HEADER TRANSFERASE 13-OCT-08 3EVW TITLE CRYSTAL STRUCTURE OF THE MIMIVIRUS NDK R107G MUTANT COMPLEXED WITH TITLE 2 DTDP COMPND MOL_ID: 1; COMPND 2 MOLECULE: NUCLEOSIDE DIPHOSPHATE KINASE; COMPND 3 CHAIN: A, B, C, D, E, F; COMPND 4 SYNONYM: NDP KINASE, NDK; COMPND 5 EC: 2.7.4.6; COMPND 6 ENGINEERED: YES; COMPND 7 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ACANTHAMOEBA POLYPHAGA MIMIVIRUS; SOURCE 3 ORGANISM_TAXID: 212035; SOURCE 4 GENE: MIMI_R418, NDK; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: ROSETTA(DE3)PLYSS; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PDIGS02 KEYWDS PHOSPHOTRANSFERASE NUCLEOTIDE BINDING, ATP-BINDING, KINASE, KEYWDS 2 MAGNESIUM, METAL-BINDING, NUCLEOTIDE METABOLISM, NUCLEOTIDE-BINDING, KEYWDS 3 PHOSPHOPROTEIN, TRANSFERASE EXPDTA X-RAY DIFFRACTION AUTHOR S.JEUDY,A.LARTIGUE,J.M.CLAVERIE,C.ABERGEL REVDAT 3 06-SEP-23 3EVW 1 REMARK REVDAT 2 20-OCT-21 3EVW 1 REMARK SEQADV LINK REVDAT 1 11-AUG-09 3EVW 0 JRNL AUTH S.JEUDY,A.LARTIGUE,J.M.CLAVERIE,C.ABERGEL JRNL TITL DISSECTING THE UNIQUE NUCLEOTIDE SPECIFICITY OF MIMIVIRUS JRNL TITL 2 NUCLEOSIDE DIPHOSPHATE KINASE. JRNL REF J.VIROL. V. 83 7142 2009 JRNL REFN ISSN 0022-538X JRNL PMID 19439473 JRNL DOI 10.1128/JVI.00511-09 REMARK 2 REMARK 2 RESOLUTION. 2.60 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE) 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) : 2.60 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 28.53 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.390 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 3 NUMBER OF REFLECTIONS : 35004 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.201 REMARK 3 R VALUE (WORKING SET) : 0.199 REMARK 3 FREE R VALUE : 0.247 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.010 REMARK 3 FREE R VALUE TEST SET COUNT : 1753 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 28.5310 - 6.0950 0.97 2622 154 0.1830 0.2050 REMARK 3 2 6.0950 - 4.8460 1.00 2604 152 0.1710 0.2210 REMARK 3 3 4.8460 - 4.2350 1.00 2560 147 0.1540 0.2100 REMARK 3 4 4.2350 - 3.8490 1.00 2568 131 0.1720 0.2400 REMARK 3 5 3.8490 - 3.5740 1.00 2567 131 0.1950 0.2380 REMARK 3 6 3.5740 - 3.3630 1.00 2559 127 0.2050 0.2470 REMARK 3 7 3.3630 - 3.1950 1.00 2553 129 0.2190 0.3090 REMARK 3 8 3.1950 - 3.0560 1.00 2569 133 0.2310 0.2960 REMARK 3 9 3.0560 - 2.9390 1.00 2566 113 0.2430 0.2870 REMARK 3 10 2.9390 - 2.8380 1.00 2515 138 0.2400 0.2910 REMARK 3 11 2.8380 - 2.7490 1.00 2535 130 0.2460 0.3090 REMARK 3 12 2.7490 - 2.6700 1.00 2543 133 0.2660 0.3600 REMARK 3 13 2.6700 - 2.6000 1.00 2490 135 0.2710 0.3520 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 : 0.34 REMARK 3 B_SOL : 43.99 REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.360 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 25.700 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 72.50 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 63.20 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 3.97200 REMARK 3 B22 (A**2) : -2.06800 REMARK 3 B33 (A**2) : -1.90300 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 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 : 0.007 6571 REMARK 3 ANGLE : 1.207 8896 REMARK 3 CHIRALITY : 0.071 974 REMARK 3 PLANARITY : 0.004 1130 REMARK 3 DIHEDRAL : 21.672 2464 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL 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 3EVW COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 21-NOV-08. REMARK 100 THE DEPOSITION ID IS D_1000049832. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 24-SEP-07 REMARK 200 TEMPERATURE (KELVIN) : 105 REMARK 200 PH : 7.5 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) : 0.979 REMARK 200 MONOCHROMATOR : SI111 AND SI311 REMARK 200 OPTICS : MIRRORS REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 35004 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.600 REMARK 200 RESOLUTION RANGE LOW (A) : 28.500 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 200 DATA REDUNDANCY : 7.000 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.09800 REMARK 200 FOR THE DATA SET : 4.6000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.60 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.74 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 7.30 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : 0.35400 REMARK 200 FOR SHELL : 2.000 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: AMORE REMARK 200 STARTING MODEL: 2B8Q REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 57.55 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.90 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 40 TO 44% MPD, 0.1M HEPES, PH 7.5, REMARK 280 VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 2 2 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z+1/2 REMARK 290 3555 -X,Y,-Z+1/2 REMARK 290 4555 X,-Y,-Z REMARK 290 5555 X+1/2,Y+1/2,Z 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 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 92.43700 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 92.43700 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 40.34500 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 75.51900 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 40.34500 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 75.51900 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 