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- PDB-2zua: Crystal structure of nucleoside diphosphate kinase from Haloarcul... -

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Basic information

Entry
Database: PDB / ID: 2zua
TitleCrystal structure of nucleoside diphosphate kinase from Haloarcula quadrata
ComponentsNucleoside diphosphate kinase
KeywordsTRANSFERASE / ferredoxin fold / Kpn loop / Kinase
Function / homology
Function and homology information


nucleoside-diphosphate kinase / UTP biosynthetic process / CTP biosynthetic process / GTP biosynthetic process / nucleoside diphosphate kinase activity / ATP binding / metal ion binding / cytoplasm
Similarity search - Function
Nucleoside diphosphate kinase-like domain / Nucleoside diphosphate kinase / 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
Nucleoside diphosphate kinase
Similarity search - Component
Biological speciesHaloarcula quadrata (Halophile)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.59 Å
AuthorsIchimura, T. / Yamamura, A. / Ohtsuka, J. / Miyazono, K. / Okai, M. / Nagata, K. / Tanokura, M.
CitationJournal: Biophys.J. / Year: 2009
Title: Molecular mechanism of distinct salt-dependent enzyme activity of two halophilic nucleoside diphosphate kinases
Authors: Yamamura, A. / Ichimura, T. / Kamekura, M. / Mizuki, T. / Usami, R. / Makino, T. / Ohtsuka, J. / Miyazono, K. / Okai, M. / Nagata, K. / Tanokura, M.
History
DepositionOct 15, 2008Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 25, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 2023Group: Data collection / Database references / 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Nucleoside diphosphate kinase
B: Nucleoside diphosphate kinase
C: Nucleoside diphosphate kinase
D: Nucleoside diphosphate kinase


Theoretical massNumber of molelcules
Total (without water)78,9464
Polymers78,9464
Non-polymers00
Water1267
1
A: Nucleoside diphosphate kinase
D: Nucleoside diphosphate kinase

A: Nucleoside diphosphate kinase
D: Nucleoside diphosphate kinase

A: Nucleoside diphosphate kinase
D: Nucleoside diphosphate kinase


Theoretical massNumber of molelcules
Total (without water)118,4206
Polymers118,4206
Non-polymers00
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
Buried area16930 Å2
ΔGint-75.3 kcal/mol
Surface area34600 Å2
MethodPISA
2
B: Nucleoside diphosphate kinase
C: Nucleoside diphosphate kinase

B: Nucleoside diphosphate kinase
C: Nucleoside diphosphate kinase

B: Nucleoside diphosphate kinase
C: Nucleoside diphosphate kinase


Theoretical massNumber of molelcules
Total (without water)118,4206
Polymers118,4206
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
Buried area16810 Å2
ΔGint-75.4 kcal/mol
Surface area34690 Å2
MethodPISA
Unit cell
Length a, b, c (Å)73.571, 73.571, 214.271
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number173
Space group name H-MP63

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Components

#1: Protein
Nucleoside diphosphate kinase


Mass: 19736.604 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Haloarcula quadrata (Halophile) / Strain: JCM 11048 / Gene: ndk / Plasmid: pET-28a(+) / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta(DE3) / References: UniProt: Q401C5
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 7 / 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: 2.12 Å3/Da / Density % sol: 41.99 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.6
Details: 100mM HEPES-NaOH, 25% PEG400, 10mM EDTA, pH7.6, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NW12A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Oct 11, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.59→50 Å / Num. obs: 20457 / % possible obs: 95.7 % / Rmerge(I) obs: 0.084 / Net I/σ(I): 30.7

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1BHN

1bhn


Resolution: 2.59→47.57 Å / Cor.coef. Fo:Fc: 0.935 / Cor.coef. Fo:Fc free: 0.88 / SU B: 14.645 / SU ML: 0.314 / Cross valid method: THROUGHOUT / ESU R Free: 0.398 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2894 990 5.1 %RANDOM
Rwork0.2218 ---
obs0.22524 18544 95.71 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 46.978 Å2
Baniso -1Baniso -2Baniso -3
1--0.1 Å2-0.05 Å20 Å2
2---0.1 Å20 Å2
3---0.15 Å2
Refinement stepCycle: LAST / Resolution: 2.59→47.57 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4894 0 0 7 4901
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0215002
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.2381.9396748
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8395607
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.57124.865296
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.47315835
X-RAY DIFFRACTIONr_dihedral_angle_4_deg25.3531536
X-RAY DIFFRACTIONr_chiral_restr0.0960.2679
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.023996
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2140.22272
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3070.23366
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1520.2162
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2080.2133
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2720.28
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.4491.53106
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.77824808
X-RAY DIFFRACTIONr_scbond_it1.0732159
X-RAY DIFFRACTIONr_scangle_it1.6944.51940
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.59→2.657 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.384 60 -
Rwork0.299 1465 -
obs--99.93 %

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