HEADER TRANSFERASE 01-JUN-07 2Q5F 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: POLY(P)/ATP NAD KINASE 1; COMPND 5 EC: 2.7.1.23; COMPND 6 ENGINEERED: YES; COMPND 7 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: LISTERIA MONOCYTOGENES EGD-E; SOURCE 3 ORGANISM_TAXID: 169963; SOURCE 4 STRAIN: EGD-E; SOURCE 5 GENE: PPNK1; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PET22B KEYWDS MUTANT, TRANSFERASE EXPDTA X-RAY DIFFRACTION AUTHOR G.PONCET-MONTANGE,L.ASSAIRI,S.AROLD,S.POCHET,G.LABESSE REVDAT 7 03-APR-24 2Q5F 1 REMARK REVDAT 6 21-FEB-24 2Q5F 1 REMARK REVDAT 5 20-OCT-21 2Q5F 1 REMARK SEQADV REVDAT 4 13-JUL-11 2Q5F 1 VERSN REVDAT 3 24-FEB-09 2Q5F 1 VERSN REVDAT 2 04-NOV-08 2Q5F 1 JRNL REVDAT 1 07-AUG-07 2Q5F 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. 1.90 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.2.0019 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) : 1.90 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 28.20 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 87.2 REMARK 3 NUMBER OF REFLECTIONS : 19066 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) : 0.189 REMARK 3 R VALUE (WORKING SET) : 0.188 REMARK 3 FREE R VALUE : 0.222 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 3.000 REMARK 3 FREE R VALUE TEST SET COUNT : 589 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) : 1.90 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.95 REMARK 3 REFLECTION IN BIN (WORKING SET) : 727 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 45.77 REMARK 3 BIN R VALUE (WORKING SET) : 0.2860 REMARK 3 BIN FREE R VALUE SET COUNT : 14 REMARK 3 BIN FREE R VALUE : 0.2640 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2056 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 38 REMARK 3 SOLVENT ATOMS : 84 REMARK 3 REMARK 3 B VALUES. REMARK 3 B VALUE TYPE : LIKELY RESIDUAL REMARK 3 FROM WILSON PLOT (A**2) : 29.25 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 27.83 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.50000 REMARK 3 B22 (A**2) : 2.42000 REMARK 3 B33 (A**2) : -1.92000 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): 0.175 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.152 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.106 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 8.046 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.956 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.950 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 2178 ; 0.010 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): 1473 ; 0.008 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 2953 ; 1.430 ; 1.976 REMARK 3 BOND ANGLES OTHERS (DEGREES): 3552 ; 1.615 ; 3.001 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 262 ;21.375 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 101 ;31.533 ;23.069 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 364 ;17.385 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 15 ;25.401 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 322 ; 0.089 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2398 ; 0.005 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 465 ; 0.003 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 346 ; 0.217 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): 1443 ; 0.212 ; 0.200 REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 1001 ; 0.178 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): 1150 ; 0.098 ; 0.200 REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 86 ; 0.118 ; 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): 7 ; 0.160 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): 29 ; 0.292 ; 0.200 REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 8 ; 0.185 ; 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): 1417 ; 0.692 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 527 ; 0.091 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 2089 ; 0.847 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 987 ; 1.431 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 861 ; 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 69 REMARK 3 ORIGIN