92.43700 REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 40.34500 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 75.51900 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 92.43700 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 40.34500 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 75.51900 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2 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: HEXAMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, C, E 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 0.00000 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 REMARK 350 BIOMOLECULE: 2 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: HEXAMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: B, D, F 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 161.38000 REMARK 350 BIOMT2 2 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 92.43700 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 TYR A -4 REMARK 465 LYS A -3 REMARK 465 LYS A -2 REMARK 465 LYS A 132 REMARK 465 MET A 133 REMARK 465 GLU A 134 REMARK 465 THR A 135 REMARK 465 ASP A 136 REMARK 465 ASN A 137 REMARK 465 TYR B -4 REMARK 465 LYS B -3 REMARK 465 LYS B -2 REMARK 465 ALA B -1 REMARK 465 GLY B 0 REMARK 465 THR B 131 REMARK 465 LYS B 132 REMARK 465 MET B 133 REMARK 465 GLU B 134 REMARK 465 THR B 135 REMARK 465 ASP B 136 REMARK 465 ASN B 137 REMARK 465 TYR C -4 REMARK 465 LYS C -3 REMARK 465 LYS C -2 REMARK 465 ALA C -1 REMARK 465 LYS C 132 REMARK 465 MET C 133 REMARK 465 GLU C 134 REMARK 465 THR C 135 REMARK 465 ASP C 136 REMARK 465 ASN C 137 REMARK 465 TYR D -4 REMARK 465 LYS D -3 REMARK 465 LYS D -2 REMARK 465 ALA D -1 REMARK 465 LYS D 132 REMARK 465 MET D 133 REMARK 465 GLU D 134 REMARK 465 THR D 135 REMARK 465 ASP D 136 REMARK 465 ASN D 137 REMARK 465 TYR E -4 REMARK 465 LYS E -3 REMARK 465 LYS E -2 REMARK 465 ALA E -1 REMARK 465 LYS E 132 REMARK 465 MET E 133 REMARK 465 GLU E 134 REMARK 465 THR E 135 REMARK 465 ASP E 136 REMARK 465 ASN E 137 REMARK 465 TYR F -4 REMARK 465 LYS F -3 REMARK 465 LYS F -2 REMARK 465 ALA F -1 REMARK 465 GLU F 130 REMARK 465 THR F 131 REMARK 465 LYS F 132 REMARK 465 MET F 133 REMARK 465 GLU F 134 REMARK 465 THR F 135 REMARK 465 ASP F 136 REMARK 465 ASN F 137 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 NH2 ARG F 43 OD1 ASP F 64 2.14 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 LEU A 1 103.00 -55.18 REMARK 500 ASN A 29 28.31 82.44 REMARK 500 ASN A 104 24.32 -153.50 REMARK 500 LEU A 110 -44.08 70.62 REMARK 500 GLU A 130 3.97 -54.09 REMARK 500 ASN B 29 43.15 70.75 REMARK 500 LYS B 40 112.89 -164.67 REMARK 500 LYS B 51 -62.81 21.14 