HEADER TRANSFERASE 19-NOV-08 3FBE TITLE CRYSTAL STRUCTURE OF THE MIMIVIRUS NDK N62L-R107G DOUBLE MUTANT TITLE 2 COMPLEXED WITH GDP 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 5 06-SEP-23 3FBE 1 REMARK REVDAT 4 20-OCT-21 3FBE 1 REMARK SEQADV REVDAT 3 24-JUL-19 3FBE 1 REMARK REVDAT 2 25-AUG-09 3FBE 1 JRNL REVDAT 1 16-JUN-09 3FBE 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. 2.40 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) : 2.40 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 : 43897 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.192 REMARK 3 R VALUE (WORKING SET) : 0.190 REMARK 3 FREE R VALUE : 0.230 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.040 REMARK 3 FREE R VALUE TEST SET COUNT : 2211 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 - 6.0300 0.97 2685 164 0.1920 0.2090 REMARK 3 2 6.0300 - 4.7930 1.00 2645 151 0.1690 0.2000 REMARK 3 3 4.7930 - 4.1900 1.00 2655 131 0.1470 0.1560 REMARK 3 4 4.1900 - 3.8070 1.00 2630 129 0.1600 0.1850 REMARK 3 5 3.8070 - 3.5350 1.00 2635 126 0.1730 0.1890 REMARK 3 6 3.5350 - 3.3270 1.00 2590 133 0.1900 0.1900 REMARK 3 7 3.3270 - 3.1610 1.00 2613 129 0.1940 0.2920 REMARK 3 8 3.1610 - 3.0230 1.00 2610 135 0.2160 0.2550 REMARK 3 9 3.0230 - 2.9070 1.00 2559 167 0.2060 0.2820 REMARK 3 10 2.9070 - 2.8070 1.00 2618 123 0.2080 0.2650 REMARK 3 11 2.8070 - 2.7190 1.00 2581 137 0.2210 0.2940 REMARK 3 12 2.7190 - 2.6410 1.00 2567 138 0.2080 0.2520 REMARK 3 13 2.6410 - 2.5720 1.00 2588 134 0.2110 0.2740 REMARK 3 14 2.5720 - 2.5090 1.00 2588 142 0.2360 0.2940 REMARK 3 15 2.5090 - 2.4520 1.00 2568 142 0.2330 0.3460 REMARK 3 16 2.4520 - 2.4000 1.00 2554 130 0.2330 0.3010 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 : 0.37 REMARK 3 B_SOL : 53.44 REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.320 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 23.190 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 48.70 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 44.06 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 1.54600 REMARK 3 B22 (A**2) : -2.40200 REMARK 3 B33 (A**2) : 0.85600 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 : 0.006 6595 REMARK 3 ANGLE : 1.111 8938 REMARK 3 CHIRALITY : 0.070 986 REMARK 3 PLANARITY : 0.004 1124 REMARK 3 DIHEDRAL : 21.384 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 3FBE COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 10-DEC-08. REMARK 100 THE DEPOSITION ID IS D_1000050381. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 09-SEP-07 REMARK 200 TEMPERATURE (KELVIN) : 105 REMARK 200 PH : 7.4 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ESRF REMARK 200 BEAMLINE : ID14-1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.934 REMARK 200 MONOCHROMATOR : DIAMOND (111), GE(220) REMARK 200 OPTICS : MIRRORS REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 210 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 43916 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.400 REMARK 200 RESOLUTION RANGE LOW (A) : 61.300 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 200 DATA REDUNDANCY : 7.200 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.07200 REMARK 200 FOR THE DATA SET : 7.7000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.40 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.53 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 6.90 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : 0.36500 REMARK 200 FOR SHELL : 2.100 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: 2B8P REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 57.05 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.86 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 40-44% MPD, 0.1M MOPS, PH 7.4, VAPOR REMARK 280 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 91.89250 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 91.89250 