FOR THE GROUP (A): 10.1460 24.2140 22.2950 REMARK 3 T TENSOR REMARK 3 T11: 0.0168 T22: 0.0683 REMARK 3 T33: -0.0514 T12: 0.0355 REMARK 3 T13: 0.0457 T23: -0.0785 REMARK 3 L TENSOR REMARK 3 L11: 2.5996 L22: 1.3343 REMARK 3 L33: 7.4694 L12: -1.1784 REMARK 3 L13: -1.6532 L23: 1.5523 REMARK 3 S TENSOR REMARK 3 S11: -0.0929 S12: -0.1530 S13: 0.0534 REMARK 3 S21: 0.1295 S22: 0.0047 S23: 0.0962 REMARK 3 S31: -0.2181 S32: -0.3511 S33: 0.0882 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 74 A 97 REMARK 3 RESIDUE RANGE : A 245 A 251 REMARK 3 ORIGIN FOR THE GROUP (A): 22.0380 25.4820 24.6440 REMARK 3 T TENSOR REMARK 3 T11: 0.2443 T22: 0.2732 REMARK 3 T33: 0.0760 T12: 0.0534 REMARK 3 T13: 0.0520 T23: -0.1354 REMARK 3 L TENSOR REMARK 3 L11: 1.7488 L22: 0.0614 REMARK 3 L33: 2.8583 L12: 0.0024 REMARK 3 L13: -0.2514 L23: -0.4165 REMARK 3 S TENSOR REMARK 3 S11: -0.0676 S12: -0.5912 S13: 0.2902 REMARK 3 S21: 0.1822 S22: 0.4443 S23: -0.1162 REMARK 3 S31: -0.1903 S32: 0.5217 S33: -0.3767 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): 31.3520 14.3330 16.4620 REMARK 3 T TENSOR REMARK 3 T11: -0.0495 T22: -0.0339 REMARK 3 T33: -0.1849 T12: -0.0389 REMARK 3 T13: 0.0174 T23: -0.0544 REMARK 3 L TENSOR REMARK 3 L11: 4.2077 L22: 13.7472 REMARK 3 L33: 6.3528 L12: 1.8073 REMARK 3 L13: 0.1448 L23: -2.8495 REMARK 3 S TENSOR REMARK 3 S11: 0.0803 S12: -0.3866 S13: 0.2577 REMARK 3 S21: 0.6417 S22: -0.0827 S23: 0.0884 REMARK 3 S31: -0.1336 S32: 0.0823 S33: 0.0024 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): 17.9020 13.2320 -4.4760 REMARK 3 T TENSOR REMARK 3 T11: -0.1394 T22: -0.0550 REMARK 3 T33: -0.1247 T12: 0.0380 REMARK 3 T13: -0.0096 T23: -0.0140 REMARK 3 L TENSOR REMARK 3 L11: 1.2700 L22: 1.8847 REMARK 3 L33: 2.8323 L12: -0.2196 REMARK 3 L13: 0.1639 L23: 0.2730 REMARK 3 S TENSOR REMARK 3 S11: 0.0735 S12: 0.0490 S13: 0.0661 REMARK 3 S21: -0.1479 S22: -0.1393 S23: 0.2741 REMARK 3 S31: -0.0947 S32: -0.3948 S33: 0.0657 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): 17.7140 8.8760 11.1630 REMARK 3 T TENSOR REMARK 3 T11: 0.1584 T22: 0.1652 REMARK 3 T33: 0.0207 T12: -0.0037 REMARK 3 T13: 0.0746 T23: 0.0436 REMARK 3 L TENSOR REMARK 3 L11: 0.0715 L22: 18.2648 REMARK 3 L33: 17.8523 L12: -1.1430 REMARK 3 L13: -1.1300 L23: 18.0573 REMARK 3 S TENSOR REMARK 3 S11: -0.2015 S12: -0.8526 S13: -0.6478 REMARK 3 S21: 1.9650 S22: -0.6087 S23: 0.5042 REMARK 3 S31: 1.3913 S32: -0.2618 S33: 0.8102 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 357 REMARK 3 ORIGIN FOR THE GROUP (A): 19.1050 14.5520 3.1790 REMARK 3 T TENSOR REMARK 3 T11: -0.0007 T22: 0.0504 REMARK 3 T33: 0.0157 T12: 0.0178 REMARK 3 T13: 0.0114 T23: -0.0042 REMARK 3 L TENSOR REMARK 3 L11: 0.1124 L22: 0.4310 REMARK 3 L33: 0.6272 L12: 0.0917 REMARK 3 L13: 0.1476 L23: 0.5073 REMARK 3 S TENSOR REMARK 3 S11: 0.0398 S12: -0.0096 S13: 0.0222 REMARK 3 S21: 0.0129 S22: 0.0047 S23: 0.0367 REMARK 3 S31: -0.0305 S32: -0.0516 S33: -0.0445 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.40 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 2Q5F COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 11-JUN-07. REMARK 100 THE DEPOSITION ID IS D_1000043171. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 13-NOV-06 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 5.5 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) : 0.933 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 210 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 19663 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.900 REMARK 200 RESOLUTION RANGE LOW (A) : 28.200 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 87.5 REMARK 200 DATA REDUNDANCY : 5.900 REMARK 200 R MERGE (I) : 0.06000 REMARK 200 R SYM (I) : 0.06300 REMARK 200 FOR THE DATA SET : 20.2000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.90 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.99 REMARK 200 COMPLETENESS FOR SHELL (%) : 51.6 REMARK 200 DATA REDUNDANCY IN SHELL : 3.90 REMARK 200 R MERGE FOR SHELL (I) : 0.48900 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.500 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: REFMAC 5.2.0019 REMARK 200 