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- PDB-6joh: The crystal of nucleoside diphosphate kinase from Aspergillus flavus -

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Basic information

Entry
Database: PDB / ID: 6joh
TitleThe crystal of nucleoside diphosphate kinase from Aspergillus flavus
ComponentsNucleoside diphosphate kinase
KeywordsTRANSFERASE
Function / homology
Function and homology information


nucleoside-diphosphate kinase / UTP biosynthetic process / CTP biosynthetic process / nucleoside diphosphate kinase activity / GTP biosynthetic process / 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 NRRL3357 (mold)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsWang, Y. / Wang, S. / Wang, S.H.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China31772105 China
CitationJournal: To Be Published
Title: Molecular and structural basis of Nucleoside Diphosphate Kinase regulating the spores and sclerotia development in Aspergillus flavus
Authors: Wang, Y. / Wang, S.H.
History
DepositionMar 21, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 29, 2020Provider: repository / Type: Initial release
Revision 1.1Nov 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 area16170 Å2
ΔGint-59 kcal/mol
Surface area33670 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 area16100 Å2
ΔGint-55 kcal/mol
Surface area33510 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 area16050 Å2
ΔGint-59 kcal/mol
Surface area33820 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 area16300 Å2
ΔGint-60 kcal/mol
Surface area33360 Å2
MethodPISA
Unit cell
Length a, b, c (Å)190.836, 169.470, 146.937
Angle α, β, γ (deg.)90.00, 92.92, 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 NRRL3357 (mold) / Strain: NRRL3357 / 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: 2.9 Å3/Da / Density % sol: 57.62 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / Details: 2.4M Sodium Citrate, 100mM 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: Sep 30, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.4→33.67 Å / Num. obs: 179636 / % possible obs: 98.86 % / Redundancy: 3.6 % / Rsym value: 0.103 / Net I/σ(I): 49.1
Reflection shellResolution: 2.4→2.49 Å / Num. unique obs: 17977 / Rsym value: 0.58

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Processing

Software
NameVersionClassification
REFMAC5.8.0232refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1NSK

1nsk


Resolution: 2.4→33.69 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.924 / SU B: 10.8 / SU ML: 0.237 / Cross valid method: THROUGHOUT / ESU R: 0.377 / ESU R Free: 0.267 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.268 8963 5 %RANDOM
Rwork0.22167 ---
obs0.22404 170403 98.85 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 55.111 Å2
Baniso -1Baniso -2Baniso -3
1-2.89 Å20 Å2-0.43 Å2
2--0.25 Å2-0 Å2
3----3.08 Å2
Refinement stepCycle: 1 / Resolution: 2.4→33.69 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms28040 0 0 0 28040
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.01328758
X-RAY DIFFRACTIONr_bond_other_d0.0010.01726896
X-RAY DIFFRACTIONr_angle_refined_deg1.6281.63938886
X-RAY DIFFRACTIONr_angle_other_deg1.2391.57862514
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.16553546
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.37922.1341434
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.633154904
X-RAY DIFFRACTIONr_dihedral_angle_4_deg24.69115168
X-RAY DIFFRACTIONr_chiral_restr0.0790.23618
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0232014
X-RAY DIFFRACTIONr_gen_planes_other0.0010.026138
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it4.6625.6314256
X-RAY DIFFRACTIONr_mcbond_other4.6615.6314255
X-RAY DIFFRACTIONr_mcangle_it6.7768.44417778
X-RAY DIFFRACTIONr_mcangle_other6.7758.44417779
X-RAY DIFFRACTIONr_scbond_it5.0826.15614502
X-RAY DIFFRACTIONr_scbond_other5.0816.15614500
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other7.6689.02621108
X-RAY DIFFRACTIONr_long_range_B_refined11.28966.80131368
X-RAY DIFFRACTIONr_long_range_B_other11.28866.80331369
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.401→2.464 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.401 625 -
Rwork0.353 11725 -
obs--92.25 %

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