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- PDB-2b8q: X-ray structure of Acanthamoeba ployphaga mimivirus nucleoside di... -

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Basic information

Entry
Database: PDB / ID: 2b8q
TitleX-ray structure of Acanthamoeba ployphaga mimivirus nucleoside diphosphate kinase complexed with TDP
ComponentsProbable nucleoside diphosphate kinase
KeywordsTRANSFERASE / NDK / TDP / phosphotranferase
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
PHOSPHATE ION / THYMIDINE-5'-DIPHOSPHATE / Nucleoside diphosphate kinase
Similarity search - Component
Biological speciesMimivirus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 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 / 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.ptnr1_label_seq_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.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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.ptnr1_label_seq_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_conn.ptnr2_label_seq_id / _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
C: Probable nucleoside diphosphate kinase
D: Probable nucleoside diphosphate kinase
E: Probable nucleoside diphosphate kinase
F: Probable nucleoside diphosphate kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)100,46319
Polymers97,8096
Non-polymers2,65413
Water2,756153
1
A: Probable nucleoside diphosphate kinase
C: Probable nucleoside diphosphate kinase
E: Probable nucleoside diphosphate kinase
hetero molecules

A: Probable nucleoside diphosphate kinase
C: Probable nucleoside diphosphate kinase
E: Probable nucleoside diphosphate kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)100,55820
Polymers97,8096
Non-polymers2,74914
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555x,-y,-z1
2
B: Probable nucleoside diphosphate kinase
D: Probable nucleoside diphosphate kinase
F: Probable nucleoside diphosphate kinase
hetero molecules

B: Probable nucleoside diphosphate kinase
D: Probable nucleoside diphosphate kinase
F: Probable nucleoside diphosphate kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)100,36818
Polymers97,8096
Non-polymers2,55912
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)80.390, 153.352, 185.491
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
Probable nucleoside diphosphate kinase / NDK / NDP kinase


Mass: 16301.495 Da / Num. of mol.: 6
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-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Mg
#3: Chemical
ChemComp-TYD / THYMIDINE-5'-DIPHOSPHATE


Mass: 402.188 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C10H16N2O11P2
#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.: 153 / 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: 3.14 Å3/Da / Density % sol: 60.5 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 44% MPD, 0.1M hepes, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.97565 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Jul 6, 2005 / Details: mirrors
RadiationMonochromator: silicon / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97565 Å / Relative weight: 1
ReflectionResolution: 2.5→66.5 Å / Num. obs: 39727 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5 % / Biso Wilson estimate: 51 Å2 / Rmerge(I) obs: 0.079 / Rsym value: 0.079 / Net I/σ(I): 5.9
Reflection shellResolution: 2.5→2.64 Å / Redundancy: 5 % / Rmerge(I) obs: 0.355 / Mean I/σ(I) obs: 2 / Rsym value: 0.355 / % possible all: 100

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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 2B8P

2b8p


Resolution: 2.5→29.55 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 2483223.13 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Details: REFMAC was also used for the refinement.
RfactorNum. reflection% reflectionSelection details
Rfree0.231 2003 5 %RANDOM
Rwork0.199 ---
obs0.199 40011 99.8 %-
all-40011 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 31.6874 Å2 / ksol: 0.324969 e/Å3
Displacement parametersBiso mean: 44.6 Å2
Baniso -1Baniso -2Baniso -3
1-8.59 Å20 Å20 Å2
2---8.09 Å20 Å2
3----0.5 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.36 Å0.3 Å
Luzzati d res low-5 Å
Luzzati sigma a0.46 Å0.35 Å
Refinement stepCycle: LAST / Resolution: 2.5→29.55 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6344 0 161 153 6658
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_deg1.5
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d22.5
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d2.34
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: 2.5→2.66 Å / Rfactor Rfree error: 0.019 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.353 333 5.1 %
Rwork0.311 6258 -
obs--100 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater.top
X-RAY DIFFRACTION3tdp.paramion.top
X-RAY DIFFRACTION4ion.paramtdp.top

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