HEADER TRANSFERASE 05-SEP-23 8QGC TITLE CRYSTAL STRUCTURE OF NAD KINASE 1 FROM LISTERIA MONOCYTOGENES IN TITLE 2 COMPLEX WITH A DI-ADENOSINE 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 BL21(DE3); SOURCE 6 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 7 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID KEYWDS TETRAMERIC NAD-KINASE, TRANSFERASE EXPDTA X-RAY DIFFRACTION AUTHOR M.GELIN,G.LABESSE,C.LIONNE REVDAT 1 19-MAR-25 8QGC 0 JRNL AUTH M.GELIN,G.LABESSE,D.CLEMENT,S.POCHET,C.LIONNE,C.LESEIGNEUR, JRNL AUTH 2 V.HUTEAU JRNL TITL CRYSTAL STRUCTURE OF NAD KINASE 1 FROM LISTERIA JRNL TITL 2 MONOCYTOGENES IN COMPLEX WITH A DI-ADENOSINE DERIVATIVE JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 2.29 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.19.1_4122 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 : GEOSTD + MONOMER LIBRARY + CDL V1.2 REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.29 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 48.21 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.1 REMARK 3 NUMBER OF REFLECTIONS : 12851 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.227 REMARK 3 R VALUE (WORKING SET) : 0.226 REMARK 3 FREE R VALUE : 0.242 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.850 REMARK 3 FREE R VALUE TEST SET COUNT : 623 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 48.2100 - 3.6400 0.99 3145 166 0.1909 0.1981 REMARK 3 2 3.6300 - 2.8900 0.99 3045 151 0.2371 0.2843 REMARK 3 3 2.8900 - 2.5200 0.99 3025 150 0.2922 0.3044 REMARK 3 4 2.5200 - 2.2900 0.99 3013 156 0.3201 0.3616 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL 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) : 0.303 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 31.880 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 45.50 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 64.71 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 : 0.010 2196 REMARK 3 ANGLE : 1.433 2980 REMARK 3 CHIRALITY : 0.093 324 REMARK 3 PLANARITY : 0.007 376 REMARK 3 DIHEDRAL : 15.968 798 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 25 ) REMARK 3 ORIGIN FOR THE GROUP (A): 8.9171 21.9238 28.3854 REMARK 3 T TENSOR REMARK 3 T11: 0.7277 T22: 0.9189 REMARK 3 T33: 0.5679 T12: 0.0576 REMARK 3 T13: 0.0428 T23: -0.1144 REMARK 3 L TENSOR REMARK 3 L11: 4.3701 L22: 2.4069 REMARK 3 L33: 5.6027 L12: -0.8108 REMARK 3 L13: -1.0239 L23: 2.0301 REMARK 3 S TENSOR REMARK 3 S11: -0.1615 S12: -0.8898 S13: -0.1290 REMARK 3 S21: -0.0731 S22: 0.0889 S23: 0.6780 REMARK 3 S31: -0.3201 S32: -0.3382 S33: 0.0869 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 26 THROUGH 37 ) REMARK 3 ORIGIN FOR THE GROUP (A): 7.0016 32.9274 25.1310 REMARK 3 T TENSOR REMARK 3 T11: 0.9698 T22: 1.3489 REMARK 3 T33: 0.8511 T12: 0.2137 REMARK 3 T13: 0.1345 T23: -0.2771 REMARK 3 L TENSOR REMARK 3 L11: 3.3637 L22: 2.1450 REMARK 3 L33: 3.2987 L12: -1.1948 REMARK 3 L13: -1.2784 L23: -1.7395 REMARK 3 S TENSOR REMARK 3 S11: 0.4871 S12: -0.9972 S13: 1.2099 REMARK 3 S21: 0.4061 S22: -0.0944 S23: -0.1386 REMARK 3 S31: -1.5204 S32: -0.7038 S33: 0.0555 