HEADER TRANSFERASE 11-APR-19 6RBU TITLE CRYSTAL STRUCTURE OF NAD KINASE 1 FROM LISTERIA MONOCYTOGENES IN TITLE 2 COMPLEXE WITH AN ADENINE DERIVATIVE 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 6RBU 1 REMARK REVDAT 2 25-MAR-20 6RBU 1 JRNL REVDAT 1 19-FEB-20 6RBU 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. 1.97 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.14_3260 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) : 1.97 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 55.29 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.330 REMARK 3 COMPLETENESS FOR RANGE (%) : 95.1 REMARK 3 NUMBER OF REFLECTIONS : 19327 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.228 REMARK 3 R VALUE (WORKING SET) : 0.226 REMARK 3 FREE R VALUE : 0.263 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.020 REMARK 3 FREE R VALUE TEST SET COUNT : 970 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 55.3140 - 3.7680 0.98 2837 158 0.1722 0.2019 REMARK 3 2 3.7680 - 2.9908 0.98 2720 130 0.1996 0.2236 REMARK 3 3 2.9908 - 2.6128 0.98 2704 141 0.2516 0.2828 REMARK 3 4 2.6128 - 2.3739 0.99 2699 150 0.2522 0.3161 REMARK 3 5 2.3739 - 2.2037 0.81 2184 121 0.4304 0.4799 REMARK 3 6 2.2037 - 2.0738 0.94 2574 119 0.3013 0.3007 REMARK 3 7 2.0738 - 1.9699 0.98 2639 151 0.2833 0.3841 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) : 0.220 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 32.050 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 48.70 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 : 7 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 1 THROUGH 26 ) REMARK 3 ORIGIN FOR THE GROUP (A): 8.6926 22.6520 28.6105 REMARK 3 T TENSOR REMARK 3 T11: 0.4270 T22: 0.5306 REMARK 3 T33: 0.3344 T12: 0.1192 REMARK 3 T13: 0.0638 T23: -0.1052 REMARK 3 L TENSOR REMARK 3 L11: 3.5625 L22: 1.2118 REMARK 3 L33: 3.4149 L12: -0.7830 REMARK 3 L13: -0.4961 L23: 0.7329 REMARK 3 S TENSOR REMARK 3 S11: -0.1769 S12: -0.6640 S13: 0.0190 REMARK 3 S21: 0.0664 S22: -0.0077 S23: 0.3692 REMARK 3 S31: -0.1997 S32: -0.3109 S33: 0.0328 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 27 THROUGH 91 ) REMARK 3 ORIGIN FOR THE GROUP (A): 13.7502 24.6253 20.5934 REMARK 3 T TENSOR REMARK 3 T11: 0.4427 T22: 0.4836 REMARK 3 T33: 0.3996 T12: 0.0765 REMARK 3 T13: 0.0496 T23: -0.1281 REMARK 3 L TENSOR REMARK 3 L11: 2.8675 L22: 1.4566 REMARK 3 L33: 2.1389 L12: -0.4481 REMARK 3 L13: -1.1366 L23: 0.5962 REMARK 3 S TENSOR REMARK 3 S11: -0.0858 S12: -0.4211 S13: 0.4083 REMARK 3 S21: 0.2110 S22: 0.0960 S23: -0.0300 REMARK 3 S31: -0.1425 S32: -0.1391 S33: -0.0120 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 92 THROUGH 120 ) REMARK 3 ORIGIN FOR THE GROUP (A): 13.9775 25.2278 4.2750 REMARK 3 T TENSOR REMARK 3 T11: 0.4240 T22: 0.3959 REMARK 3 T33: 0.5052 T12: 0.0967 REMARK 3 T13: 0.0952 T23: -0.0230 REMARK 3 L TENSOR REMARK 3 L11: 1.4363 L22: 1.1581 REMARK 3 L33: 0.6416 L12: -0.2351 REMARK 3 L13: -0.8378 L23: -0.2827 REMARK 3 S TENSOR REMARK 3 S11: 0.1348 S12: -0.0321 S13: 0.8336 REMARK 3 S21: -0.0086 S22: -0.1467 S23: 0.5018 REMARK 3 S31: -0.6803 S32: -0.6769 S33: -0.0636 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 121 