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- PDB-2b8p: Crystal structure of Acanthamoeba polyphaga mimivirus NDK, the fi... -

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Basic information

Entry
Database: PDB / ID: 2b8p
TitleCrystal structure of Acanthamoeba polyphaga mimivirus NDK, the first viral nucleoside diphosphate kinase
ComponentsProbable nucleoside diphosphate kinase
KeywordsTRANSFERASE / NDK / phosphotransferase / nucleotide binding
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 (NDPK)-like domain profile. / Nucleoside diphosphate kinase, active site / Nucleoside diphosphate kinase (NDPK) active site signature. / Nucleoside diphosphate kinase / 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 (NDPK)-like domain profile. / Nucleoside diphosphate kinase, active site / Nucleoside diphosphate kinase (NDPK) active site signature. / Nucleoside diphosphate kinase / 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
Nucleoside diphosphate kinase
Similarity search - Component
Biological speciesMimivirus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.55 Å
AuthorsJeudy, S. / 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 10, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 15, 2005Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 23, 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 / 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 / _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: Probable nucleoside diphosphate kinase
B: Probable nucleoside diphosphate kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,7336
Polymers36,3492
Non-polymers3844
Water1,36976
1
A: Probable nucleoside diphosphate kinase
B: Probable nucleoside diphosphate kinase
hetero molecules

A: Probable nucleoside diphosphate kinase
B: Probable nucleoside diphosphate kinase
hetero molecules

A: Probable nucleoside diphosphate kinase
B: Probable nucleoside diphosphate kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)110,20018
Polymers109,0476
Non-polymers1,15312
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_456z-1/2,-x+1/2,-y+11
crystal symmetry operation12_565-y+1/2,-z+1,x+1/21
Unit cell
Length a, b, c (Å)99.425, 99.425, 99.425
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number198
Space group name H-MP213
Components on special symmetry positions
IDModelComponents
11A-5034-

HOH

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Components

#1: Protein Probable nucleoside diphosphate kinase / NDK / NDP kinase


Mass: 18174.498 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mimivirus / Genus: Mimivirus / Gene: NDK / Plasmid: pDIGS02 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta(DE3)pLysS / References: UniProt: Q5UQL3, nucleoside-diphosphate kinase
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 76 / Source method: isolated from a natural source / Formula: H2O

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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: 2.26 Å3/Da / Density % sol: 45.5 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: Ammonium sulfate 1.6M, MES 0.1M, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.97563 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Dec 3, 2004 / Details: mirrors
RadiationMonochromator: silicon / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97563 Å / Relative weight: 1
ReflectionResolution: 2.55→70.36 Å / Num. obs: 8922 / % possible obs: 95.9 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 4.3 % / Biso Wilson estimate: 37.7 Å2 / Rmerge(I) obs: 0.059 / Rsym value: 0.059 / Net I/σ(I): 9.7
Reflection shellResolution: 2.55→2.64 Å / Redundancy: 1.7 % / Rmerge(I) obs: 0.256 / Mean I/σ(I) obs: 2.9 / Rsym value: 0.256 / % possible all: 94.1

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Processing

Software
NameVersionClassification
CNS1.1refinement
MOSFLMdata reduction
CCP4(SCALA)data scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1K44

1k44


Resolution: 2.55→24.12 Å / Rfactor Rfree error: 0.008 / Data cutoff high absF: 1541510.84 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.252 1067 10.3 %RANDOM
Rwork0.202 ---
obs0.202 10346 94.8 %-
all-8922 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 52.1508 Å2 / ksol: 0.376597 e/Å3
Displacement parametersBiso mean: 44.2 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.38 Å0.29 Å
Luzzati d res low-5 Å
Luzzati sigma a0.37 Å0.3 Å
Refinement stepCycle: LAST / Resolution: 2.55→24.12 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2083 0 20 76 2179
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d21.5
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.75
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
LS refinement shellResolution: 2.55→2.71 Å / Rfactor Rfree error: 0.026 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.342 178 10.7 %
Rwork0.262 1484 -
obs--93 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater.top
X-RAY DIFFRACTION3ion.paramion.top

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