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- PDB-6xp4: Nucleoside Diphosphate Kinase from Aspergillus fumgiatus Af293 -

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Basic information

Entry
Database: PDB / ID: 6xp4
TitleNucleoside Diphosphate Kinase from Aspergillus fumgiatus Af293
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
Nucleoside diphosphate kinase
Similarity search - Component
Biological speciesAspergillus fumigatus Af293 (mold)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2 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 7, 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

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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


Theoretical massNumber of molelcules
Total (without water)108,3406
Polymers108,3406
Non-polymers00
Water35,6881981
1
B: Nucleoside diphosphate kinase
D: Nucleoside diphosphate kinase
F: Nucleoside diphosphate kinase

E: Nucleoside diphosphate kinase

A: Nucleoside diphosphate kinase
C: Nucleoside diphosphate kinase


Theoretical massNumber of molelcules
Total (without water)108,3406
Polymers108,3406
Non-polymers00
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_655x+1,y,z1
crystal symmetry operation3_555-x,y+1/2,-z+1/21
Buried area16170 Å2
ΔGint-79 kcal/mol
Surface area34420 Å2
MethodPISA
Unit cell
Length a, b, c (Å)93.430, 101.640, 114.100
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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1981 / 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: 2.5 Å3/Da / Density % sol: 50.81 %
Crystal growTemperature: 289.15 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: 21% PEG 3350, 0.45 M sodium malonate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX1 / Wavelength: 0.9537 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Apr 18, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 2→49.75 Å / Num. obs: 68713 / % possible obs: 93.1 % / Redundancy: 11.2 % / CC1/2: 0.998 / Rmerge(I) obs: 0.09 / Rpim(I) all: 0.027 / Rrim(I) all: 0.094 / Net I/σ(I): 21.1 / Num. measured all: 768998 / Scaling rejects: 352
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
2-2.049.10.3473545238840.9510.1160.3676.686.6
9.8-49.7511.60.0384947340.9990.0090.03241.699.4

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.88 Å49.75 Å
Translation2.88 Å49.75 Å

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Processing

Software
NameVersionClassification
PHENIX1.16_3549refinement
Aimless0.6.3data scaling
PHASER2.8.2phasing
PDB_EXTRACT3.25data extraction
iMOSFLM7.0.072data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4KPC

4kpc


Resolution: 2→49.749 Å / SU ML: 0.16 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 17.61 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1879 3462 5.04 %
Rwork0.1286 65192 -
obs0.1317 68654 92.78 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 80.66 Å2 / Biso mean: 16.9352 Å2 / Biso min: 1.66 Å2
Refinement stepCycle: final / Resolution: 2→49.749 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7158 0 0 1981 9139
Biso mean---30.27 -
Num. residues----929
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2-2.02740.2011410.1438237686
2.0274-2.05640.20891410.142236186
2.0564-2.08710.24041410.145239686
2.0871-2.11970.20081180.1372243487
2.1197-2.15440.211490.1307245189
2.1544-2.19160.19781300.1356243688
2.1916-2.23140.20771300.1377248889
2.2314-2.27440.20761380.1372248090
2.2744-2.32080.2051300.1335252190
2.3208-2.37120.18311330.1342249290
2.3712-2.42640.18481400.137254390
2.4264-2.48710.22491400.135252791
2.4871-2.55430.2231060.1434256791
2.5543-2.62950.20431310.1383254992
2.6295-2.71440.21361480.14260793
2.7144-2.81140.1811390.1344260893
2.8114-2.92390.20631130.1422267294
2.9239-3.0570.1981570.1277267496
3.057-3.21810.19611660.1296273497
3.2181-3.41970.16431450.1201278999
3.4197-3.68360.16741330.11142843100
3.6836-4.05420.17361850.10252821100
4.0542-4.64050.13281550.10052859100
4.6405-5.8450.17311180.12462925100
5.845-49.7490.17831350.15093039100

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