THROUGH 184 ) REMARK 3 ORIGIN FOR THE GROUP (A): 20.7270 11.4387 -3.7497 REMARK 3 T TENSOR REMARK 3 T11: 0.2653 T22: 0.2726 REMARK 3 T33: 0.2794 T12: 0.0179 REMARK 3 T13: 0.0180 T23: 0.0041 REMARK 3 L TENSOR REMARK 3 L11: 1.6515 L22: 0.8395 REMARK 3 L33: 2.7152 L12: -0.2045 REMARK 3 L13: -0.2449 L23: 0.4950 REMARK 3 S TENSOR REMARK 3 S11: 0.0254 S12: 0.1496 S13: 0.0381 REMARK 3 S21: -0.0248 S22: -0.0769 S23: 0.1552 REMARK 3 S31: -0.0577 S32: -0.2173 S33: 0.0498 REMARK 3 TLS GROUP : 5 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 185 THROUGH 198 ) REMARK 3 ORIGIN FOR THE GROUP (A): 25.4612 1.3015 -12.6787 REMARK 3 T TENSOR REMARK 3 T11: 0.5518 T22: 0.4003 REMARK 3 T33: 0.3167 T12: 0.0308 REMARK 3 T13: -0.0190 T23: 0.0050 REMARK 3 L TENSOR REMARK 3 L11: 1.7796 L22: 3.5954 REMARK 3 L33: 3.8500 L12: 0.6374 REMARK 3 L13: 0.3104 L23: 0.6655 REMARK 3 S TENSOR REMARK 3 S11: 0.0622 S12: 0.2862 S13: -0.3173 REMARK 3 S21: -0.7275 S22: 0.2641 S23: 0.1206 REMARK 3 S31: 0.2745 S32: -0.1921 S33: -0.0543 REMARK 3 TLS GROUP : 6 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 199 THROUGH 216 ) REMARK 3 ORIGIN FOR THE GROUP (A): 17.2444 15.3717 -10.5435 REMARK 3 T TENSOR REMARK 3 T11: 0.3688 T22: 0.3986 REMARK 3 T33: 0.3647 T12: 0.0290 REMARK 3 T13: -0.0152 T23: 0.0228 REMARK 3 L TENSOR REMARK 3 L11: 2.4628 L22: 1.2597 REMARK 3 L33: 2.2605 L12: -1.0501 REMARK 3 L13: -0.4679 L23: -1.1268 REMARK 3 S TENSOR REMARK 3 S11: 0.1835 S12: 0.3081 S13: -0.2389 REMARK 3 S21: -0.0913 S22: -0.0617 S23: 0.2615 REMARK 3 S31: 0.3100 S32: -0.6746 S33: -0.0318 REMARK 3 TLS GROUP : 7 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 217 THROUGH 264 ) REMARK 3 ORIGIN FOR THE GROUP (A): 18.9128 17.0716 7.2467 REMARK 3 T TENSOR REMARK 3 T11: 0.2853 T22: 0.2694 REMARK 3 T33: 0.2910 T12: 0.0164 REMARK 3 T13: 0.0778 T23: -0.0232 REMARK 3 L TENSOR REMARK 3 L11: 2.0398 L22: 1.6594 REMARK 3 L33: 2.3485 L12: -0.7462 REMARK 3 L13: -0.0653 L23: 0.5497 REMARK 3 S TENSOR REMARK 3 S11: -0.0145 S12: -0.3601 S13: 0.1947 REMARK 3 S21: 0.1425 S22: -0.0231 S23: 0.1624 REMARK 3 S31: -0.2392 S32: -0.5311 S33: 0.0678 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 6RBU COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 11-APR-19. REMARK 100 THE DEPOSITION ID IS D_1292101715. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 04-OCT-18 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 : MASSIF-1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.966000 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS3 2M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : AIMLESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 25869 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.448 REMARK 200 RESOLUTION RANGE LOW (A) : 55.292 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 93.8 REMARK 200 DATA REDUNDANCY : 4.300 REMARK 200 R MERGE (I) : 0.03300 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 19.3000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.45 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.62 REMARK 200 COMPLETENESS FOR SHELL (%) : 82.8 REMARK 200 DATA REDUNDANCY IN SHELL : 5.40 REMARK 200 R MERGE FOR SHELL (I) : 0.68700 