI/PSI- REMARK 500 CHOLOGY: RAMACHANDRAN REVISITED. STRUCTURE 4, 1395 - 1400 REMARK 500 REMARK 500 M RES CSSEQI PSI PHI REMARK 500 TYR A 27 -167.43 -127.79 REMARK 500 MET A 29 93.12 85.15 REMARK 500 LEU A 72 81.95 39.95 REMARK 500 ASP A 77 -23.68 102.72 REMARK 500 GLU A 94 66.30 -104.24 REMARK 500 LYS A 113 121.99 -19.07 REMARK 500 LYS A 114 63.58 73.90 REMARK 500 ASN A 122 -71.47 -96.93 REMARK 500 ASP A 141 -10.06 77.27 REMARK 500 ALA A 162 -130.99 -109.48 REMARK 500 HIS A 204 -12.57 73.73 REMARK 500 ASN A 213 -96.85 -115.89 REMARK 500 ASP A 214 88.67 32.04 REMARK 500 ASP A 222 -123.39 55.56 REMARK 500 PHE A 248 -78.78 121.52 REMARK 500 ILE A 262 -60.27 -93.84 REMARK 500 GLU A 263 165.97 173.16 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 HIS A 71 LEU A 72 72.62 REMARK 500 ASN A 213 ASP A 214 79.52 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 NAP A 273 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 301 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2I1W RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF NAD KINASE 1 FROM LISTERIA MONOCYTOGENES REMARK 900 RELATED ID: 2I29 RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF NAD KINASE 1 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 2I2A A 1 264 UNP Q8Y8D7 PPNK1_LISMO 1 264 SEQADV 2I2A LEU A 265 UNP Q8Y8D7 CLONING ARTIFACT SEQADV 2I2A GLU A 266 UNP Q8Y8D7 CLONING ARTIFACT SEQADV 2I2A HIS A 267 UNP Q8Y8D7 EXPRESSION TAG SEQADV 2I2A HIS A 268 UNP Q8Y8D7 EXPRESSION TAG SEQADV 2I2A HIS A 269 UNP Q8Y8D7 EXPRESSION TAG SEQADV 2I2A HIS A 270 UNP Q8Y8D7 EXPRESSION TAG SEQADV 2I2A HIS A 271 UNP Q8Y8D7 EXPRESSION TAG SEQADV 2I2A 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 NAP A 273 48 HET GOL A 301 6 HETNAM NAP NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE HETNAM GOL GLYCEROL HETSYN NAP 2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 2 NAP C21 H28 N7 O17 P3 FORMUL 3 GOL C3 H8 O3 FORMUL 4 HOH *123(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 ARG A 58 ILE A 62 5 5 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 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 TYR A 109 -1 N THR A 105 O TYR A 118 SHEET 3 B 6 VAL A 231 ARG A 247 -1 O GLU A 237 N LYS A 104 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 SER A 155 O GLN A 180 SHEET 4 C 6 GLU A 123 SER A 128 -1 N SER A 124 O MET A 154 SHEET 5 C 6 PHE A 217 VAL A 221 -1 O GLN A 218 N LYS A 127 SHEET 6 C 6 LEU A 224 HIS A 228 -1 O HIS A 228 N PHE A 217 CISPEP 1 ASP A 28 MET A 29 0 -21.27 CISPEP 2 ALA A 76 ASP A 77 0 7.49 CISPEP 3 ILE A 111 GLY A 112 0 11.18 CISPEP 4 LYS A 113 LYS A 114 0 24.72 CISPEP 5 GLY A 130 GLY A 131 0 -14.90 CISPEP 6 ARG A 247 PHE A 248 0 -13.74 SITE 1 AC1 19 GLY A 44 ASP A 45 GLY A 46 PHE A 74 SITE 2 AC1 19 TYR A 75 ASN A 122 GLU A 123 ASP A 150 SITE 3 AC1 19 SER A 158 THR A 161 ALA A 162 TYR A 163 SITE 4 AC1 19 SER A 166 ALA A 185 ILE A 187 HIS A 223 SITE 5 AC1 19 HOH A 326 HOH A 389 HOH A 421 SITE 1 AC2 7 HIS A 173 HIS A 205 PRO A 252 PHE A 253 SITE 2 AC2 7 HOH A 391 HOH A 392 HOH A 397 CRYST1 61.902 77.429 117.797 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 0.016155 0.000000 0.000000 0.00000 SCALE2 0.000000 0.012915 0.000000 0.00000 SCALE3 0.000000 0.000000 0.008489 0.00000