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- PDB-3gp9: Crystal structure of the Mimivirus NDK complexed with GDP -

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Basic information

Entry
Database: PDB / ID: 3gp9
TitleCrystal structure of the Mimivirus NDK complexed with GDP
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
GUANOSINE-5'-DIPHOSPHATE / PHOSPHATE ION / Nucleoside diphosphate kinase
Similarity search - Component
Biological speciesAcanthamoeba polyphaga mimivirus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 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
DepositionMar 23, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 11, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Sep 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

Downloads & links

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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)101,18424
Polymers97,8096
Non-polymers3,37518
Water12,214678
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)101,18424
Polymers97,8096
Non-polymers3,37518
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)101,18424
Polymers97,8096
Non-polymers3,37518
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)79.482, 152.951, 183.858
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-563-

HOH

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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-GDP / GUANOSINE-5'-DIPHOSPHATE


Type: RNA linking / Mass: 443.201 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C10H15N5O11P2 / Comment: GDP, energy-carrying molecule*YM
#3: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: PO4
#4: Chemical
ChemComp-MG / MAGNESIUM ION


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


Mass: 18.015 Da / Num. of mol.: 678 / 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: 2.86 Å3/Da / Density % sol: 56.94 %
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: 105 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 1.064 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 23, 2007 / Details: mirrors
RadiationMonochromator: Si(311) and Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.064 Å / Relative weight: 1
ReflectionResolution: 1.8→70.5 Å / Num. obs: 102912 / % possible obs: 99.4 % / Redundancy: 3.9 % / Biso Wilson estimate: 24.4 Å2 / Rsym value: 0.063 / Net I/σ(I): 6.4
Reflection shellResolution: 1.9→2 Å / Redundancy: 3.9 % / Mean I/σ(I) obs: 3.2 / Num. unique all: 12476 / Rsym value: 0.233 / % possible all: 99.4

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
AMoREphasing
PHENIX(phenix.refine)refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2b8q

2b8q


Resolution: 1.8→70.527 Å / Occupancy max: 1 / Occupancy min: 0.64 / SU ML: 0.24 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 21.8 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.22 5150 5 %random
Rwork0.188 97762 --
obs0.19 102912 99.31 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 54.686 Å2 / ksol: 0.361 e/Å3
Displacement parametersBiso max: 184.1 Å2 / Biso mean: 28.391 Å2 / Biso min: 12.52 Å2
Baniso -1Baniso -2Baniso -3
1--1.776 Å20 Å20 Å2
2--0.533 Å20 Å2
3---1.243 Å2
Refinement stepCycle: LAST / Resolution: 1.8→70.527 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6331 0 204 678 7213
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0056655
X-RAY DIFFRACTIONf_angle_d0.9939020
X-RAY DIFFRACTIONf_chiral_restr0.069984
X-RAY DIFFRACTIONf_plane_restr0.0031135
X-RAY DIFFRACTIONf_dihedral_angle_d19.1922492
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.8-1.8210.3011790.26932003379100
1.821-1.8420.271650.25432953460100
1.842-1.8640.2791770.24932113388100
1.864-1.8880.291640.23232773441100
1.888-1.9130.2411730.22132493422100
1.913-1.9390.2421840.20832333417100
1.939-1.9670.2551680.19732473415100
1.967-1.9960.2461580.21132673425100
1.996-2.0270.2491710.20932383409100
2.027-2.060.2261720.19932593431100
2.06-2.0960.2491410.19633073448100
2.096-2.1340.231690.20332383407100
2.134-2.1750.2221640.19132663430100
2.175-2.220.231800.18932543434100
2.22-2.2680.2451820.19432713453100
2.268-2.3210.2281610.19132593420100
2.321-2.3790.2111540.18732463400100
2.379-2.4430.2361570.19333003457100
2.443-2.5150.2381700.20332493419100
2.515-2.5960.2631800.21532633443100
2.596-2.6890.221630.2013283344699
2.689-2.7960.2442090.2013205341499
2.796-2.9240.2281820.1943254343699
2.924-3.0780.2351780.1973289346799
3.078-3.2710.1931710.1783247341899
3.271-3.5230.1981740.1673260343499
3.523-3.8780.1891770.1633276345399
3.878-4.4390.1641960.1533217341397
4.439-5.5920.1751490.1523247339696
5.592-70.5820.2311820.1893355353796

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