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 (%): 45.65 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.26 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 31.27600 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 37.99400 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 59.12350 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 31.27600 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 37.99400 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 59.12350 REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 31.27600 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 37.99400 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 59.12350 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 31.27600 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 37.99400 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 59.12350 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 62.55200 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 62.55200 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 418 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 ILE A 111 REMARK 465 GLY A 112 REMARK 465 LYS A 113 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 LYS A 85 CG CD CE NZ REMARK 470 ARG A 190 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 -70.67 -100.80 REMARK 500 ALA A 162 -125.69 -110.05 REMARK 500 ASN A 189 -159.95 -147.70 REMARK 500 HIS A 204 -10.70 74.77 REMARK 500 ASN A 213 -82.69 -128.86 REMARK 500 ASP A 222 -123.99 53.73 REMARK 500 GLU A 263 148.83 178.53 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 JYK A 302 DBREF 6RBU A 1 264 UNP Q8Y8D7 NADK1_LISMO 1 264 SEQADV 6RBU LEU A 265 UNP Q8Y8D7 EXPRESSION TAG SEQADV 6RBU GLU A 266 UNP Q8Y8D7 EXPRESSION TAG SEQADV 6RBU HIS A 267 UNP Q8Y8D7 EXPRESSION TAG SEQADV 6RBU HIS A 268 UNP Q8Y8D7 EXPRESSION TAG SEQADV 6RBU HIS A 269 UNP Q8Y8D7 EXPRESSION TAG SEQADV 6RBU HIS A 270 UNP Q8Y8D7 EXPRESSION TAG SEQADV 6RBU HIS A 271 UNP Q8Y8D7 EXPRESSION TAG SEQADV 6RBU 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 JYK A 302 16 HETNAM CIT CITRIC ACID HETNAM JYK 9-(2-AZIDOETHYL)-8-BROMANYL-PURIN-6-AMINE FORMUL 2 CIT C6 H8 O7 FORMUL 3 JYK C7 H7 BR N8 FORMUL 4 HOH *85(H2 O) HELIX 1 AA1 ASP A 10 GLY A 25 1 16 HELIX 2 AA2 GLY A 44 TYR A 55 1 12 HELIX 3 AA3 ARG A 58 ILE A 62 5 5 HELIX 4 AA4 ARG A 79 ALA A 81 5 3 HELIX 5 AA5 GLU A 82 GLY A 93 1 12 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 GLU A 115 ALA A 120 0 SHEET 2 AA2 6 GLN A 96 TYR A 109 -1 N VAL A 107 O ALA A 116 SHEET 3 AA2 6 VAL A 231 ARG A 247 -1 O ARG A 247 N GLN A 96 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 SER A 220 N THR A 125 SHEET 6 AA3 6 LEU A 224 HIS A 228 -1 O HIS A 228 N PHE A 217 SITE 1 AC1 9 VAL A 98 TYR A 100 HIS A 173 ARG A 247 SITE 2 AC1 9 PHE A 251 PRO A 252 PHE A 253 ARG A 256 SITE 3 AC1 9 HOH A 447 SITE 1 AC2 9 ASP A 45 LEU A 49 PHE A 74 TYR A 75 SITE 2 AC2 9 ASN A 122 SER A 158 THR A 161 ALA A 162 SITE 3 AC2 9 ILE A 187 CRYST1 62.552 75.988 118.247 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 0.015987 0.000000 0.000000 0.00000 SCALE2 0.000000 0.013160 0.000000 0.00000 SCALE3 0.000000 0.000000 0.008457 0.00000