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 38 THROUGH 68 ) REMARK 3 ORIGIN FOR THE GROUP (A): 12.3757 23.3123 15.7166 REMARK 3 T TENSOR REMARK 3 T11: 0.5989 T22: 0.6269 REMARK 3 T33: 0.5073 T12: 0.1381 REMARK 3 T13: 0.0310 T23: -0.0869 REMARK 3 L TENSOR REMARK 3 L11: 4.0207 L22: 2.3952 REMARK 3 L33: 5.4573 L12: 0.1776 REMARK 3 L13: -1.6325 L23: 1.9705 REMARK 3 S TENSOR REMARK 3 S11: 0.1921 S12: -0.1981 S13: 0.6021 REMARK 3 S21: 0.0514 S22: -0.3211 S23: 0.0618 REMARK 3 S31: -0.6932 S32: -0.0583 S33: -0.0059 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 69 THROUGH 92 ) REMARK 3 ORIGIN FOR THE GROUP (A): 20.5177 21.4912 26.4041 REMARK 3 T TENSOR REMARK 3 T11: 0.6363 T22: 0.9953 REMARK 3 T33: 0.7309 T12: 0.1062 REMARK 3 T13: 0.0908 T23: -0.2005 REMARK 3 L TENSOR REMARK 3 L11: 4.0849 L22: 0.9856 REMARK 3 L33: 5.4502 L12: -1.5352 REMARK 3 L13: -1.7580 L23: 1.3285 REMARK 3 S TENSOR REMARK 3 S11: 0.0830 S12: -1.4716 S13: 1.5356 REMARK 3 S21: 0.4161 S22: 1.2102 S23: -0.9582 REMARK 3 S31: -0.9030 S32: 1.0483 S33: -0.0745 REMARK 3 TLS GROUP : 5 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 93 THROUGH 167 ) REMARK 3 ORIGIN FOR THE GROUP (A): 17.5888 15.0260 -2.2380 REMARK 3 T TENSOR REMARK 3 T11: 0.2820 T22: 0.3950 REMARK 3 T33: 0.3522 T12: 0.0544 REMARK 3 T13: 0.0294 T23: 0.0148 REMARK 3 L TENSOR REMARK 3 L11: 1.6011 L22: 2.4507 REMARK 3 L33: 4.3272 L12: -1.1590 REMARK 3 L13: -0.2458 L23: 0.5100 REMARK 3 S TENSOR REMARK 3 S11: 0.1816 S12: 0.0852 S13: 0.1297 REMARK 3 S21: -0.1403 S22: -0.1615 S23: 0.1514 REMARK 3 S31: -0.4322 S32: -0.4071 S33: 0.0375 REMARK 3 TLS GROUP : 6 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 168 THROUGH 238 ) REMARK 3 ORIGIN FOR THE GROUP (A): 18.3266 11.9488 -6.1637 REMARK 3 T TENSOR REMARK 3 T11: 0.3714 T22: 0.4640 REMARK 3 T33: 0.4059 T12: 0.0857 REMARK 3 T13: -0.0089 T23: 0.0148 REMARK 3 L TENSOR REMARK 3 L11: 2.2278 L22: 1.5563 REMARK 3 L33: 3.9399 L12: -0.2742 REMARK 3 L13: -0.3612 L23: -0.5768 REMARK 3 S TENSOR REMARK 3 S11: 0.0412 S12: 0.1558 S13: 0.2033 REMARK 3 S21: -0.1864 S22: -0.1079 S23: 0.4826 REMARK 3 S31: -0.1656 S32: -0.5262 S33: 0.0547 REMARK 3 TLS GROUP : 7 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 239 THROUGH 263 ) REMARK 3 ORIGIN FOR THE GROUP (A): 27.1701 19.8620 15.9295 REMARK 3 T TENSOR REMARK 3 T11: 0.5374 T22: 0.4644 REMARK 3 T33: 0.4401 T12: -0.0088 REMARK 3 T13: 0.0796 T23: -0.0785 REMARK 3 L TENSOR REMARK 3 L11: 3.2231 L22: 2.3692 REMARK 3 L33: 3.6369 L12: -1.4036 REMARK 3 L13: 0.5569 L23: -0.0372 REMARK 3 S TENSOR REMARK 3 S11: -0.0054 S12: -0.3058 S13: 0.4711 REMARK 3 S21: 0.4840 S22: -0.1736 S23: -0.1352 REMARK 3 S31: -0.6030 S32: 0.0836 S33: 0.0067 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 8QGC COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 07-SEP-23. REMARK 100 THE DEPOSITION ID IS D_1292133132. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 07-NOV-14 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 4.8-5.1 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) : 0.97625 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 12864 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.290 REMARK 200 RESOLUTION RANGE LOW (A) : 48.210 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.4 REMARK 200 DATA REDUNDANCY : 4.600 REMARK 200 R MERGE (I) : 0.06700 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 13.5000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.29 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.37 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : 4.60 REMARK 200 R MERGE FOR SHELL (I) : 0.78400 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, PHENIX REMARK 200 STARTING MODEL: 8A9V REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 45.21 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.25 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 30 MM NABR, 220 MM KCITRATE, GLYCEROL REMARK 280 6%, 15-16% W/V PEG400, VAPOR DIFFUSION, HANGING DROP, REMARK 280 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 31.55350 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 37.36400 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 59.11950 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 31.55350 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 37.36400 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 59.11950 REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 31.55350 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 37.36400 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 59.11950 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 31.55350 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 37.36400 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 59.11950 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 63.10700 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 63.10700 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 416 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 110 REMARK 465 ILE A 111 REMARK 465 GLY A 112 REMARK 465 LYS A 113 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 LYS A 85 CG CD CE NZ REMARK 470 LYS A 114 CG CD CE NZ REMARK 470 GLN A 232 CG CD OE1 NE2 REMARK 470 ARG A 247 CG CD NE CZ NH1 NH2 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND LENGTHS 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,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3) 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 RES CSSEQI ATM2 DEVIATION REMARK 500 PHE A 253 CB PHE A 253 CG -0.115 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 28 75.07 -118.44 REMARK 500 ASP A 77 57.24 -108.00 REMARK 500 GLU A 94 24.57 49.94 REMARK 500 ASN A 122 -60.17 -100.28 REMARK 500 ALA A 162 -129.40 -102.81 REMARK 500 HIS A 204 -11.98 78.13 REMARK 500 VAL A 212 -61.09 -97.89 REMARK 500 ASN A 213 -79.21 -119.88 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 8A9V RELATED DB: PDB DBREF 8QGC A 1 264 UNP Q8Y8D7 NADK1_LISMO 1 264 SEQADV 8QGC LEU A 265 UNP Q8Y8D7 EXPRESSION TAG SEQADV 8QGC GLU A 266 UNP Q8Y8D7 EXPRESSION TAG SEQADV 8QGC HIS A 267 UNP Q8Y8D7 EXPRESSION TAG SEQADV 8QGC HIS A 268 UNP Q8Y8D7 EXPRESSION TAG SEQADV 8QGC HIS A 269 UNP Q8Y8D7 EXPRESSION TAG SEQADV 