REMARK 500 SER B 54 -9.05 -55.68 REMARK 500 PHE B 59 -60.72 -23.78 REMARK 500 ASN B 109 24.85 -140.80 REMARK 500 LEU B 110 -42.94 76.17 REMARK 500 ASN C 29 32.82 77.02 REMARK 500 ILE C 92 -1.56 -59.59 REMARK 500 ASN C 104 38.08 -154.27 REMARK 500 LEU C 110 -45.41 77.80 REMARK 500 GLU C 130 50.13 -60.10 REMARK 500 ASN D 104 51.45 -151.97 REMARK 500 LEU D 110 -47.97 77.96 REMARK 500 GLU D 130 86.04 -67.61 REMARK 500 ASN E 29 25.25 82.56 REMARK 500 ASN E 104 21.72 -155.23 REMARK 500 LEU E 110 -44.02 77.45 REMARK 500 ASN F 104 55.08 -146.08 REMARK 500 LEU F 110 -49.53 79.63 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 MG C 162 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 TYD C 138 O1A REMARK 620 2 TYD C 138 O2B 58.4 REMARK 620 N 1 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG E 164 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 TYD E 138 O2B REMARK 620 2 TYD E 138 O1A 65.8 REMARK 620 N 1 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG A 160 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG B 161 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG C 162 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG D 163 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG E 164 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG F 165 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE TYD A 138 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE TYD B 138 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE TYD C 138 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE TYD D 138 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE TYD E 138 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE TYD F 138 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2B8P RELATED DB: PDB DBREF 3EVW A 2 137 UNP Q5UQL3 NDK_MIMIV 2 137 DBREF 3EVW B 2 137 UNP Q5UQL3 NDK_MIMIV 2 137 DBREF 3EVW C 2 137 UNP Q5UQL3 NDK_MIMIV 2 137 DBREF 3EVW D 2 137 UNP Q5UQL3 NDK_MIMIV 2 137 DBREF 3EVW E 2 137 UNP Q5UQL3 NDK_MIMIV 2 137 DBREF 3EVW F 2 137 UNP Q5UQL3 NDK_MIMIV 2 137 SEQADV 3EVW TYR A -4 UNP Q5UQL3 EXPRESSION TAG SEQADV 3EVW LYS A -3 UNP Q5UQL3 EXPRESSION TAG SEQADV 3EVW LYS A -2 UNP Q5UQL3 EXPRESSION TAG SEQADV 3EVW ALA A -1 UNP Q5UQL3 EXPRESSION TAG SEQADV 3EVW GLY A 0 UNP Q5UQL3 EXPRESSION TAG SEQADV 3EVW LEU A 1 UNP Q5UQL3 EXPRESSION TAG SEQADV 3EVW GLY A 107 UNP Q5UQL3 ARG 107 ENGINEERED MUTATION SEQADV 3EVW TYR B -4 UNP Q5UQL3 EXPRESSION TAG SEQADV 3EVW LYS B -3 UNP Q5UQL3 EXPRESSION TAG SEQADV 3EVW LYS B -2 UNP Q5UQL3 EXPRESSION TAG SEQADV 3EVW ALA B -1 UNP Q5UQL3 EXPRESSION TAG SEQADV 3EVW GLY B 0 UNP Q5UQL3 EXPRESSION TAG SEQADV 3EVW LEU B 1 UNP Q5UQL3 EXPRESSION TAG SEQADV 3EVW