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- PDB-3ena: Crystal structure of the mimivirus NDK +Kpn-N62L-R107G triple mut... -

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Basic information

Entry
Database: PDB / ID: 3ena
TitleCrystal structure of the mimivirus NDK +Kpn-N62L-R107G triple mutant complexed with dGDP
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
2'-DEOXYGUANOSINE-5'-DIPHOSPHATE / Nucleoside diphosphate kinase
Similarity search - Component
Biological speciesAcanthamoeba polyphaga mimivirus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 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 25, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 11, 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 1.3Oct 20, 2021Group: Database references / Derived calculations
Category: database_2 / struct_conn ...database_2 / 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 / _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
Revision 1.4Sep 6, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,9586
Polymers33,0552
Non-polymers9034
Water4,468248
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)101,87518
Polymers99,1666
Non-polymers2,70912
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
Unit cell
Length a, b, c (Å)70.358, 70.358, 104.295
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-285-

HOH

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Components

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


Mass: 16527.703 Da / Num. of mol.: 2 / Mutation: +Kpn, N62L, R107G
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-DGI / 2'-DEOXYGUANOSINE-5'-DIPHOSPHATE


Type: DNA linking / Mass: 427.201 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H15N5O10P2
#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.: 248 / 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: 2.25 Å3/Da / Density % sol: 45.44 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.6
Details: 0.8 to 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: ID14-1 / Wavelength: 0.934 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Sep 9, 2007
RadiationMonochromator: Diamond (111), Ge(220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.934 Å / Relative weight: 1
ReflectionResolution: 1.6→52.6 Å / Num. obs: 38444 / % possible obs: 99.8 % / Redundancy: 5 % / Biso Wilson estimate: 16.26 Å2 / Rmerge(I) obs: 0.042 / Net I/σ(I): 11.2
Reflection shellResolution: 1.6→1.69 Å / Redundancy: 4.2 % / Rmerge(I) obs: 0.229 / Mean I/σ(I) obs: 3.3 / Num. unique all: 5608

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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: 1.6→52.611 Å / Occupancy max: 1 / Occupancy min: 0.9 / SU ML: 0.21 / Cross valid method: THROUGHOUT / σ(F): 1.6 / Phase error: 18.2 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.202 1922 5 %
Rwork0.168 36522 -
obs0.17 38444 99.67 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 50.181 Å2 / ksol: 0.378 e/Å3
Displacement parametersBiso max: 47.13 Å2 / Biso mean: 16.354 Å2 / Biso min: 6.3 Å2
Baniso -1Baniso -2Baniso -3
1--0.198 Å2-0 Å20 Å2
2---0.198 Å20 Å2
3---0.396 Å2
Refinement stepCycle: LAST / Resolution: 1.6→52.611 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2121 0 56 248 2425
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072221
X-RAY DIFFRACTIONf_angle_d1.1913012
X-RAY DIFFRACTIONf_chiral_restr0.07329
X-RAY DIFFRACTIONf_plane_restr0.005382
X-RAY DIFFRACTIONf_dihedral_angle_d17.731830
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.6-1.640.2321380.17826072745100
1.64-1.6840.1961430.17126012744100
1.684-1.7340.2451180.16626322750100
1.734-1.790.2091400.16126122752100
1.79-1.8540.2071290.16526232752100
1.854-1.9280.2411290.16325972726100
1.928-2.0160.2021340.1726232757100
2.016-2.1220.181390.16526012740100
2.122-2.2550.2271450.15726042749100
2.255-2.4290.1991430.16926362779100
2.429-2.6740.2211440.18125942738100
2.674-3.0610.2261550.18126082763100
3.061-3.8560.1771230.1592614273799
3.856-52.640.171420.1562570271297

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