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 39.62150 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 76.44850 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 39.62150 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 76.44850 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 91.89250 REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 39.62150 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 76.44850 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 91.89250 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 39.62150 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 76.44850 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 300 REMARK: HOMOHEXAMER 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 158.48600 REMARK 350 BIOMT2 2 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 91.89250 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 GLU B 130 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: 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 29 30.99 71.69 REMARK 500 GLU A 55 50.03 -106.31 REMARK 500 ASN A 104 30.42 -148.08 REMARK 500 LEU A 110 -41.76 73.68 REMARK 500 GLU A 130 28.57 -76.14 REMARK 500 ASN B 104 21.40 -145.17 REMARK 500 LEU B 110 -45.62 74.94 REMARK 500 ASN C 29 22.13 81.93 REMARK 500 PRO C 95 150.45 -47.60 REMARK 500 LEU C 110 -45.42 71.56 REMARK 500 GLU C 130 71.64 -61.18 REMARK 500 ASN D 29 20.18 82.13 REMARK 500 LYS D 40 119.88 -161.61 REMARK 500 LEU D 110 -39.94 72.96 REMARK 500 GLU D 130 14.26 -56.52 REMARK 500 ASN E 29 27.85 81.96 REMARK 500 GLU E 52 -33.21 -39.76 REMARK 500 ASN E 104 10.04 -146.35 REMARK 500 LEU E 110 -43.90 77.71 REMARK 500 GLU E 130 50.15 -65.85 REMARK 500 ASN F 29 34.69 73.15 REMARK 500 ASN F 104 21.72 -144.48 REMARK 500 LEU F 110 -41.62 70.42 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 MG A 160 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GDP A 138 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GDP B 138 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG C 162 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GDP C 138 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG D 163 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GDP D 138 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG E 164 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GDP E 138 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG F 165 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GDP F 138 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2B8P RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF THE MIMIVIRUS NDK DBREF 3FBE A 2 137 UNP Q5UQL3 NDK_MIMIV 2 137 DBREF 3FBE B 2 137 UNP Q5UQL3 NDK_MIMIV 2 137 DBREF 3FBE C 2 137 UNP Q5UQL3 NDK_MIMIV 2 137 DBREF 3FBE D 2 137 UNP Q5UQL3 NDK_MIMIV 2 137 DBREF 3FBE E 2 137 UNP Q5UQL3 NDK_MIMIV 2 137 DBREF 3FBE F 2 137 UNP Q5UQL3 NDK_MIMIV 2 137 SEQADV 3FBE TYR A -4 UNP Q5UQL3 EXPRESSION TAG SEQADV 3FBE LYS A -3 UNP Q5UQL3 EXPRESSION TAG SEQADV 3FBE LYS A -2 UNP Q5UQL3 EXPRESSION TAG SEQADV 3FBE ALA A -1 UNP Q5UQL3 EXPRESSION TAG SEQADV 3FBE GLY A 0 UNP Q5UQL3 EXPRESSION TAG SEQADV 3FBE LEU A 1 UNP Q5UQL3 EXPRESSION TAG SEQADV 3FBE LEU A 62 UNP Q5UQL3 ASN 62 ENGINEERED MUTATION SEQADV 3FBE GLY A 107 UNP Q5UQL3 ARG 107 ENGINEERED MUTATION SEQADV 3FBE TYR B -4 UNP Q5UQL3 EXPRESSION TAG SEQADV 3FBE LYS B -3 UNP Q5UQL3 EXPRESSION TAG SEQADV 3FBE LYS B -2 UNP Q5UQL3 EXPRESSION TAG SEQADV 3FBE ALA B -1 UNP Q5UQL3 EXPRESSION TAG SEQADV 3FBE GLY B 0 UNP Q5UQL3 EXPRESSION TAG SEQADV 3FBE LEU B 1 UNP Q5UQL3 EXPRESSION TAG SEQADV 3FBE LEU B 62 UNP Q5UQL3 ASN 62 ENGINEERED MUTATION SEQADV 3FBE GLY B 107 UNP Q5UQL3 ARG 107 ENGINEERED MUTATION SEQADV 3FBE TYR C -4 UNP Q5UQL3 EXPRESSION TAG SEQADV 3FBE LYS C -3 UNP Q5UQL3 EXPRESSION TAG SEQADV 3FBE LYS C -2 UNP Q5UQL3 EXPRESSION TAG SEQADV 3FBE ALA C -1 UNP Q5UQL3 EXPRESSION TAG SEQADV 3FBE GLY C 0 UNP Q5UQL3 EXPRESSION TAG SEQADV 3FBE