HEADER TRANSFERASE 16-APR-19 6RG7 TITLE CRYSTAL STRUCTURE OF NAD KINASE 1 FROM LISTERIA MONOCYTOGENES IN TITLE 2 COMPLEXE WITH AN INHIBITOR COMPND MOL_ID: 1; COMPND 2 MOLECULE: NAD KINASE 1; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: ATP-DEPENDENT NAD KINASE; COMPND 5 EC: 2.7.1.23; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: LISTERIA MONOCYTOGENES EGD-E; SOURCE 3 ORGANISM_TAXID: 169963; SOURCE 4 GENE: NADK1, LMO0968; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS TETRAMERIC NAD KINASE, TRANSFERASE EXPDTA X-RAY DIFFRACTION AUTHOR M.GELIN,G.LABESSE REVDAT 3 15-MAY-24 6RG7 1 REMARK REVDAT 2 25-MAR-20 6RG7 1 JRNL REVDAT 1 19-FEB-20 6RG7 0 JRNL AUTH M.GELIN,J.PAOLETTI,M.A.NAHORI,V.HUTEAU,C.LESEIGNEUR, JRNL AUTH 2 G.JOUVION,L.DUGUE,D.CLEMENT,J.L.PONS,L.ASSAIRI,S.POCHET, JRNL AUTH 3 G.LABESSE,O.DUSSURGET JRNL TITL FROM SUBSTRATE TO FRAGMENTS TO INHIBITOR ACTIVEIN JRNL TITL 2 VIVOAGAINSTSTAPHYLOCOCCUS AUREUS. JRNL REF ACS INFECT DIS. V. 6 422 2020 JRNL REFN ESSN 2373-8227 JRNL PMID 32017533 JRNL DOI 10.1021/ACSINFECDIS.9B00368 REMARK 2 REMARK 2 RESOLUTION. 2.08 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.13_2998 REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VINCENT CHEN,IAN REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE-KUNSTLEVE, REMARK 3 : LI-WEI HUNG,ROBERT IMMORMINO,TOM IOERGER, REMARK 3 : AIRLIE MCCOY,ERIK MCKEE,NIGEL MORIARTY, REMARK 3 : REETAL PAI,RANDY READ,JANE RICHARDSON, REMARK 3 : DAVID RICHARDSON,TOD ROMO,JIM SACCHETTINI, REMARK 3 : NICHOLAS SAUTER,JACOB SMITH,LAURENT REMARK 3 : STORONI,TOM TERWILLIGER,PETER ZWART REMARK 3 REMARK 3 REFINEMENT TARGET : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.08 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 34.94 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.330 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.3 REMARK 3 NUMBER OF REFLECTIONS : 17064 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.206 REMARK 3 R VALUE (WORKING SET) : 0.205 REMARK 3 FREE R VALUE : 0.228 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.080 REMARK 3 FREE R VALUE TEST SET COUNT : 867 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (IN BINS). REMARK 3 BIN RESOLUTION RANGE COMPL. NWORK NFREE RWORK RFREE REMARK 3 1 34.9436 - 3.7783 0.99 2845 149 0.1683 0.1718 REMARK 3 2 3.7783 - 2.9995 1.00 2733 153 0.1910 0.2293 REMARK 3 3 2.9995 - 2.6205 1.00 2723 147 0.2336 0.2675 REMARK 3 4 2.6205 - 2.3810 1.00 2706 155 0.2313 0.2717 REMARK 3 5 2.3810 - 2.2103 0.99 2684 130 0.3021 0.3555 REMARK 3 6 2.2103 - 2.0800 0.93 2506 133 0.2943 0.3216 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : NULL REMARK 3 SOLVENT RADIUS : 1.11 REMARK 3 SHRINKAGE RADIUS : 0.90 REMARK 3 K_SOL : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.260 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 27.980 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 33.91 