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- PDB-3elh: X-ray structure of Acanthamoeba ployphaga mimivirus nucleoside di... -

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Basic information

Entry
Database: PDB / ID: 3elh
TitleX-ray structure of Acanthamoeba ployphaga mimivirus nucleoside diphosphate kinase complexed with dUDP
ComponentsNucleoside diphosphate kinase
KeywordsTRANSFERASE / nucleoside diphosphate kinase mimivirus 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
DEOXYURIDINE-5'-DIPHOSPHATE / Nucleoside diphosphate kinase
Similarity search - Component
Biological speciesAcanthamoeba polyphaga mimivirus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 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
DepositionSep 22, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 16, 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 / 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: Nucleoside diphosphate kinase
B: Nucleoside diphosphate kinase
C: Nucleoside diphosphate kinase
D: Nucleoside diphosphate kinase
E: Nucleoside diphosphate kinase
F: Nucleoside diphosphate kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)100,28418
Polymers97,8096
Non-polymers2,47512
Water2,720151
1
A: Nucleoside diphosphate kinase
C: Nucleoside diphosphate kinase
E: Nucleoside diphosphate kinase
hetero molecules

A: Nucleoside diphosphate kinase
C: Nucleoside diphosphate kinase
E: Nucleoside diphosphate kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)100,28418
Polymers97,8096
Non-polymers2,47512
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555x,-y,-z1
2
B: Nucleoside diphosphate kinase
D: Nucleoside diphosphate kinase
F: Nucleoside diphosphate kinase
hetero molecules

B: Nucleoside diphosphate kinase
D: Nucleoside diphosphate kinase
F: Nucleoside diphosphate kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)100,28418
Polymers97,8096
Non-polymers2,47512
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_755-x+2,y,-z+1/21
Unit cell
Length a, b, c (Å)80.717, 153.576, 185.795
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

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


Mass: 16301.495 Da / Num. of mol.: 6
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-DUD / DEOXYURIDINE-5'-DIPHOSPHATE


Mass: 388.162 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C9H14N2O11P2
#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 151 / 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: 2.94 Å3/Da / Density % sol: 58.21 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.4
Details: 40 to 44% MPD, 0.1M MOPS, pH 7.4, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 1.064 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: May 22, 2007
RadiationMonochromator: Si111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.064 Å / Relative weight: 1
ReflectionResolution: 2.4→70.7 Å / Num. obs: 43019 / % possible obs: 99.3 % / Redundancy: 4.8 % / Biso Wilson estimate: 52.823 Å2 / Rsym value: 0.6 / Net I/σ(I): 8.2
Reflection shellResolution: 2.4→2.53 Å / Redundancy: 5 % / Mean I/σ(I) obs: 2 / Num. unique all: 6280 / Rsym value: 0.378 / % possible all: 99.6

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Processing

Software
NameVersionClassification
PHENIXrefinement
AMoREphasing
REFMAC5refinement
MOSFLMdata reduction
SCALAdata scaling
ADSCQuantumdata collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2B8Q

2b8q


Resolution: 2.4→19.872 Å / Occupancy max: 1 / Occupancy min: 1 / SU ML: 0.33 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 24.93 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.231 2274 5.05 %RANDOM
Rwork0.193 42733 --
obs0.195 45007 99.13 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 52.992 Å2 / ksol: 0.361 e/Å3
Displacement parametersBiso max: 102.1 Å2 / Biso mean: 46.689 Å2 / Biso min: 27.91 Å2
Baniso -1Baniso -2Baniso -3
1-0.056 Å20 Å20 Å2
2---0.04 Å20 Å2
3----0.016 Å2
Refinement stepCycle: LAST / Resolution: 2.4→19.872 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6338 0 150 151 6639
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0066608
X-RAY DIFFRACTIONf_angle_d1.0888940
X-RAY DIFFRACTIONf_chiral_restr0.066980
X-RAY DIFFRACTIONf_plane_restr0.0041136
X-RAY DIFFRACTIONf_dihedral_angle_d23.6552494
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.4-2.45210.3091400.2454262099
2.4521-2.5090.29191400.2477264799
2.509-2.57160.37461230.24642682100
2.5716-2.6410.27841440.2442650100
2.641-2.71860.30051480.23582654100
2.7186-2.80610.32281390.24822668100
2.8061-2.90610.28451290.2376266899
2.9061-3.0220.26531350.2221265199
3.022-3.15910.30361400.22712662100
3.1591-3.32490.22651320.2044269099
3.3249-3.53210.22711440.1868265899
3.5321-3.80310.20141520.1883266199
3.8031-4.18260.21331370.1661268199
4.1826-4.78040.18181340.1519269398
4.7804-5.99530.20351560.1644269299
5.9953-19.87240.16551810.1561275698

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