GLY B 107 UNP Q5UQL3 ARG 107 ENGINEERED MUTATION SEQADV 3EVW TYR C -4 UNP Q5UQL3 EXPRESSION TAG SEQADV 3EVW LYS C -3 UNP Q5UQL3 EXPRESSION TAG SEQADV 3EVW LYS C -2 UNP Q5UQL3 EXPRESSION TAG SEQADV 3EVW ALA C -1 UNP Q5UQL3 EXPRESSION TAG SEQADV 3EVW GLY C 0 UNP Q5UQL3 EXPRESSION TAG SEQADV 3EVW LEU C 1 UNP Q5UQL3 EXPRESSION TAG SEQADV 3EVW GLY C 107 UNP Q5UQL3 ARG 107 ENGINEERED MUTATION SEQADV 3EVW TYR D -4 UNP Q5UQL3 EXPRESSION TAG SEQADV 3EVW LYS D -3 UNP Q5UQL3 EXPRESSION TAG SEQADV 3EVW LYS D -2 UNP Q5UQL3 EXPRESSION TAG SEQADV 3EVW ALA D -1 UNP Q5UQL3 EXPRESSION TAG SEQADV 3EVW GLY D 0 UNP Q5UQL3 EXPRESSION TAG SEQADV 3EVW LEU D 1 UNP Q5UQL3 EXPRESSION TAG SEQADV 3EVW GLY D 107 UNP Q5UQL3 ARG 107 ENGINEERED MUTATION SEQADV 3EVW TYR E -4 UNP Q5UQL3 EXPRESSION TAG SEQADV 3EVW LYS E -3 UNP Q5UQL3 EXPRESSION TAG SEQADV 3EVW LYS E -2 UNP Q5UQL3 EXPRESSION TAG SEQADV 3EVW ALA E -1 UNP Q5UQL3 EXPRESSION TAG SEQADV 3EVW GLY E 0 UNP Q5UQL3 EXPRESSION TAG SEQADV 3EVW LEU E 1 UNP Q5UQL3 EXPRESSION TAG SEQADV 3EVW GLY E 107 UNP Q5UQL3 ARG 107 ENGINEERED MUTATION SEQADV 3EVW TYR F -4 UNP Q5UQL3 EXPRESSION TAG SEQADV 3EVW LYS F -3 UNP Q5UQL3 EXPRESSION TAG SEQADV 3EVW LYS F -2 UNP Q5UQL3 EXPRESSION TAG SEQADV 3EVW ALA F -1 UNP Q5UQL3 EXPRESSION TAG SEQADV 3EVW GLY F 0 UNP Q5UQL3 EXPRESSION TAG SEQADV 3EVW LEU F 1 UNP Q5UQL3 EXPRESSION TAG SEQADV 3EVW GLY F 107 UNP Q5UQL3 ARG 107 ENGINEERED MUTATION SEQRES 1 A 142 TYR LYS LYS ALA GLY LEU GLN ARG THR LEU VAL LEU ILE SEQRES 2 A 142 LYS PRO ASP ALA PHE GLU ARG SER LEU VAL ALA GLU ILE SEQRES 3 A 142 MET GLY ARG ILE GLU LYS LYS ASN PHE LYS ILE VAL SER SEQRES 4 A 142 MET LYS PHE TRP SER LYS ALA PRO ARG ASN LEU ILE GLU SEQRES 5 A 142 GLN HIS TYR LYS GLU HIS SER GLU GLN SER TYR PHE ASN SEQRES 6 A 142 ASP ASN CYS ASP PHE MET VAL SER GLY PRO ILE ILE SER SEQRES 7 A 142 ILE VAL TYR GLU GLY THR ASP ALA ILE SER LYS ILE ARG SEQRES 8 A 142 ARG LEU GLN GLY ASN ILE LEU THR PRO GLY THR ILE ARG SEQRES 9 A 142 GLY ASP LEU ALA ASN ASP ILE GLY GLU ASN LEU ILE HIS SEQRES 10 A 142 ALA SER ASP SER GLU ASP SER ALA VAL ASP GLU ILE SER SEQRES 11 A 142 ILE TRP PHE PRO GLU THR LYS MET GLU THR ASP ASN SEQRES 1 B 142 TYR LYS LYS ALA GLY LEU GLN ARG THR LEU VAL LEU ILE SEQRES 2 B 142 LYS PRO ASP ALA PHE GLU ARG SER LEU VAL ALA GLU ILE SEQRES 3 B 142 MET GLY ARG ILE GLU LYS LYS ASN PHE LYS ILE VAL SER SEQRES 4 B 142 MET LYS PHE TRP SER LYS ALA PRO ARG ASN LEU ILE GLU SEQRES 5 B 142 GLN HIS TYR LYS GLU HIS SER GLU GLN SER TYR PHE ASN SEQRES 6 B 142 ASP ASN CYS ASP PHE MET VAL SER GLY PRO ILE ILE SER SEQRES 7 B 142 ILE VAL TYR GLU GLY THR ASP ALA ILE SER LYS ILE ARG SEQRES 8 B 142 ARG LEU GLN GLY ASN ILE LEU THR PRO