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- PDB-3evo: Crystal structure of the Mimivirus NDK +Kpn mutant complexed with dTDP -

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Basic information

Entry
Database: PDB / ID: 3evo
TitleCrystal structure of the Mimivirus NDK +Kpn mutant complexed with dTDP
ComponentsNucleoside diphosphate kinase
KeywordsTRANSFERASE / phosphotransferase nucleotide binding / ATP-binding / Kinase / Magnesium / Metal-binding / Nucleotide metabolism / Nucleotide-binding / Phosphoprotein
Function / homology
Function and homology information


nucleoside-diphosphate kinase / UTP biosynthetic process / CTP biosynthetic process / nucleoside diphosphate kinase activity / GTP biosynthetic process / ATP binding / metal ion binding
Similarity search - Function
Nucleoside diphosphate kinase-like domain / Nucleoside diphosphate kinase, active site / Nucleoside diphosphate kinase (NDPK) active site signature. / Nucleoside diphosphate kinase / Nucleoside diphosphate kinase (NDPK)-like domain profile. / Nucleoside diphosphate kinase-like domain / Nucleoside diphosphate kinase / NDK / Nucleoside diphosphate kinase-like domain superfamily / Alpha-Beta Plaits ...Nucleoside diphosphate kinase-like domain / Nucleoside diphosphate kinase, active site / Nucleoside diphosphate kinase (NDPK) active site signature. / Nucleoside diphosphate kinase / Nucleoside diphosphate kinase (NDPK)-like domain profile. / Nucleoside diphosphate kinase-like domain / Nucleoside diphosphate kinase / NDK / Nucleoside diphosphate kinase-like domain superfamily / Alpha-Beta Plaits / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
THYMIDINE-5'-DIPHOSPHATE / Nucleoside diphosphate kinase
Similarity search - Component
Biological speciesAcanthamoeba polyphaga mimivirus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsJeudy, S. / Lartigue, A. / Claverie, J.M. / Abergel, C.
CitationJournal: J.Virol. / Year: 2009
Title: Dissecting the unique nucleotide specificity of mimivirus nucleoside diphosphate kinase.
Authors: Jeudy, S. / Lartigue, A. / Claverie, J.M. / Abergel, C.
History
DepositionOct 13, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 25, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jul 24, 2019Group: Data collection / Refinement description / Category: software
Item: _software.classification / _software.name / _software.version
Revision 1.3Sep 6, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Nucleoside diphosphate kinase
B: Nucleoside diphosphate kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,1116
Polymers33,2582
Non-polymers8534
Water7,530418
1
A: Nucleoside diphosphate kinase
B: Nucleoside diphosphate kinase
hetero molecules

A: Nucleoside diphosphate kinase
B: Nucleoside diphosphate kinase
hetero molecules

A: Nucleoside diphosphate kinase
B: Nucleoside diphosphate kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)102,33218
Polymers99,7736
Non-polymers2,55912
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-y+1,x-y,z1
crystal symmetry operation3_665-x+y+1,-x+1,z1
Buried area2930 Å2
ΔGint-44 kcal/mol
Surface area12490 Å2
Unit cell
Length a, b, c (Å)69.759, 69.759, 103.262
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number173
Space group name H-MP63
Components on special symmetry positions
IDModelComponents
11A-210-

HOH

21A-250-

HOH

31A-279-

HOH

41B-197-

HOH

51B-338-

HOH

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Components

#1: Protein Nucleoside diphosphate kinase / NDP kinase / NDK


Mass: 16628.791 Da / Num. of mol.: 2 / Mutation: +Kpn
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Acanthamoeba polyphaga mimivirus / Gene: MIMI_R418, NDK / Plasmid: pDIGS02 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta(DE3)pLysS / References: UniProt: Q5UQL3, nucleoside-diphosphate kinase
#2: Chemical ChemComp-TYD / THYMIDINE-5'-DIPHOSPHATE


Mass: 402.188 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H16N2O11P2
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 418 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsRESIDUES 92-94 ILT WERE REPLACED BY RESIDUES 92-98 TNPLASA.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.18 Å3/Da / Density % sol: 43.6 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.6
Details: 1.1M sodium citrate, 0.1M Tris, pH 7.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 105 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-3 / Wavelength: 0.931 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jun 26, 2007 / Details: mirrors
RadiationMonochromator: Diamond (111), Ge(220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.931 Å / Relative weight: 1
ReflectionResolution: 1.5→35 Å / Num. obs: 43329 / % possible obs: 95.2 % / Redundancy: 6 % / Biso Wilson estimate: 16.3 Å2 / Rsym value: 0.036 / Net I/σ(I): 11.9
Reflection shellResolution: 1.5→1.58 Å / Redundancy: 2.5 % / Mean I/σ(I) obs: 3 / Num. unique all: 3652 / Rsym value: 0.254 / % possible all: 74.6

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Processing

Software
NameVersionClassification
PHENIXrefinement
AMoREphasing
REFMAC5.2refinement
MOSFLMdata reduction
SCALAdata scaling
ADSCQuantumdata collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2b8p

2b8p


Resolution: 1.5→29.907 Å / Occupancy max: 1 / Occupancy min: 0.7 / SU ML: 0.13 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 17.86 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.185 2187 5.05 %RANDOM
Rwork0.16 41142 --
obs0.161 43329 95.21 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 48.399 Å2 / ksol: 0.389 e/Å3
Displacement parametersBiso max: 68.36 Å2 / Biso mean: 18.421 Å2 / Biso min: 6.34 Å2
Baniso -1Baniso -2Baniso -3
1-0.157 Å2-0 Å2-0 Å2
2--0.157 Å2-0 Å2
3----0.314 Å2
Refinement stepCycle: LAST / Resolution: 1.5→29.907 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2126 0 52 418 2596
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072220
X-RAY DIFFRACTIONf_angle_d1.3363008
X-RAY DIFFRACTIONf_chiral_restr0.08328
X-RAY DIFFRACTIONf_plane_restr0.005384
X-RAY DIFFRACTIONf_dihedral_angle_d19.694836
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 16

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.5-1.5330.2371000.2171859195969
1.533-1.5680.2471270.1912056218377
1.568-1.6070.2191330.1782283241685
1.607-1.6510.211460.1642486263293
1.651-1.6990.1921550.1532664281999
1.699-1.7540.1711380.1526962834100
1.754-1.8170.1831280.15126772805100
1.817-1.890.1951440.16127442888100
1.89-1.9760.1851290.1626892818100
1.976-2.080.1761470.15826962843100
2.08-2.210.1911390.15726842823100
2.21-2.3810.2011370.16327192856100
2.381-2.620.2121170.16427312848100
2.62-2.9990.171350.1727142849100
2.999-3.7770.1661440.14127322876100
3.777-29.9130.1681680.15127122880100

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