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- PDB-3gpa: Crystal structure of the Mimivirus NDK N62L mutant complexed with CDP -

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Basic information

Entry
Database: PDB / ID: 3gpa
TitleCrystal structure of the Mimivirus NDK N62L mutant complexed with CDP
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
CYTIDINE-5'-DIPHOSPHATE / PHOSPHATE ION / Nucleoside diphosphate kinase
Similarity search - Component
Biological speciesAcanthamoeba polyphaga mimivirus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 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 1.2Jul 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 / pdbx_struct_conn_angle ...database_2 / 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_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_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
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
C: Nucleoside diphosphate kinase
E: Nucleoside diphosphate kinase
B: Nucleoside diphosphate kinase
D: Nucleoside diphosphate kinase
F: Nucleoside diphosphate kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)100,46319
Polymers97,8036
Non-polymers2,66013
Water6,612367
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)100,55820
Polymers97,8036
Non-polymers2,75514
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)100,36818
Polymers97,8036
Non-polymers2,56512
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)79.640, 152.421, 184.653
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: 16300.550 Da / Num. of mol.: 6 / Mutation: N62L
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-CDP / CYTIDINE-5'-DIPHOSPHATE


Mass: 403.176 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C9H15N3O11P2
#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 367 / 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: 57.06 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: Hepes 0.1M, 40 to 44% MPD, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 105 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Sep 10, 2007 / Details: mirrors
RadiationMonochromator: Si(111) and Si(311) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2→77 Å / Num. obs: 73214 / % possible obs: 96.5 % / Redundancy: 4.5 % / Biso Wilson estimate: 37 Å2 / Rsym value: 0.052 / Net I/σ(I): 8.8
Reflection shellResolution: 2→2.11 Å / Redundancy: 3 % / Mean I/σ(I) obs: 1.7 / Num. unique all: 6904 / Rsym value: 0.454 / % possible all: 96.5

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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: 2b8q

2b8q


Resolution: 2→70.446 Å / Occupancy max: 1 / Occupancy min: 1 / SU ML: 0.26 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 24.02 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.229 3668 5.01 %random
Rwork0.192 69546 --
obs0.194 73214 96.32 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 52.865 Å2 / ksol: 0.382 e/Å3
Displacement parametersBiso max: 75.35 Å2 / Biso mean: 37.689 Å2 / Biso min: 20 Å2
Baniso -1Baniso -2Baniso -3
1-0.831 Å20 Å20 Å2
2---0.394 Å20 Å2
3----0.437 Å2
Refinement stepCycle: LAST / Resolution: 2→70.446 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6301 0 161 367 6829
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0076581
X-RAY DIFFRACTIONf_angle_d1.2168906
X-RAY DIFFRACTIONf_chiral_restr0.075982
X-RAY DIFFRACTIONf_plane_restr0.0041125
X-RAY DIFFRACTIONf_dihedral_angle_d21.9212482
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 26

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2-2.0260.3311100.2852155226580
2.026-2.0540.3021040.2722320242483
2.054-2.0830.2821050.2612366247186
2.083-2.1150.3061110.2622450256189
2.115-2.1480.291450.2562523266892
2.148-2.1830.311390.2322629276897
2.183-2.220.2791480.21827502898100
2.22-2.2610.2851510.21727552906100
2.261-2.3040.2811600.20927152875100
2.304-2.3510.2521470.21427432890100
2.351-2.4020.2421300.2127802910100
2.402-2.4580.2741450.2072750289599
2.458-2.520.3121430.2182744288799
2.52-2.5880.2461260.2192750287699
2.588-2.6640.2481490.2112752290199
2.664-2.750.281520.2162742289499
2.75-2.8480.2541300.2182771290199
2.848-2.9630.2581410.2172762290399
2.963-3.0970.2961440.2192747289199
3.097-3.2610.2351330.192760289399
3.261-3.4650.2311670.1762776294399
3.465-3.7320.1881470.1662758290599
3.732-4.1080.1841670.1562746291399
4.108-4.7020.1721390.1412763290298
4.702-5.9240.1711640.1582766293098
5.924-70.490.1991710.1752773294494

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