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 45.77 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : NULL REMARK 3 B22 (A**2) : NULL REMARK 3 B33 (A**2) : NULL REMARK 3 B12 (A**2) : NULL REMARK 3 B13 (A**2) : NULL REMARK 3 B23 (A**2) : NULL REMARK 3 REMARK 3 TWINNING INFORMATION. REMARK 3 FRACTION: NULL REMARK 3 OPERATOR: NULL REMARK 3 REMARK 3 DEVIATIONS FROM IDEAL VALUES. REMARK 3 RMSD COUNT REMARK 3 BOND : NULL NULL REMARK 3 ANGLE : NULL NULL REMARK 3 CHIRALITY : NULL NULL REMARK 3 PLANARITY : NULL NULL REMARK 3 DIHEDRAL : NULL NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 9 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 1 THROUGH 26 ) REMARK 3 ORIGIN FOR THE GROUP (A): 9.0021 22.9046 28.4988 REMARK 3 T TENSOR REMARK 3 T11: 0.4797 T22: 0.6179 REMARK 3 T33: 0.3964 T12: 0.1251 REMARK 3 T13: 0.0437 T23: -0.1574 REMARK 3 L TENSOR REMARK 3 L11: 2.9734 L22: 3.0782 REMARK 3 L33: 5.0411 L12: -1.0646 REMARK 3 L13: -1.0047 L23: 1.1649 REMARK 3 S TENSOR REMARK 3 S11: -0.1605 S12: -0.6914 S13: 0.0519 REMARK 3 S21: 0.0406 S22: 0.0243 S23: 0.3616 REMARK 3 S31: -0.0616 S32: -0.3658 S33: 0.1636 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 27 THROUGH 79 ) REMARK 3 ORIGIN FOR THE GROUP (A): 13.0608 23.9451 18.6594 REMARK 3 T TENSOR REMARK 3 T11: 0.4374 T22: 0.4254 REMARK 3 T33: 0.3777 T12: 0.0825 REMARK 3 T13: 0.0433 T23: -0.1121 REMARK 3 L TENSOR REMARK 3 L11: 2.5429 L22: 2.1157 REMARK 3 L33: 4.4737 L12: -0.6550 REMARK 3 L13: -1.8541 L23: 1.8501 REMARK 3 S TENSOR REMARK 3 S11: -0.0449 S12: -0.2257 S13: 0.3233 REMARK 3 S21: 0.0994 S22: -0.1241 S23: 0.1807 REMARK 3 S31: -0.3403 S32: -0.3931 S33: 0.0403 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 80 THROUGH 120 ) REMARK 3 ORIGIN FOR THE GROUP (A): 16.0688 25.1900 12.0264 REMARK 3 T TENSOR REMARK 3 T11: 0.3969 T22: 0.3641 REMARK 3 T33: 0.4598 T12: 0.1626 REMARK 3 T13: 0.0236 T23: -0.0255 REMARK 3 L TENSOR REMARK 3 L11: 1.8108 L22: 1.9063 REMARK 3 L33: 4.8007 L12: -0.1490 REMARK 3 L13: -0.9947 L23: 0.9974 REMARK 3 S TENSOR REMARK 3 S11: 0.0349 S12: -0.0799 S13: 0.4875 REMARK 3 S21: 0.0545 S22: 0.0471 S23: 0.1495 REMARK 3 S31: -0.8181 S32: -0.1334 S33: 0.0727 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 121 THROUGH 141 ) REMARK 3 ORIGIN FOR THE GROUP (A): 15.2973 10.1412 -7.2709 REMARK 3 T TENSOR REMARK 3 T11: 0.2632 T22: 0.3330 REMARK 3 T33: 0.3290 T12: 0.0052 REMARK 3 T13: -0.0285 T23: -0.0069 REMARK 3 L TENSOR REMARK 3 L11: 2.2585 L22: 2.1953 REMARK 3 L33: 6.2125 L12: -0.9744 REMARK 3 L13: -0.7755 L23: 1.9137 REMARK 3 S TENSOR REMARK 3 S11: 0.0444 S12: 0.1237 S13: -0.1213 REMARK 3 S21: 0.0324 S22: -0.1629 S23: 0.3604 REMARK 3 S31: 0.3162 S32: -0.5386 S33: 0.2181 REMARK 3 TLS GROUP : 5 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 142 THROUGH 184 ) REMARK 3 ORIGIN FOR THE GROUP (A): 23.3120 11.8141 -2.0296 REMARK 3 T TENSOR REMARK 3 T11: 0.1814 T22: 0.1953 REMARK 3 