8QGC HIS A 270 UNP Q8Y8D7 EXPRESSION TAG SEQADV 8QGC HIS A 271 UNP Q8Y8D7 EXPRESSION TAG SEQADV 8QGC 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 UYP A 302 51 HETNAM CIT CITRIC ACID HETNAM UYP 1-[[(2~{R},3~{S},4~{R},5~{R})-5-[8-[3-[[(2~{R},3~{S}, HETNAM 2 UYP 4~{R},5~{R})-5-(6-AMINOPURIN-9-YL)-3,4-BIS(OXIDANYL) HETNAM 3 UYP OXOLAN-2-YL]METHYL-METHYL-AMINO]PROP-1-YNYL]-6-AZANYL- HETNAM 4 UYP PURIN-9-YL]-3,4-BIS(OXIDANYL)OXOLAN-2-YL]METHYL]-3- HETNAM 5 UYP PHENYL-UREA FORMUL 2 CIT C6 H8 O7 FORMUL 3 UYP C31 H35 N13 O7 FORMUL 4 HOH *31(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 ARG A 58 GLU A 61 5 4 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 6 TYR A 3 SER A 7 0 SHEET 2 AA1 6 ILE A 38 GLY A 43 1 O ILE A 40 N MET A 4 SHEET 3 AA1 6 ALA A 63 HIS A 68 1 O ILE A 67 N GLY A 43 SHEET 4 AA1 6 GLU A 233 ARG A 247 1 O ALA A 246 N PHE A 64 SHEET 5 AA1 6 GLN A 96 LYS A 108 -1 N VAL A 98 O PHE A 245 SHEET 6 AA1 6 ALA A 116 ALA A 120 -1 O ALA A 116 N VAL A 107 SHEET 1 AA2 7 TYR A 3 SER A 7 0 SHEET 2 AA2 7 ILE A 38 GLY A 43 1 O ILE A 40 N MET A 4 SHEET 3 AA2 7 ALA A 63 HIS A 68 1 O ILE A 67 N GLY A 43 SHEET 4 AA2 7 GLU A 233 ARG A 247 1 O ALA A 246 N PHE A 64 SHEET 5 AA2 7 VAL A 207 PRO A 211 -1 N VAL A 207 O TYR A 236 SHEET 6 AA2 7 PHE A 133 ILE A 139 -1 N VAL A 138 O SER A 208 SHEET 7 AA2 7 ILE A 142 GLY A 149 -1 O PHE A 144 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 CRYST1 63.107 74.728 118.239 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 0.015846 0.000000 0.000000 0.00000 SCALE2 0.000000 0.013382 0.000000 0.00000 SCALE3 0.000000 0.000000 0.008457 0.00000 CONECT 2076 2077 2078 2079 CONECT 2077 2076 CONECT 2078 2076 CONECT 2079 2076 2080 CONECT 2080 2079 2081 2082 2086 CONECT 2081 2080 CONECT 2082 2080 2083 CONECT 2083 2082 2084 2085 CONECT 2084 2083 CONECT 2085 2083 CONECT 2086 2080 2087 2088 CONECT 2087 2086 CONECT 2088 2086 CONECT 2089 2090 2094 2124 CONECT 2090 2089 2091 2123 CONECT 2091 2090 2093 2122 CONECT 2092 2099 2123 2124 CONECT 2093 2091 2095 CONECT 2094 2089 2095 CONECT 2095 2093 2094 CONECT 2096 2125 CONECT 2097 2098 2125 CONECT 2098 2097 2099 CONECT 2099 2092 2098 CONECT 2100 2111 2124 2133 CONECT 2101 2102 2110 2133 CONECT 2102 2101 2126 CONECT 2103 2126 2127 2134 CONECT 2104 2105 2109 2127 CONECT 2105 2104 2106 CONECT 2106 2105 2107 CONECT 2107 2106 2108 CONECT 2108 2107 2109 CONECT 2109 2104 2108 CONECT 2110 2101 2111 2135 CONECT 2111 2100 2110 2136 CONECT 2112 2113 2125 CONECT 2113 2112 2116 2137 CONECT 2114 2115 2128 2137 CONECT 2115 2114 2116 2138 CONECT 2116 2113 2115 2139 CONECT 2117 2128 2129 CONECT 2118 2119 2121 2129 CONECT 2119 2118 2128 2130 CONECT 2120 2130 2131 CONECT 2121 2118 2131 2132 CONECT 2122 2091 CONECT 2123 2090 2092 CONECT 2124 2089 2092 2100 CONECT 2125 2096 2097 2112 CONECT 2126 2102 2103 CONECT 2127 2103 2104 CONECT 2128 2114 2117 2119 CONECT 2129 2117 2118 CONECT 2130 2119 2120 CONECT 2131 2120 2121 CONECT 2132 2121 CONECT 2133 2100 2101 CONECT 2134 2103 CONECT 2135 2110 CONECT 2136 2111 CONECT 2137 2113 2114 CONECT 2138 2115 CONECT 2139 2116 MASTER 409 0 2 8 19 0 0 6 2155 1 64 21 END