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- PDB-6xpu: Nucleoside Diphosphate Kinase from Aspergillus fumgiatus Af293 bo... -

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Basic information

Entry
Database: PDB / ID: 6xpu
TitleNucleoside Diphosphate Kinase from Aspergillus fumgiatus Af293 bound to IDP
ComponentsNucleoside diphosphate kinase
KeywordsTRANSFERASE / Nucleoside diphosphate kinase / phosphotransferase / kinase
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 (NDPK)-like domain profile. / 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
Similarity search - Domain/homology
INOSINE-5'-DIPHOSPHATE / Nucleoside diphosphate kinase
Similarity search - Component
Biological speciesAspergillus fumigatus Af293 (mold)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.9 Å
AuthorsNguyen, S. / Bruning, J.B.
CitationJournal: Febs J. / Year: 2021
Title: Nucleoside selectivity of Aspergillus fumigatus nucleoside-diphosphate kinase.
Authors: Nguyen, S. / Jovcevski, B. / Pukala, T.L. / Bruning, J.B.
History
DepositionJul 9, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 4, 2020Provider: repository / Type: Initial release
Revision 1.1Apr 14, 2021Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year / _citation_author.identifier_ORCID
Revision 1.2Oct 18, 2023Group: Advisory / Data collection ...Advisory / 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 / pdbx_unobs_or_zero_occ_atoms
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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,5279
Polymers54,1703
Non-polymers1,3576
Water14,808822
1
A: Nucleoside diphosphate kinase
B: Nucleoside diphosphate kinase
C: Nucleoside diphosphate kinase
hetero molecules

A: Nucleoside diphosphate kinase
B: Nucleoside diphosphate kinase
C: Nucleoside diphosphate kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)111,05518
Polymers108,3406
Non-polymers2,71512
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,y,-z1
Buried area21420 Å2
ΔGint-178 kcal/mol
Surface area32800 Å2
MethodPISA
Unit cell
Length a, b, c (Å)52.900, 70.307, 119.133
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21221
Components on special symmetry positions
IDModelComponents
11A-383-

HOH

21B-542-

HOH

31B-578-

HOH

41C-412-

HOH

51C-459-

HOH

61C-486-

HOH

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Components

#1: Protein Nucleoside diphosphate kinase / NDP kinase


Mass: 18056.674 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aspergillus fumigatus Af293 (mold) / Strain: ATCC MYA-4609 / Af293 / CBS 101355 / FGSC A1100 / Gene: ndk1, AFUA_5G03490 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q7Z8P9, nucleoside-diphosphate kinase
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-IDP / INOSINE-5'-DIPHOSPHATE


Mass: 428.186 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C10H14N4O11P2 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 822 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.04 Å3/Da / Density % sol: 39.85 %
Crystal growTemperature: 289.15 K / Method: vapor diffusion, hanging drop / Details: 19.5% PEG 3350, 0.20 M NaCl, 0.1 M HEPES pH 7.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX1 / Wavelength: 0.954 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Jul 5, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.954 Å / Relative weight: 1
ReflectionResolution: 1.9→42.271 Å / Num. obs: 35832 / % possible obs: 100 % / Redundancy: 14 % / CC1/2: 0.999 / Rmerge(I) obs: 0.091 / Rpim(I) all: 0.025 / Rrim(I) all: 0.095 / Net I/σ(I): 20.7
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
1.9-1.94140.5753136322460.9480.1580.5975100
9.11-42.2711.60.02645393900.9990.0080.02750.699.3

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation6.29 Å42.27 Å
Translation6.29 Å42.27 Å

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Processing

Software
NameVersionClassification
PHENIX1.16_3549refinement
Aimless0.7.1data scaling
PHASER2.8.2phasing
PDB_EXTRACT3.25data extraction
XDS20161205data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6XP7

6xp7


Resolution: 1.9→42.27 Å / SU ML: 0.22 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 23.68 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2273 1797 5.04 %
Rwork0.1776 33871 -
obs0.1801 35668 99.66 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 80.05 Å2 / Biso mean: 24.6721 Å2 / Biso min: 11.57 Å2
Refinement stepCycle: final / Resolution: 1.9→42.27 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3560 0 84 822 4466
Biso mean--26.77 33.35 -
Num. residues----458
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.9-1.95140.3211350.25132560100
1.9514-2.00880.26741290.21312560100
2.0088-2.07360.26891440.20732549100
2.0736-2.14770.2421220.20352615100
2.1477-2.23370.29341300.2128254399
2.2337-2.33540.26961220.2127259199
2.3354-2.45850.25811600.20642565100
2.4585-2.61250.2851480.20832569100
2.6125-2.81420.25371320.19672613100
2.8142-3.09730.25331400.18552610100
3.0973-3.54530.20661480.15372639100
3.5453-4.46590.16611450.13062648100
4.4659-42.270.18211420.15282809100

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