LEU C 1 UNP Q5UQL3 EXPRESSION TAG SEQADV 3FBE LEU C 62 UNP Q5UQL3 ASN 62 ENGINEERED MUTATION SEQADV 3FBE GLY C 107 UNP Q5UQL3 ARG 107 ENGINEERED MUTATION SEQADV 3FBE TYR D -4 UNP Q5UQL3 EXPRESSION TAG SEQADV 3FBE LYS D -3 UNP Q5UQL3 EXPRESSION TAG SEQADV 3FBE LYS D -2 UNP Q5UQL3 EXPRESSION TAG SEQADV 3FBE ALA D -1 UNP Q5UQL3 EXPRESSION TAG SEQADV 3FBE GLY D 0 UNP Q5UQL3 EXPRESSION TAG SEQADV 3FBE LEU D 1 UNP Q5UQL3 EXPRESSION TAG SEQADV 3FBE LEU D 62 UNP Q5UQL3 ASN 62 ENGINEERED MUTATION SEQADV 3FBE GLY D 107 UNP Q5UQL3 ARG 107 ENGINEERED MUTATION SEQADV 3FBE TYR E -4 UNP Q5UQL3 EXPRESSION TAG SEQADV 3FBE LYS E -3 UNP Q5UQL3 EXPRESSION TAG SEQADV 3FBE LYS E -2 UNP Q5UQL3 EXPRESSION TAG SEQADV 3FBE ALA E -1 UNP Q5UQL3 EXPRESSION TAG SEQADV 3FBE GLY E 0 UNP Q5UQL3 EXPRESSION TAG SEQADV 3FBE LEU E 1 UNP Q5UQL3 EXPRESSION TAG SEQADV 3FBE LEU E 62 UNP Q5UQL3 ASN 62 ENGINEERED MUTATION SEQADV 3FBE GLY E 107 UNP Q5UQL3 ARG 107 ENGINEERED MUTATION SEQADV 3FBE TYR F -4 UNP Q5UQL3 EXPRESSION TAG SEQADV 3FBE LYS F -3 UNP Q5UQL3 EXPRESSION TAG SEQADV 3FBE LYS F -2 UNP Q5UQL3 EXPRESSION TAG SEQADV 3FBE ALA F -1 UNP Q5UQL3 EXPRESSION TAG SEQADV 3FBE GLY F 0 UNP Q5UQL3 EXPRESSION TAG SEQADV 3FBE LEU F 1 UNP Q5UQL3 EXPRESSION TAG SEQADV 3FBE LEU F 62 UNP Q5UQL3 ASN 62 ENGINEERED MUTATION SEQADV 3FBE 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 LEU 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 LEU 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 LEU 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 LEU 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 LEU 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 LEU 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 GDP A 138 28 HET GDP B 138 28 HET MG C 162 1 HET GDP C 138 28 HET MG D 163 1 HET GDP D 138 28 HET MG E 164 1 HET GDP E 138 28 HET MG F 165 1 HET GDP F 138 28 HETNAM MG MAGNESIUM ION HETNAM GDP GUANOSINE-5'-DIPHOSPHATE FORMUL 7 MG 5(MG 2+) FORMUL 8 GDP 6(C10 H15 N5 O11 P2) FORMUL 18 HOH *150(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 TYR B 50 1 9 HELIX 12 12 LYS B 51 SER B 54 5 4 HELIX 13 13 TYR B 58 VAL B 67 1 10 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 SER D 68 1 11 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 54 5 4 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 SER F 54 5 4 HELIX 45 45 TYR F 58 VAL F 67 1 10 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 SER A 34 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 ILE B 71 N TRP B 38 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 GLU C 77 N LYS C 31 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 VAL D 33 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 ILE F 71 N TRP F 38 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 SITE 1 AC1 4 LYS A 9 TYR A 50 HIS A 112 GDP A 138 SITE 1 AC2 10 LYS A 9 HIS A 53 TYR A 58 ARG A 86 SITE 2 AC2 10 GLN A 89 ARG A 99 ILE A 106 GLY A 107 SITE 3 AC2 10 ASN A 109 MG A 160 SITE 1 AC3 7 HIS B 53 LEU B 62 ARG B 86 GLN B 89 SITE 2 AC3 7 GLY B 90 ARG B 99 ILE B 106 SITE 1 AC4 2 ARG C 86 GDP C 138 SITE 1 AC5 9 LYS C 9 HIS C 53 LEU C 62 ARG C 86 SITE 2 AC5 9 ARG C 99 ILE C 106 GLY C 107 ASN C 109 SITE 3 AC5 9 MG C 162 SITE 1 AC6 4 LYS D 9 TYR D 50 HIS D 112 GDP D 138 SITE 1 AC7 11 LYS D 9 HIS D 53 TYR D 58 LEU D 62 SITE 2 AC7 11 ARG D 86 GLN D 89 ARG D 99 ILE D 106 SITE 3 AC7 11 GLY D 107 ASN D 109 MG D 163 SITE 1 AC8 3 ARG E 86 ASP E 115 GDP E 138 SITE 1 AC9 10 LYS E 9 HIS E 53 LEU E 62 ARG E 86 SITE 2 AC9 10 ARG E 99 ILE E 106 GLY E 107 ASN E 109 SITE 3 AC9 10 HOH E 150 MG E 164 SITE 1 BC1 3 ARG F 86 ASP F 115 GDP F 138 SITE 1 BC2 8 LYS F 9 HIS F 53 ARG F 86 ARG F 99 SITE 2 BC2 8 ILE F 106 GLY F 107 ASN F 109 MG F 165 CRYST1 79.243 152.897 183.785 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 0.012619 0.000000 0.000000 0.00000 SCALE2 0.000000 0.006540 0.000000 0.00000 SCALE3 0.000000 0.000000 0.005441 0.00000