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- PDB-3ee3: Crystal structure of Acanthamoeba polyphaga mimivirus nucleoside ... -

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Basic information

Entry
Database: PDB / ID: 3ee3
TitleCrystal structure of Acanthamoeba polyphaga mimivirus nucleoside diphosphate kinase complexed with CDP
ComponentsNucleoside diphosphate kinase
KeywordsTRANSFERASE / phosphotransferase ATP-binding mimivirus / 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 / 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 4, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 16, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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)100,37418
Polymers97,8096
Non-polymers2,56512
Water2,828157
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)100,37418
Polymers97,8096
Non-polymers2,56512
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)100,37418
Polymers97,8096
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)82.419, 154.419, 187.039
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: NDK, MIMI_R418 / Plasmid: pDIS02 / 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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 157 / 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: 3.04 Å3/Da / Density % sol: 59.57 %
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: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 1.064 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 24, 2007 / Details: mirrors
RadiationMonochromator: Si(311) and Si(111) cut / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.064 Å / Relative weight: 1
ReflectionResolution: 2.4→95.3 Å / Num. all: 45481 / Num. obs: 45481 / % possible obs: 99.7 % / Redundancy: 4.7 % / Biso Wilson estimate: 56.3 Å2 / Rsym value: 0.077 / Net I/σ(I): 6
Reflection shellResolution: 2.4→2.53 Å / Redundancy: 4.8 % / Mean I/σ(I) obs: 1.7 / Num. unique all: 6609 / Rsym value: 0.433 / % possible all: 99.9

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
AMoREphasing
REFMAC5.2.0005refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.4→20 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.938 / SU B: 7.5 / SU ML: 0.17 / Cross valid method: THROUGHOUT / ESU R: 0.29 / ESU R Free: 0.221 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.23347 2366 5.1 %RANDOM
Rwork0.1944 ---
obs0.19635 44357 99.59 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 47.789 Å2
Baniso -1Baniso -2Baniso -3
1-0.08 Å20 Å20 Å2
2---0.12 Å20 Å2
3---0.04 Å2
Refinement stepCycle: LAST / Resolution: 2.4→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6312 0 156 157 6625
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0226594
X-RAY DIFFRACTIONr_angle_refined_deg1.5421.9838928
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7615780
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.85124.286315
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.887151185
X-RAY DIFFRACTIONr_dihedral_angle_4_deg25.6981548
X-RAY DIFFRACTIONr_chiral_restr0.10.2981
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.024914
X-RAY DIFFRACTIONr_nbd_refined0.2080.22552
X-RAY DIFFRACTIONr_nbtor_refined0.2990.24401
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1470.2309
X-RAY DIFFRACTIONr_metal_ion_refined0.0780.21
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2220.267
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1770.24
X-RAY DIFFRACTIONr_mcbond_it0.7321.54076
X-RAY DIFFRACTIONr_mcangle_it1.30926363
X-RAY DIFFRACTIONr_scbond_it1.85732897
X-RAY DIFFRACTIONr_scangle_it3.0184.52565
LS refinement shellResolution: 2.4→2.461 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.364 176 -
Rwork0.293 3198 -
obs--99.82 %

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