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- PDB-1nb2: Crystal Structure of Nucleoside Diphosphate Kinase from Bacillus ... -

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Basic information

Entry
Database: PDB / ID: 1nb2
TitleCrystal Structure of Nucleoside Diphosphate Kinase from Bacillus Halodenitrificans
ComponentsNucleoside Diphosphate Kinase
KeywordsTRANSFERASE / Nucleoside Diphosphate Kinase / Bacillus Halodenitrifians
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 / cytoplasm
Similarity search - Function
Nucleoside diphosphate kinase-like domain / 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
Nucleoside diphosphate kinase
Similarity search - Component
Biological speciesVirgibacillus halodenitrificans (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsChen, C.-J. / Liu, M.-Y. / Chang, W.-C. / Chang, T. / Wang, B.-C. / Le Gall, J.
CitationJournal: J.Struct.Biol. / Year: 2003
Title: Crystal structure of a nucleoside diphosphate kinase from Bacillus halodenitrificans: coexpression of its activity with a Mn-superoxide dismutase.
Authors: Chen, C.-J. / Liu, M.-Y. / Chang, T. / Chang, W.-C. / Wang, B.-C. / Le Gall, J.
History
DepositionDec 2, 2002Deposition site: RCSB / Processing site: PDBJ
Revision 1.0May 6, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 13, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Nucleoside Diphosphate Kinase


Theoretical massNumber of molelcules
Total (without water)14,8841
Polymers14,8841
Non-polymers00
Water61334
1
A: Nucleoside Diphosphate Kinase
x 6


Theoretical massNumber of molelcules
Total (without water)89,3026
Polymers89,3026
Non-polymers00
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555z,x,y1
crystal symmetry operation9_555y,z,x1
crystal symmetry operation14_666-y+5/4,-x+5/4,-z+5/41
crystal symmetry operation19_666-x+5/4,-z+5/4,-y+5/41
crystal symmetry operation24_666-z+5/4,-y+5/4,-x+5/41
Unit cell
Length a, b, c (Å)114.07, 114.07, 114.07
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number212
Space group name H-MP4332
DetailsThe biological assembly is a hexamer generated from the monomer in the asymmetric unit by the crystallographic operations.

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Components

#1: Protein Nucleoside Diphosphate Kinase


Mass: 14883.729 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Virgibacillus halodenitrificans (bacteria)
References: UniProt: Q7SIA9, nucleoside-diphosphate kinase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 34 / 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: 4.15 Å3/Da / Density % sol: 70.39 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6
Details: Sodium Formate, MES, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Crystal grow
*PLUS
Temperature: 18 ℃ / pH: 6.5 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
15.0 mg/mlprotein1drop
24.2 Msodium formate1reservoir
30.1 MMES1reservoirpH6.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: BL17B2 / Wavelength: 1.116 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Nov 14, 2001 / Details: mirrors
RadiationMonochromator: SAGITALLY FOCUSED Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.116 Å / Relative weight: 1
ReflectionResolution: 2.2→20 Å / Num. all: 24296 / Num. obs: 21145 / % possible obs: 87.03 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 7 % / Rsym value: 0.056 / Net I/σ(I): 16.1
Reflection shellResolution: 2.2→2.24 Å / Redundancy: 1.6 % / Mean I/σ(I) obs: 3.4 / Num. unique all: 813 / Rsym value: 0.26 / % possible all: 64
Reflection
*PLUS
% possible obs: 95.6 % / Redundancy: 7.03 % / Rmerge(I) obs: 0.062
Reflection shell
*PLUS
% possible obs: 64 % / Mean I/σ(I) obs: 3.8

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
CNS1refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.2→15 Å / Cross valid method: THROUGHOUT / σ(F): 1 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.254 2115 -RANDOM
Rwork0.213 ---
all0.234 24296 --
obs0.229 21145 87.03 %-
Refinement stepCycle: LAST / Resolution: 2.2→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1026 0 0 34 1060
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.734
X-RAY DIFFRACTIONc_bond_d0.009
Refinement
*PLUS
Lowest resolution: 25 Å / Rfactor Rfree: 0.252 / Rfactor Rwork: 0.211
Solvent computation
*PLUS
Displacement parameters
*PLUS

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