T33: 0.1896 T12: 0.0152 REMARK 3 T13: 0.0046 T23: 0.0016 REMARK 3 L TENSOR REMARK 3 L11: 1.5845 L22: 1.6579 REMARK 3 L33: 4.2399 L12: -0.3528 REMARK 3 L13: -0.0902 L23: 1.0717 REMARK 3 S TENSOR REMARK 3 S11: 0.0325 S12: 0.1298 S13: 0.1494 REMARK 3 S21: -0.1575 S22: 0.0555 S23: 0.1158 REMARK 3 S31: -0.2688 S32: -0.1221 S33: 0.0257 REMARK 3 TLS GROUP : 6 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 185 THROUGH 198 ) REMARK 3 ORIGIN FOR THE GROUP (A): 25.2946 1.4952 -12.5043 REMARK 3 T TENSOR REMARK 3 T11: 0.5252 T22: 0.5130 REMARK 3 T33: 0.2931 T12: 0.0354 REMARK 3 T13: -0.0265 T23: -0.0309 REMARK 3 L TENSOR REMARK 3 L11: 4.7751 L22: 3.8410 REMARK 3 L33: 2.9237 L12: 0.5379 REMARK 3 L13: -0.2841 L23: -1.6589 REMARK 3 S TENSOR REMARK 3 S11: -0.1679 S12: 0.8315 S13: -0.2296 REMARK 3 S21: -0.8775 S22: 0.0990 S23: 0.0762 REMARK 3 S31: 0.6117 S32: -0.2737 S33: -0.0939 REMARK 3 TLS GROUP : 7 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 199 THROUGH 216 ) REMARK 3 ORIGIN FOR THE GROUP (A): 17.5248 15.6935 -10.2648 REMARK 3 T TENSOR REMARK 3 T11: 0.3430 T22: 0.4226 REMARK 3 T33: 0.3605 T12: 0.1012 REMARK 3 T13: -0.0424 T23: 0.0758 REMARK 3 L TENSOR REMARK 3 L11: 3.2133 L22: 2.8356 REMARK 3 L33: 4.2876 L12: -0.4370 REMARK 3 L13: 0.4323 L23: -0.0144 REMARK 3 S TENSOR REMARK 3 S11: 0.0971 S12: 0.5018 S13: 0.1204 REMARK 3 S21: -0.0117 S22: 0.0223 S23: 0.5460 REMARK 3 S31: -0.1666 S32: -0.4386 S33: 0.1086 REMARK 3 TLS GROUP : 8 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 217 THROUGH 252 ) REMARK 3 ORIGIN FOR THE GROUP (A): 14.4131 18.7348 3.0584 REMARK 3 T TENSOR REMARK 3 T11: 0.3091 T22: 0.4041 REMARK 3 T33: 0.4157 T12: 0.1293 REMARK 3 T13: 0.0386 T23: -0.0408 REMARK 3 L TENSOR REMARK 3 L11: 2.2655 L22: 2.6785 REMARK 3 L33: 4.0597 L12: -0.1250 REMARK 3 L13: 0.5981 L23: 0.3386 REMARK 3 S TENSOR REMARK 3 S11: 0.0048 S12: -0.1121 S13: 0.2437 REMARK 3 S21: -0.0451 S22: -0.1454 S23: 0.5569 REMARK 3 S31: -0.4472 S32: -0.7475 S33: 0.1578 REMARK 3 TLS GROUP : 9 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 253 THROUGH 264 ) REMARK 3 ORIGIN FOR THE GROUP (A): 31.5367 12.7254 17.6089 REMARK 3 T TENSOR REMARK 3 T11: 0.3771 T22: 0.3477 REMARK 3 T33: 0.2676 T12: 0.0403 REMARK 3 T13: 0.0063 T23: -0.0401 REMARK 3 L TENSOR REMARK 3 L11: 6.0134 L22: 7.3902 REMARK 3 L33: 4.5144 L12: -0.1169 REMARK 3 L13: 0.6210 L23: 1.4464 REMARK 3 S TENSOR REMARK 3 S11: -0.2988 S12: -1.0494 S13: -0.0534 REMARK 3 S21: 1.1285 S22: 0.2067 S23: -0.7777 REMARK 3 S31: 0.2832 S32: 0.1083 S33: -0.0456 REMARK 3 REMARK 3 NCS DETAILS REMARK 3 NUMBER OF NCS GROUPS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 6RG7 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 16-APR-19. REMARK 100 THE DEPOSITION ID IS D_1292101861. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 11-DEC-12 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 5.