GLY THR ILE ARG SEQRES 9 B 142 GLY ASP LEU ALA ASN ASP ILE GLY GLU ASN LEU ILE HIS SEQRES 10 B 142 ALA SER ASP SER GLU ASP SER ALA VAL ASP GLU ILE SER SEQRES 11 B 142 ILE TRP PHE PRO GLU THR LYS MET GLU THR ASP ASN SEQRES 1 C 142 TYR LYS LYS ALA GLY LEU GLN ARG THR LEU VAL LEU ILE SEQRES 2 C 142 LYS PRO ASP ALA PHE GLU ARG SER LEU VAL ALA GLU ILE SEQRES 3 C 142 MET GLY ARG ILE GLU LYS LYS ASN PHE LYS ILE VAL SER SEQRES 4 C 142 MET LYS PHE TRP SER LYS ALA PRO ARG ASN LEU ILE GLU SEQRES 5 C 142 GLN HIS TYR LYS GLU HIS SER GLU GLN SER TYR PHE ASN SEQRES 6 C 142 ASP ASN CYS ASP PHE MET VAL SER GLY PRO ILE ILE SER SEQRES 7 C 142 ILE VAL TYR GLU GLY THR ASP ALA ILE SER LYS ILE ARG SEQRES 8 C 142 ARG LEU GLN GLY ASN ILE LEU THR PRO GLY THR ILE ARG SEQRES 9 C 142 GLY ASP LEU ALA ASN ASP ILE GLY GLU ASN LEU ILE HIS SEQRES 10 C 142 ALA SER ASP SER GLU ASP SER ALA VAL ASP GLU ILE SER SEQRES 11 C 142 ILE TRP PHE PRO GLU THR LYS MET GLU THR ASP ASN SEQRES 1 D 142 TYR LYS LYS ALA GLY LEU GLN ARG THR LEU VAL LEU ILE SEQRES 2 D 142 LYS PRO ASP ALA PHE GLU ARG SER LEU VAL ALA GLU ILE SEQRES 3 D 142 MET GLY ARG ILE GLU LYS LYS ASN PHE LYS ILE VAL SER SEQRES 4 D 142 MET LYS PHE TRP SER LYS ALA PRO ARG ASN LEU ILE GLU SEQRES 5 D 142 GLN HIS TYR LYS GLU HIS SER GLU GLN SER TYR PHE ASN SEQRES 6 D 142 ASP ASN CYS ASP PHE MET VAL SER GLY PRO ILE ILE SER SEQRES 7 D 142 ILE VAL TYR GLU GLY THR ASP ALA ILE SER LYS ILE ARG SEQRES 8 D 142 ARG LEU GLN GLY ASN ILE LEU THR PRO GLY THR ILE ARG SEQRES 9 D 142 GLY ASP LEU ALA ASN ASP ILE GLY GLU ASN LEU ILE HIS SEQRES 10 D 142 ALA SER ASP SER GLU ASP SER ALA VAL ASP GLU ILE SER SEQRES 11 D 142 ILE TRP PHE PRO GLU THR LYS MET GLU THR ASP ASN SEQRES 1 E 142 TYR LYS LYS ALA GLY LEU GLN ARG THR LEU VAL LEU ILE SEQRES 2 E 142 LYS PRO ASP ALA PHE GLU ARG SER LEU VAL ALA GLU ILE SEQRES 3 E 142 MET GLY ARG ILE GLU LYS LYS ASN PHE LYS ILE VAL SER SEQRES 4 E 142 MET LYS PHE TRP SER LYS ALA PRO ARG ASN LEU ILE GLU SEQRES 5 E 142 GLN HIS TYR LYS GLU HIS SER GLU GLN SER TYR PHE ASN SEQRES 6 E 142 ASP ASN CYS ASP PHE MET VAL SER GLY PRO ILE ILE SER SEQRES 7 E 142 ILE VAL TYR GLU GLY THR ASP ALA ILE SER LYS ILE ARG SEQRES 8 E 142 ARG LEU GLN GLY ASN ILE LEU THR PRO GLY THR ILE ARG SEQRES 9 E 142 GLY ASP LEU ALA ASN ASP ILE GLY GLU ASN LEU ILE HIS SEQRES 10 E 142 ALA SER ASP SER GLU ASP SER ALA VAL ASP GLU ILE SER SEQRES 11 E 142 ILE TRP PHE PRO GLU THR LYS MET GLU THR ASP ASN SEQRES 1 F 142 TYR LYS LYS ALA GLY LEU GLN ARG THR LEU VAL LEU ILE SEQRES 2 F 142 LYS PRO ASP ALA PHE GLU ARG SER LEU VAL ALA GLU ILE SEQRES 3 F 142 MET GLY ARG ILE GLU LYS LYS ASN PHE LYS ILE VAL SER SEQRES 4 F 142 MET LYS PHE TRP SER LYS ALA PRO ARG