STARTING MODEL: PDB2I2C REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 45.46 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.26 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PEG400 15-20% W/V, KCITRATE 50 MM, KCL REMARK 280 300 MM, PH 5.5, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 291K 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 31.47950 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 37.54400 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 59.24500 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 31.47950 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 37.54400 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 59.24500 REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 31.47950 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 37.54400 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 59.24500 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 31.47950 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 37.54400 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 59.24500 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: 12680 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 38750 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -60.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 2 -1.000000 0.000000 0.000000 62.95900 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 62.95900 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 LYS A 114 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 35 CG CD OE1 OE2 REMARK 470 LYS A 85 CG CD CE NZ REMARK 470 GLN A 96 CG CD OE1 NE2 REMARK 470 GLN A 232 CG CD OE1 NE2 REMARK 470 GLU A 263 CG CD OE1 OE2 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND ANGLES REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 ASP A 77 N - CA - C ANGL. DEV. = 22.4 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 HIS A 71 -159.42 79.27 REMARK 500 ASN A 122 -65.62 -99.05 REMARK 500 SER A 129 20.85 -52.13 REMARK 500 ALA A 162 -129.00 -101.85 REMARK 500 HIS A 204 -5.75 77.58 REMARK 500 ASN A 213 -79.42 -118.48 REMARK 500 ASP A 222 -123.61 52.00 REMARK 500 ILE A 226 102.23 -175.67 REMARK 500 GLU A 263 145.67 -174.71 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 GLY A 70 HIS A 71 35.18 REMARK 500 ALA A 76 ASP A 77 121.91 REMARK 500 SER A 128 SER A 129 133.43 REMARK 500 PRO A 132 PHE A 133 144.42 REMARK 500 VAL A 191 TYR A 192 -141.53 REMARK 500 SER A 225 ILE A 226 -119.22 REMARK 500 ARG A 247 PHE A 248 -143.34 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 DTA A 273 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2I2C RELATED DB: PDB REMARK 900 WILDE-TYPE ENZYME DBREF 2Q5F A 1 264 UNP Q8Y8D7 PPNK1_LISMO 1 264 SEQADV 2Q5F GLU A 223 UNP Q8Y8D7 HIS 223 ENGINEERED MUTATION SEQADV 2Q5F LEU A 265 UNP Q8Y8D7 CLONING ARTIFACT SEQADV 2Q5F GLU A 266 UNP Q8Y8D7 CLONING ARTIFACT SEQADV 2Q5F HIS A 267 UNP Q8Y8D7 CLONING ARTIFACT SEQADV 2Q5F HIS A 268 UNP Q8Y8D7 CLONING ARTIFACT SEQADV 2Q5F HIS A 269 UNP Q8Y8D7 CLONING ARTIFACT SEQADV 2Q5F HIS A 270 UNP Q8Y8D7 CLONING ARTIFACT SEQADV 2Q5F HIS A 271 UNP Q8Y8D7 CLONING ARTIFACT SEQADV 2Q5F HIS A 272 UNP Q8Y8D7 CLONING ARTIFACT 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 GLU 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 DTA A 273 38 HETNAM DTA (2S,3S,4R,5R,2'S,3'S,4'R,5'R)-2,2'- HETNAM 2 DTA [DITHIOBIS(METHYLENE)]BIS[5-(6-AMINO-9H-PURIN-9-YL) HETNAM 3 DTA TETRAHYDROFURAN-3,4-DIOL] HETSYN DTA DI-(5'-THIOADENOSINE) FORMUL 2 DTA C20 H24 N10 O6 S2 FORMUL 3 HOH *84(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 ILE A 62 5 7 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 LEU A 209 O ILE A 234 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 SITE 1 AC1 16 ASP A 45 PHE A 74 TYR A 75 ASN A 122 SITE 2 AC1 16 GLU A 123 ASP A 150 SER A 158 THR A 161 SITE 3 AC1 16 ALA A 162 TYR A 163 SER A 166 ALA A 185 SITE 4 AC1 16 ILE A 187 HOH A 303 HOH A 317 HOH A 324 CRYST1 62.959 75.088 118.490 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 0.015883 0.000000 0.000000 0.00000 SCALE2 0.000000 0.013318 0.000000 0.00000 SCALE3 0.000000 0.000000 0.008440 0.00000