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ESRF REMARK 200 BEAMLINE : ID14-4 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.979288 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315R REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM REMARK 200 DATA SCALING SOFTWARE : AIMLESS 0.7.1 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 17163 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.080 REMARK 200 RESOLUTION RANGE LOW (A) : 34.940 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.0 REMARK 200 DATA REDUNDANCY : 6.700 REMARK 200 R MERGE (I) : 0.06500 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 15.2000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.08 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.14 REMARK 200 COMPLETENESS FOR SHELL (%) : 91.3 REMARK 200 DATA REDUNDANCY IN SHELL : 4.30 REMARK 200 R MERGE FOR SHELL (I) : 0.44200 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: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHENIX REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 45.75 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.27 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 30 MM NABR, 220 MM KCITRATE, GLYCEROL REMARK 280 6%, 15-16% W/V PEG400, PH 5.0, EVAPORATION, TEMPERATURE 291.15K 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 31.47400 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 37.85650 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 59.07400 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 31.47400 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 37.85650 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 59.07400 REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 31.47400 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 37.85650 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 59.07400 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 31.47400 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 37.85650 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 59.07400 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 APPLY THE FOLLOWING TO CHAINS: A REMARK 350 BIOMT1 2 -1.000000 0.000000 0.000000 62.94800 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 APPLY THE FOLLOWING TO CHAINS: A REMARK 350 BIOMT1 3 -1.000000 0.000000 0.000000 62.94800 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 APPLY THE FOLLOWING TO CHAINS: A 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 412 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 484 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 93 REMARK 465 GLU A 94 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 11 CG CD OE1 OE2 REMARK 470 LYS A 85 CG CD CE NZ REMARK 470 LYS A 92 CG CD CE NZ REMARK 470 ARG A 190 CB CG CD NE CZ NH1 NH2 REMARK 470 GLN A 232 CG CD OE1 NE2 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: 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 ASN