HEADER TRANSFERASE 01-NOV-15 5EJI TITLE CRYSTAL STRUCTURE OF NAD KINASE W78F MUTANT FROM LISTERIA TITLE 2 MONOCYTOGENES IN COMPLEX WITH NADP/MN++/PPI 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; SOURCE 3 ORGANISM_TAXID: 1639; 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; SOURCE 8 EXPRESSION_SYSTEM_PLASMID: PLA15.3.3 KEYWDS GRAM-POSITIVE NAD KINASE, ALLOSTERY, CITRATE, TRANSFERASE EXPDTA X-RAY DIFFRACTION AUTHOR G.PONCET-MONTANGE,L.ASSAIRI,M.GELIN,S.POCHET,G.LABESSE REVDAT 2 06-SEP-17 5EJI 1 REMARK REVDAT 1 09-NOV-16 5EJI 0 JRNL AUTH G.PONCET-MONTANGE,L.ASSAIRI,M.GELIN,S.POCHET,G.LABESSE JRNL TITL CRYSTAL STRUCTURE OF NAD KINASE W78F MUTANT FROM LISTERIA JRNL TITL 2 MONOCYTOGENES IN COMPLEX WITH NADP/MN++/PPI JRNL REF TO BE PUBLISHED JRNL REFN REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH G.PONCET-MONTANGE,L.ASSAIRI,M.GELIN,S.POCHET,G.LABESSE REMARK 1 TITL MOLECULAR BASIS OF NAD KINASE CATALYSIS REVEALS CITRATE IS REMARK 1 TITL 2 AN ALLOSTERIC REGULATOR. REMARK 1 REF TO BE PUBLISHED REMARK 1 REFN REMARK 2 REMARK 2 RESOLUTION. 2.29 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 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 : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.29 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 63.08 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 0.180 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.7 REMARK 3 NUMBER OF REFLECTIONS : 12906 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.179 REMARK 3 R VALUE (WORKING SET) : 0.177 REMARK 3 FREE R VALUE : 0.237 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 2.930 REMARK 3 FREE R VALUE TEST SET COUNT : 709 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 63.1040 - 3.9183 1.00 4774 142 0.1500 0.1929 REMARK 3 2 3.9183 - 3.1100 1.00 4734 127 0.1609 0.2252 REMARK 3 3 3.1100 - 2.7169 1.00 4735 157 0.2144 0.3066 REMARK 3 4 2.7169 - 2.4685 1.00 4757 127 0.2337 0.2574 REMARK 3 5 2.4685 - 2.2916 0.94 4486 156 0.2677 0.3561 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) : 0.260 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 29.860 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 56.61 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 : 0.008 2185 REMARK 3 ANGLE : 1.071 2963 REMARK 3 CHIRALITY : 0.052 319 REMARK 3 PLANARITY : 0.006 372 REMARK 3 DIHEDRAL : 16.673 782 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 2 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 1 THROUGH 101 ) REMARK 3 ORIGIN FOR THE GROUP (A): 13.6534 24.0503 22.9923 REMARK 3 T TENSOR REMARK 3 T11: 0.5075 T22: 0.5693 REMARK 3 T33: 0.4434 T12: 0.0565 REMARK 3 T13: 0.0379 T23: -0.1400 REMARK 3 L TENSOR REMARK 3 L11: 0.3348 L22: 0.0801 REMARK 3 L33: 0.2357 L12: -0.0196 REMARK 3 L13: -0.2501 L23: 0.1216 REMARK 3 S TENSOR REMARK 3 S11: 0.0359 S12: -0.3809 S13: 0.1507 REMARK 3 S21: -0.0803 S22: -0.0110 S23: -0.0342 REMARK 3 S31: 0.0590 S32: 0.1004 S33: 0.0003 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 102 THROUGH 264 ) REMARK 3 ORIGIN FOR THE GROUP (A): 19.4071 13.6196 -1.7224 REMARK 3 T TENSOR REMARK 3 T11: 0.1069 T22: 0.1109 REMARK 3 T33: 0.1697 T12: 0.0578 REMARK 3 T13: -0.0183 T23: -0.0207 REMARK 3 L TENSOR REMARK 3 L11: 0.3575 L22: 0.2385 REMARK 3 L33: 0.5727 L12: 0.0445 REMARK 3 L13: -0.5165 L23: -0.1014 REMARK 3 S TENSOR REMARK 3 S11: 0.0213 S12: 0.0924 S13: 0.1399 REMARK 3 S21: 0.0802 S22: -0.0746 S23: 0.1382 REMARK 3 S31: -0.0320 S32: -0.0979 S33: -0.0049 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 5EJI COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 02-NOV-15. REMARK 100 THE DEPOSITION ID IS D_1000215021. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 16-SEP-06 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 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 : 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 4 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : NULL REMARK 200 DATA SCALING SOFTWARE : SCALA 3.3.21 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 13007 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.829 REMARK 200 RESOLUTION RANGE LOW (A) : 63.069 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 4.100 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.06100 REMARK 200 FOR THE DATA SET : 12.5000 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) : 2.41 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 4.10 REMARK 200 R MERGE FOR SHELL (I) : 0.56100 REMARK 200 R SYM FOR SHELL (I) : 0.56100 REMARK 200 FOR SHELL : 1.300 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: NULL REMARK 200 SOFTWARE USED: NULL REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 45.70 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.27 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 50 MM SODIUM BROMIDE, 150 MM TRI REMARK 280 -SODIUM CITRATE DIHYDRATE, PH 5.1-5.4, 14-16% W/V POLYETHYLENE REMARK 280 GLYCOL 400, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 294K 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 31.73300 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 37.19450 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 59.50600 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 31.73300 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 37.19450 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 59.50600 REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 31.73300 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 37.19450 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 59.50600 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 31.73300 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 37.19450 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 59.50600 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 REMARK 350 TOTAL BURIED SURFACE AREA: 16930 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 38290 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -78.0 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 63.46600 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 63.46600 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 434 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 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 GLN A 96 CG CD OE1 NE2 REMARK 470 GLN A 232 CG CD OE1 NE2 REMARK 470 LYS A 241 CG CD CE NZ REMARK 470 ARG A 249 CG CD NE CZ NH1 NH2 REMARK 470 GLU A 263 CG CD OE1 OE2 REMARK 470 ASP A 264 CG OD1 OD2 REMARK 480 REMARK 480 ZERO OCCUPANCY ATOM REMARK 480 THE FOLLOWING RESIDUES HAVE ATOMS MODELED WITH ZERO REMARK 480 OCCUPANCY. THE LOCATION AND PROPERTIES OF THESE ATOMS REMARK 480 MAY NOT BE RELIABLE. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 480 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 480 M RES C SSEQI ATOMS REMARK 480 TYR A 109 C 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 415 O HOH A 424 2.13 REMARK 500 O HOH A 431 O HOH A 434 2.17 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15 REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375 REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS. REMARK 500 REMARK 500 DISTANCE CUTOFF: REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE REMARK 500 OD2 ASP A 150 OH TYR A 163 4555 2.17 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 -62.01 -93.43 REMARK 500 TYR A 109 -154.42 -125.27 REMARK 500 ASN A 122 -66.40 -98.70 REMARK 500 SER A 129 30.40 -78.18 REMARK 500 ALA A 162 -129.08 -102.34 REMARK 500 ASN A 213 -81.06 -127.17 REMARK 500 ASP A 222 -130.30 52.26 REMARK 500 GLU A 263 147.93 -172.42 REMARK 500 REMARK 500 REMARK: NULL REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MN A 302 MN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 NAP A 301 O1A REMARK 620 2 NAP A 301 O3X 108.6 REMARK 620 3 POP A 303 O4 63.9 110.1 REMARK 620 4 POP A 303 O 134.1 94.1 71.0 REMARK 620 N 1 2 3 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 301 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MN A 302 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue POP A 303 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue CIT A 304 DBREF 5EJI A 1 264 UNP Q8Y8D7 NADK1_LISMO 1 264 SEQADV 5EJI PHE A 78 UNP Q8Y8D7 TRP 78 ENGINEERED MUTATION SEQADV 5EJI LEU A 265 UNP Q8Y8D7 EXPRESSION TAG SEQADV 5EJI GLU A 266 UNP Q8Y8D7 EXPRESSION TAG SEQADV 5EJI HIS A 267 UNP Q8Y8D7 EXPRESSION TAG SEQADV 5EJI HIS A 268 UNP Q8Y8D7 EXPRESSION TAG SEQADV 5EJI HIS A 269 UNP Q8Y8D7 EXPRESSION TAG SEQADV 5EJI HIS A 270 UNP Q8Y8D7 EXPRESSION TAG SEQADV 5EJI HIS A 271 UNP Q8Y8D7 EXPRESSION TAG SEQADV 5EJI 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 PHE 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 301 48 HET MN A 302 1 HET POP A 303 9 HET CIT A 304 13 HETNAM NAP NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE HETNAM MN MANGANESE (II) ION HETNAM POP PYROPHOSPHATE 2- HETNAM CIT CITRIC ACID HETSYN NAP 2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE FORMUL 2 NAP C21 H28 N7 O17 P3 FORMUL 3 MN MN 2+ FORMUL 4 POP H2 O7 P2 2- FORMUL 5 CIT C6 H8 O7 FORMUL 6 HOH *34(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 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 6 TYR A 3 SER A 7 0 SHEET 2 AA1 6 ILE A 38 GLY A 43 1 O ILE A 42 N THR A 6 SHEET 3 AA1 6 ALA A 63 HIS A 68 1 O ILE A 67 N SER A 41 SHEET 4 AA1 6 GLU A 233 ARG A 247 1 O HIS A 244 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 42 N THR A 6 SHEET 3 AA2 7 ALA A 63 HIS A 68 1 O ILE A 67 N SER A 41 SHEET 4 AA2 7 GLU A 233 ARG A 247 1 O HIS A 244 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 147 N VAL A 135 SHEET 1 AA3 6 LEU A 199 PRO A 202 0 SHEET 2 AA3 6 ALA A 178 MET A 184 -1 N LEU A 181 O LEU A 199 SHEET 3 AA3 6 GLY A 151 SER A 155 -1 N GLY A 151 O MET A 184 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 LINK O1A NAP A 301 MN MN A 302 1555 1555 2.76 LINK O3X NAP A 301 MN MN A 302 1555 1555 2.08 LINK MN MN A 302 O4 POP A 303 1555 1555 2.32 LINK MN MN A 302 O POP A 303 1555 1555 2.08 SITE 1 AC1 20 GLY A 44 ASP A 45 GLY A 46 LEU A 49 SITE 2 AC1 20 LEU A 72 GLY A 73 PHE A 74 TYR A 75 SITE 3 AC1 20 ASN A 122 GLU A 123 ASP A 150 SER A 158 SITE 4 AC1 20 THR A 161 ALA A 162 TYR A 163 SER A 166 SITE 5 AC1 20 ALA A 185 ILE A 187 MN A 302 POP A 303 SITE 1 AC2 2 NAP A 301 POP A 303 SITE 1 AC3 6 GLY A 44 ASP A 45 GLY A 46 THR A 47 SITE 2 AC3 6 NAP A 301 MN A 302 SITE 1 AC4 9 TYR A 100 HIS A 173 HIS A 204 HIS A 205 SITE 2 AC4 9 ARG A 247 PHE A 251 PRO A 252 PHE A 253 SITE 3 AC4 9 ARG A 256 CRYST1 63.466 74.389 119.012 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 0.015756 0.000000 0.000000 0.00000 SCALE2 0.000000 0.013443 0.000000 0.00000 SCALE3 0.000000 0.000000 0.008402 0.00000