ASN LEU ILE GLU SEQRES 5 F 142 GLN HIS TYR LYS GLU HIS SER GLU GLN SER TYR PHE ASN SEQRES 6 F 142 ASP ASN CYS ASP PHE MET VAL SER GLY PRO ILE ILE SER SEQRES 7 F 142 ILE VAL TYR GLU GLY THR ASP ALA ILE SER LYS ILE ARG SEQRES 8 F 142 ARG LEU GLN GLY ASN ILE LEU THR PRO GLY THR ILE ARG SEQRES 9 F 142 GLY ASP LEU ALA ASN ASP ILE GLY GLU ASN LEU ILE HIS SEQRES 10 F 142 ALA SER ASP SER GLU ASP SER ALA VAL ASP GLU ILE SER SEQRES 11 F 142 ILE TRP PHE PRO GLU THR LYS MET GLU THR ASP ASN HET MG A 160 1 HET TYD A 138 25 HET MG B 161 1 HET TYD B 138 25 HET MG C 162 1 HET TYD C 138 25 HET MG D 163 1 HET TYD D 138 25 HET MG E 164 1 HET TYD E 138 25 HET MG F 165 1 HET TYD F 138 25 HETNAM MG MAGNESIUM ION HETNAM TYD THYMIDINE-5'-DIPHOSPHATE FORMUL 7 MG 6(MG 2+) FORMUL 8 TYD 6(C10 H16 N2 O11 P2) FORMUL 19 HOH *33(H2 O) HELIX 1 1 LYS A 9 ARG A 15 1 7 HELIX 2 2 LEU A 17 LYS A 28 1 12 HELIX 3 3 PRO A 42 TYR A 50 1 9 HELIX 4 4 LYS A 51 SER A 54 5 4 HELIX 5 5 TYR A 58 VAL A 67 1 10 HELIX 6 6 ASP A 80 GLY A 90 1 11 HELIX 7 7 THR A 97 ALA A 103 1 7 HELIX 8 8 SER A 116 PHE A 128 1 13 HELIX 9 9 LYS B 9 ARG B 15 1 7 HELIX 10 10 LEU B 17 LYS B 28 1 12 HELIX 11 11 PRO B 42 LYS B 51 1 10 HELIX 12 12 GLU B 52 SER B 54 5 3 HELIX 13 13 TYR B 58 MET B 66 1 9 HELIX 14 14 ASP B 80 GLY B 90 1 11 HELIX 15 15 THR B 97 ALA B 103 1 7 HELIX 16 16 SER B 116 PHE B 128 1 13 HELIX 17 17 LYS C 9 ARG C 15 1 7 HELIX 18 18 LEU C 17 LYS C 28 1 12 HELIX 19 19 PRO C 42 TYR C 50 1 9 HELIX 20 20 LYS C 51 SER C 54 5 4 HELIX 21 21 TYR C 58 VAL C 67 1 10 HELIX 22 22 ASP C 80 GLY C 90 1 11 HELIX 23 23 THR C 97 ALA C 103 1 7 HELIX 24 24 SER C 116 PHE C 128 1 13 HELIX 25 25 LYS D 9 ARG D 15 1 7 HELIX 26 26 LEU D 17 LYS D 28 1 12 HELIX 27 27 PRO D 42 TYR D 50 1 9 HELIX 28 28 LYS D 51 SER D 54 5 4 HELIX 29 29 TYR D 58 VAL D 67 1 10 HELIX 30 30 ASP D 80 GLY D 90 1 11 HELIX 31 31 THR D 97 ALA D 103 1 7 HELIX 32 32 SER D 116 PHE D 128 1 13 HELIX 33 33 LYS E 9 ARG E 15 1 7 HELIX 34 34 LEU E 17 LYS E 28 1 12 HELIX 35 35 PRO E 42 TYR E 50 1 9 HELIX 36 36 LYS E 51 SER E 57 5 7 HELIX 37 37 TYR E 58 VAL E 67 1 10 HELIX 38 38 ASP E 80 GLY E 90 1 11 HELIX 39 39 THR E 97 ALA E 103 1 7 HELIX 40 40 SER E 116 PHE E 128 1 13 HELIX 41 41 LYS F 9 ARG F 15 1 7 HELIX 42 42 LEU F 17 LYS F 28 1 12 HELIX 43 43 PRO F 42 TYR F 50 1 9 HELIX 44 44 LYS F 51 GLN F 56 5 6 HELIX 45 45 TYR F 58 MET F 66 1 9 HELIX 46 46 ASP F 80 GLY F 90 1 11 HELIX 47 47 THR F 97 ALA F 103 1 7 HELIX 48 48 SER F 116 PHE F 128 1 13 SHEET 1 A 4 LYS A 31 TRP A 38 0 SHEET 2 A 4 ILE A 71 THR A 79 -1 O VAL A 75 N VAL A 33 SHEET 3 A 4 LEU A 1 ILE A 8 -1 N VAL A 6 O ILE A 74 SHEET 4 A 4 ILE A 111 ALA A 113 -1 O HIS A 112 N LEU A 7 SHEET 1 B 