A 122 -70.71 -97.81 REMARK 500 ALA A 162 -125.57 -110.94 REMARK 500 VAL A 191 -78.10 -113.22 REMARK 500 HIS A 204 -9.36 76.54 REMARK 500 ASN A 213 -70.78 -129.34 REMARK 500 ASP A 222 -124.11 56.26 REMARK 500 ILE A 262 -60.48 -95.97 REMARK 500 GLU A 263 157.69 176.79 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 CIT A 301 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue K2H A 302 DBREF 6RG7 A 1 264 UNP Q8Y8D7 NADK1_LISMO 1 264 SEQADV 6RG7 LEU A 265 UNP Q8Y8D7 EXPRESSION TAG SEQADV 6RG7 GLU A 266 UNP Q8Y8D7 EXPRESSION TAG SEQADV 6RG7 HIS A 267 UNP Q8Y8D7 EXPRESSION TAG SEQADV 6RG7 HIS A 268 UNP Q8Y8D7 EXPRESSION TAG SEQADV 6RG7 HIS A 269 UNP Q8Y8D7 EXPRESSION TAG SEQADV 6RG7 HIS A 270 UNP Q8Y8D7 EXPRESSION TAG SEQADV 6RG7 HIS A 271 UNP Q8Y8D7 EXPRESSION TAG SEQADV 6RG7 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 CIT A 301 13 HET K2H A 302 33 HETNAM CIT CITRIC ACID HETNAM K2H (2~{R},3~{R},4~{S},5~{R})-2-(6-AMINOPURIN-9-YL)-5-[[3- HETNAM 2 K2H (6-AZANYL-9~{H}-PURIN-8-YL)PROP-2-YNYL-METHYL- HETNAM 3 K2H AMINO]METHYL]OXOLANE-3,4-DIOL FORMUL 2 CIT C6 H8 O7 FORMUL 3 K2H C19 H21 N11 O3 FORMUL 4 HOH *88(H2 O) HELIX 1 AA1 ASP A 10 GLU A 26 1 17 HELIX 2 AA2 GLY A 44 TYR A 55 1 12 HELIX 3 AA3 GLU A 56 ILE A 62 5 7 HELIX 4 AA4 ARG A 79 ALA A 81 5 3 HELIX 5 AA5 GLU A 82 LYS A 92 1 11 HELIX 6 AA6 PRO A 157 THR A 161 5 5 HELIX 7 AA7 ALA A 162 LEU A 167 1 6 HELIX 8 AA8 PRO A 252 ILE A 262 1 11 SHEET 1 AA1 5 GLU A 30 TYR A 31 0 SHEET 2 AA1 5 LYS A 2 SER A 7 1 N TYR A 3 O GLU A 30 SHEET 3 AA1 5 ILE A 38 GLY A 43 1 O ILE A 40 N THR A 6 SHEET 4 AA1 5 ALA A 63 HIS A 68 1 O ILE A 67 N SER A 41 SHEET 5 AA1 5 ALA A 76 TRP A 78 1 O TRP A 78 N HIS A 68 SHEET 1 AA2 6 ALA A 116 ALA A 120 0 SHEET 2 AA2 6 GLN A 96 LYS A 108 -1 N VAL A 107 O ALA A 116 SHEET 3 AA2 6 GLU A 233 ARG A 247 -1 O PHE A 245 N VAL A 98 SHEET 4 AA2 6 VAL A 207 PRO A 211 -1 N LEU A 209 O ILE A 234 SHEET 5 AA2 6 PHE A 133 ILE A 139 -1 N VAL A 138 O SER A 208 SHEET 6 AA2 6 ILE A 142 GLY A 149 -1 O GLU A 145 N VAL A 137 SHEET 1 AA3 6 LEU A 199 PRO A 202 0 SHEET 2 AA3 6 ALA A 178 MET A 184 -1 N MET A 179 O PHE A 201 SHEET 3 AA3 6 GLY A 151 SER A 155 -1 N SER A 155 O GLN A 180 SHEET 4 AA3 6 GLU A 123 SER A 128 -1 N SER A 124 O MET A 154 SHEET 5 AA3 6 PHE A 217 VAL A 221 -1 O GLN A 218 N LYS A 127 SHEET 6 AA3 6 LEU A 224 HIS A 228 -1 O ILE A 226 N ILE A 219 SITE 1 AC1 10 VAL A 98 TYR A 100 HIS A 173 ARG A 247 SITE 2 AC1 10 PHE A 251 PRO A 252 PHE A 253 ARG A 256 SITE 3 AC1 10 HOH A 406 HOH A 408 SITE 1 AC2 16 GLY A 46 LEU A 49 PHE A 74 TYR A 75 SITE 2 AC2 16 ASN A 122 GLU A 123 ASP A 150 SER A 158 SITE 3 AC2 16 THR A 161 ALA A 162 TYR A 163 SER A 166 SITE 4 AC2 16 ALA A 185 ILE A 187 HOH A 445 HOH A 446 CRYST1 62.948 75.713 118.148 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 0.015886 0.000000 0.000000 0.00000 SCALE2 0.000000 0.013208 0.000000 0.00000 SCALE3 0.000000 0.000000 0.008464 0.00000