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

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Basic information

Entry
Database: PDB / ID: 6xpw
TitleNucleoside Diphosphate Kinase from Aspergillus fumgiatus Af293 bound to CDP
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, active site / Nucleoside diphosphate kinase (NDPK) active site signature. / 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
Similarity search - Domain/homology
CYTIDINE-5'-DIPHOSPHATE / PHOSPHATE ION / 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: 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

Downloads & links

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Assembly

Deposited unit
A: Nucleoside diphosphate kinase
B: Nucleoside diphosphate kinase
C: Nucleoside diphosphate kinase
E: Nucleoside diphosphate kinase
G: Nucleoside diphosphate kinase
H: Nucleoside diphosphate kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)109,21812
Polymers108,3406
Non-polymers8786
Water34,8771936
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: mass spectrometry, Mass spectra shows a predominant hexameric species, gel filtration, The elution time of NDK corresponded to a hexamer, relative to sizing standards
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area17970 Å2
ΔGint-116 kcal/mol
Surface area34170 Å2
MethodPISA
Unit cell
Length a, b, c (Å)90.694, 101.800, 113.898
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
Nucleoside diphosphate kinase / NDP kinase


Mass: 18056.674 Da / Num. of mol.: 6
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-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: PO4
#3: Chemical ChemComp-CDP / CYTIDINE-5'-DIPHOSPHATE


Mass: 403.176 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H15N3O11P2 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1936 / 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: 2.43 Å3/Da / Density % sol: 49.31 %
Crystal growTemperature: 289.15 K / Method: vapor diffusion, hanging drop / Details: 20% PEG 3350, 0.3 M Ammonium sulphate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9537 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Aug 14, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 1.9→46.471 Å / Num. obs: 83554 / % possible obs: 99.9 % / Redundancy: 13.2 % / CC1/2: 0.998 / Rmerge(I) obs: 0.148 / Rpim(I) all: 0.042 / Rrim(I) all: 0.154 / Net I/σ(I): 13.5
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
1.9-1.9413.30.6496029045260.9310.1830.6754.599.6
9.87-46.4711.60.04580916960.9990.0130.0472899.3

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation5.56 Å46.47 Å
Translation5.56 Å46.47 Å

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Processing

Software
NameVersionClassification
PHENIX1.16_3549refinement
Aimless0.7.2data scaling
PHASER2.8.2phasing
PDB_EXTRACT3.25data extraction
XDS20161205data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6XP7

6xp7


Resolution: 1.9→46.471 Å / SU ML: 0.16 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 16.18 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1802 4276 5.12 %
Rwork0.1305 79201 -
obs0.1331 83477 99.81 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 105.37 Å2 / Biso mean: 24.3769 Å2 / Biso min: 2.07 Å2
Refinement stepCycle: final / Resolution: 1.9→46.471 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7212 0 50 1936 9198
Biso mean--39.34 39.15 -
Num. residues----932
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.9-1.92160.29041280.1796262199
1.9216-1.94420.20081240.15972625100
1.9442-1.96790.1891500.147258599
1.9679-1.99280.21951310.14462622100
1.9928-2.0190.18651330.13052612100
2.019-2.04670.17971630.1303255199
2.0467-2.07590.16221390.12742624100
2.0759-2.10690.16251480.12982611100
2.1069-2.13980.16751490.11972609100
2.1398-2.17490.17651490.12982585100
2.1749-2.21240.20411300.13912652100
2.2124-2.25270.20741590.14182576100
2.2527-2.2960.18771320.14372608100
2.296-2.34290.2231340.13592641100
2.3429-2.39380.19421340.13632647100
2.3938-2.44950.17351430.13232607100
2.4495-2.51070.19281370.13452646100
2.5107-2.57860.17431420.13672631100
2.5786-2.65450.1981550.13922628100
2.6545-2.74010.19751570.13342616100
2.7401-2.83810.18711380.13792649100
2.8381-2.95170.21221390.13582636100
2.9517-3.0860.17491390.12552661100
3.086-3.24870.20251530.12582673100
3.2487-3.45210.1671350.12072632100
3.4521-3.71860.17061630.11512665100
3.7186-4.09260.14641260.10862708100
4.0926-4.68430.14381420.09872696100
4.6843-5.89980.14761600.13432717100
5.8998-46.4710.18791440.16162867100

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