4 LYS B 31 TRP B 38 0 SHEET 2 B 4 ILE B 71 GLY B 78 -1 O VAL B 75 N SER B 34 SHEET 3 B 4 GLN B 2 ILE B 8 -1 N VAL B 6 O ILE B 74 SHEET 4 B 4 ILE B 111 ALA B 113 -1 O HIS B 112 N LEU B 7 SHEET 1 C 4 LYS C 31 TRP C 38 0 SHEET 2 C 4 ILE C 71 THR C 79 -1 O VAL C 75 N SER C 34 SHEET 3 C 4 LEU C 1 ILE C 8 -1 N VAL C 6 O ILE C 74 SHEET 4 C 4 ILE C 111 ALA C 113 -1 O HIS C 112 N LEU C 7 SHEET 1 D 4 LYS D 31 TRP D 38 0 SHEET 2 D 4 ILE D 71 THR D 79 -1 O VAL D 75 N SER D 34 SHEET 3 D 4 LEU D 1 ILE D 8 -1 N ILE D 8 O ILE D 72 SHEET 4 D 4 ILE D 111 ALA D 113 -1 O HIS D 112 N LEU D 7 SHEET 1 E 4 LYS E 31 TRP E 38 0 SHEET 2 E 4 ILE E 71 THR E 79 -1 O VAL E 75 N VAL E 33 SHEET 3 E 4 LEU E 1 ILE E 8 -1 N VAL E 6 O ILE E 74 SHEET 4 E 4 ILE E 111 ALA E 113 -1 O HIS E 112 N LEU E 7 SHEET 1 F 4 LYS F 31 TRP F 38 0 SHEET 2 F 4 ILE F 71 THR F 79 -1 O VAL F 75 N VAL F 33 SHEET 3 F 4 LEU F 1 ILE F 8 -1 N VAL F 6 O ILE F 74 SHEET 4 F 4 ILE F 111 ALA F 113 -1 O HIS F 112 N LEU F 7 LINK O2B TYD A 138 MG MG A 160 1555 1555 2.19 LINK O2B TYD B 138 MG MG B 161 1555 1555 2.38 LINK O1A TYD C 138 MG MG C 162 1555 1555 2.47 LINK O2B TYD C 138 MG MG C 162 1555 1555 2.34 LINK O2B TYD D 138 MG MG D 163 1555 1555 2.37 LINK O2B TYD E 138 MG MG E 164 1555 1555 2.36 LINK O1A TYD E 138 MG MG E 164 1555 1555 2.43 LINK O2B TYD F 138 MG MG F 165 1555 1555 2.48 SITE 1 AC1 2 ARG A 86 TYD A 138 SITE 1 AC2 3 ARG B 86 ASP B 115 TYD B 138 SITE 1 AC3 3 ARG C 86 ASP C 115 TYD C 138 SITE 1 AC4 3 ARG D 86 ASP D 115 TYD D 138 SITE 1 AC5 2 ARG E 86 TYD E 138 SITE 1 AC6 2 ASP F 115 TYD F 138 SITE 1 AC7 12 LYS A 9 TYR A 50 HIS A 53 TYR A 58 SITE 2 AC7 12 ASN A 62 ARG A 86 GLN A 89 ARG A 99 SITE 3 AC7 12 ILE A 106 GLY A 107 ASN A 109 MG A 160 SITE 1 AC8 10 LYS B 9 HIS B 53 TYR B 58 ASN B 62 SITE 2 AC8 10 ARG B 86 ARG B 99 ILE B 106 GLY B 107 SITE 3 AC8 10 ASN B 109 MG B 161 SITE 1 AC9 12 LYS C 9 TYR C 50 HIS C 53 TYR C 58 SITE 2 AC9 12 ASN C 62 ARG C 86 GLN C 89 ARG C 99 SITE 3 AC9 12 ILE C 106 GLY C 107 ASN C 109 MG C 162 SITE 1 BC1 12 LYS D 9 TYR D 50 HIS D 53 TYR D 58 SITE 2 BC1 12 ASN D 62 ARG D 86 GLN D 89 ARG D 99 SITE 3 BC1 12 ILE D 106 GLY D 107 ASN D 109 MG D 163 SITE 1 BC2 11 LYS E 9 TYR E 50 HIS E 53 TYR E 58 SITE 2 BC2 11 ASN E 62 ARG E 86 ARG E 99 ILE E 106 SITE 3 BC2 11 GLY E 107 ASN E 109 MG E 164 SITE 1 BC3 11 LYS F 9 TYR F 50 HIS F 53 TYR F 58 SITE 2 BC3 11 ARG F 86 GLN F 89 ARG F 99 ILE F 106 SITE 3 BC3 11 GLY F 107 ASN F 109 MG F 165 CRYST1 80.690 151.038 184.874 90.00 90.00 90.00 C 2 2 21 48 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 0.012393 0.000000 0.000000 0.00000 SCALE2 0.000000 0.006621 0.000000 0.00000 SCALE3 0.000000 0.000000 0.005409 0.00000