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- PDB-6k3h: Crystallographic Analysis of Nucleoside Diphosphate Kinase (NDK) ... -

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Basic information

Entry
Database: PDB / ID: 6k3h
TitleCrystallographic Analysis of Nucleoside Diphosphate Kinase (NDK) from Aspergillus Flavus
ComponentsNucleoside diphosphate kinase
KeywordsTRANSFERASE / Nucleoside Diphosphate Kinase / Aspergillus Flavus / Filamentous fungi
Function / homology
Function and homology information


: / nucleoside-diphosphate kinase / CTP biosynthetic process / UTP biosynthetic process / GTP biosynthetic process / nucleoside diphosphate kinase activity / ATP 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-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 speciesAspergillus flavus (mold)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.179 Å
AuthorsWang, Y. / Wang, S. / Wang, S.H.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China31772105 China
CitationJournal: J.Biol.Chem. / Year: 2019
Title: Molecular and structural basis of nucleoside diphosphate kinase-mediated regulation of spore and sclerotia development in the fungusAspergillus flavus.
Authors: Wang, Y. / Wang, S. / Nie, X. / Yang, K. / Xu, P. / Wang, X. / Liu, M. / Yang, Y. / Chen, Z. / Wang, S.
History
DepositionMay 18, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 3, 2019Provider: repository / Type: Initial release
Revision 1.1Jul 10, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed ..._citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
Revision 1.2Aug 28, 2019Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Nov 22, 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
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
B: Nucleoside diphosphate kinase
C: Nucleoside diphosphate kinase
D: Nucleoside diphosphate kinase
E: Nucleoside diphosphate kinase
F: Nucleoside diphosphate kinase
G: Nucleoside diphosphate kinase
H: Nucleoside diphosphate kinase
I: Nucleoside diphosphate kinase
J: Nucleoside diphosphate kinase
K: Nucleoside diphosphate kinase
L: Nucleoside diphosphate kinase
M: Nucleoside diphosphate kinase
N: Nucleoside diphosphate kinase
Q: Nucleoside diphosphate kinase
R: Nucleoside diphosphate kinase
U: Nucleoside diphosphate kinase
V: Nucleoside diphosphate kinase
W: Nucleoside diphosphate kinase
X: Nucleoside diphosphate kinase
O: Nucleoside diphosphate kinase
P: Nucleoside diphosphate kinase
S: Nucleoside diphosphate kinase
T: Nucleoside diphosphate kinase


Theoretical massNumber of molelcules
Total (without water)412,48024
Polymers412,48024
Non-polymers00
Water00
1
A: Nucleoside diphosphate kinase
B: Nucleoside diphosphate kinase
C: Nucleoside diphosphate kinase
D: Nucleoside diphosphate kinase
M: Nucleoside diphosphate kinase
N: Nucleoside diphosphate kinase


Theoretical massNumber of molelcules
Total (without water)103,1206
Polymers103,1206
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area15970 Å2
ΔGint-55 kcal/mol
Surface area32980 Å2
MethodPISA
2
E: Nucleoside diphosphate kinase
F: Nucleoside diphosphate kinase
G: Nucleoside diphosphate kinase
H: Nucleoside diphosphate kinase
O: Nucleoside diphosphate kinase
P: Nucleoside diphosphate kinase


Theoretical massNumber of molelcules
Total (without water)103,1206
Polymers103,1206
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area15840 Å2
ΔGint-56 kcal/mol
Surface area33700 Å2
MethodPISA
3
I: Nucleoside diphosphate kinase
J: Nucleoside diphosphate kinase
K: Nucleoside diphosphate kinase
L: Nucleoside diphosphate kinase
Q: Nucleoside diphosphate kinase
R: Nucleoside diphosphate kinase


Theoretical massNumber of molelcules
Total (without water)103,1206
Polymers103,1206
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area15790 Å2
ΔGint-57 kcal/mol
Surface area33830 Å2
MethodPISA
4
U: Nucleoside diphosphate kinase
V: Nucleoside diphosphate kinase
W: Nucleoside diphosphate kinase
X: Nucleoside diphosphate kinase
S: Nucleoside diphosphate kinase
T: Nucleoside diphosphate kinase


Theoretical massNumber of molelcules
Total (without water)103,1206
Polymers103,1206
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area15960 Å2
ΔGint-53 kcal/mol
Surface area33440 Å2
MethodPISA
Unit cell
Length a, b, c (Å)189.781, 168.439, 146.099
Angle α, β, γ (deg.)90.00, 92.98, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein ...
Nucleoside diphosphate kinase


Mass: 17186.676 Da / Num. of mol.: 24
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aspergillus flavus (strain ATCC 200026 / FGSC A1120 / NRRL 3357 / JCM 12722 / SRRC 167) (mold)
Strain: ATCC 200026 / FGSC A1120 / NRRL 3357 / JCM 12722 / SRRC 167
Gene: AFLA_006300 / Production host: Escherichia coli (E. coli) / References: UniProt: B8NQF0, nucleoside-diphosphate kinase

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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: 2.85 Å3/Da / Density % sol: 56.88 %
Crystal growTemperature: 289.15 K / Method: vapor diffusion, sitting drop / pH: 8.5 / Details: 2.4 M Sodium Citrate, 100 mM HEPES, pH 8.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 1, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.17→94.762 Å / Num. obs: 241762 / % possible obs: 99.3 % / Redundancy: 3.7 % / Rmerge(I) obs: 0.097 / Net I/σ(I): 6.18
Reflection shellResolution: 2.17→2.2 Å / Rmerge(I) obs: 1.264 / Num. unique obs: 11107

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Processing

Software
NameVersionClassification
PHENIX(1.14_3260: ???)refinement
DIALSdata reduction
DIALSdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1NSK

1nsk


Resolution: 2.179→94.762 Å / SU ML: 0.37 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 34.37 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2807 11865 5.02 %RANDOM
Rwork0.2304 ---
obs0.233 236473 99.29 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.179→94.762 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms28318 0 0 0 28318
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00829027
X-RAY DIFFRACTIONf_angle_d0.95239218
X-RAY DIFFRACTIONf_dihedral_angle_d3.36917345
X-RAY DIFFRACTIONf_chiral_restr0.0544182
X-RAY DIFFRACTIONf_plane_restr0.0065061
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1795-2.20430.39053530.34066905X-RAY DIFFRACTION92
2.2043-2.23020.39144080.34347543X-RAY DIFFRACTION100
2.2302-2.25740.42684160.37987447X-RAY DIFFRACTION99
2.2574-2.2860.38764160.32757452X-RAY DIFFRACTION100
2.286-2.31610.37183940.31117539X-RAY DIFFRACTION100
2.3161-2.34780.35183790.30947505X-RAY DIFFRACTION100
2.3478-2.38130.36554120.30627441X-RAY DIFFRACTION100
2.3813-2.41690.34454060.30977456X-RAY DIFFRACTION100
2.4169-2.45460.3553910.30287526X-RAY DIFFRACTION100
2.4546-2.49490.35383590.29097619X-RAY DIFFRACTION100
2.4949-2.53790.3763720.29857492X-RAY DIFFRACTION100
2.5379-2.58410.36413970.29377459X-RAY DIFFRACTION100
2.5841-2.63380.35793870.29067536X-RAY DIFFRACTION100
2.6338-2.68750.37943910.30197500X-RAY DIFFRACTION100
2.6875-2.7460.35533790.29137548X-RAY DIFFRACTION100
2.746-2.80990.33573770.27797526X-RAY DIFFRACTION100
2.8099-2.88010.33383880.29037541X-RAY DIFFRACTION100
2.8801-2.9580.38773750.29687528X-RAY DIFFRACTION100
2.958-3.04510.32723980.26827480X-RAY DIFFRACTION100
3.0451-3.14330.34254120.26667514X-RAY DIFFRACTION100
3.1433-3.25570.31474130.2717543X-RAY DIFFRACTION100
3.2557-3.38610.32984080.25797510X-RAY DIFFRACTION100
3.3861-3.54020.28493850.22777548X-RAY DIFFRACTION100
3.5402-3.72680.27144140.22167562X-RAY DIFFRACTION100
3.7268-3.96030.22664230.19767510X-RAY DIFFRACTION100
3.9603-4.26610.23573910.18097453X-RAY DIFFRACTION99
4.2661-4.69540.20443790.1627513X-RAY DIFFRACTION99
4.6954-5.37480.21184100.17147519X-RAY DIFFRACTION100
5.3748-6.77140.20434280.17457604X-RAY DIFFRACTION100
6.7714-94.85150.21154040.16867289X-RAY DIFFRACTION95

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