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

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Basic information

Entry
Database: PDB / ID: 6xpv
TitleNucleoside Diphosphate Kinase from Aspergillus fumgiatus Af293 bound to dTDP
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
THYMIDINE-5'-DIPHOSPHATE / Nucleoside diphosphate kinase
Similarity search - Component
Biological speciesAspergillus fumigatus Af293 (mold)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.3 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)110,75312
Polymers108,3406
Non-polymers2,4136
Water21,0241167
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 area19820 Å2
ΔGint-106 kcal/mol
Surface area33100 Å2
MethodPISA
Unit cell
Length a, b, c (Å)67.223, 126.073, 136.062
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-TYD / THYMIDINE-5'-DIPHOSPHATE


Mass: 402.188 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C10H16N2O11P2 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1167 / 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: 2.66 Å3/Da / Density % sol: 53.77 %
Crystal growTemperature: 289.15 K / Method: vapor diffusion, hanging drop / Details: 18.5% PEG 3350, 0.15 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: 2.3→47.82 Å / Num. obs: 52220 / % possible obs: 100 % / Redundancy: 14.1 % / CC1/2: 0.998 / Rmerge(I) obs: 0.138 / Rpim(I) all: 0.038 / Rrim(I) all: 0.143 / Net I/σ(I): 14.3 / Num. measured all: 735544 / Scaling rejects: 231
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
2.3-2.3714.50.7726469744520.9390.2080.83.2100
9.48-47.8212.40.043105568540.9990.0130.04533.399.2

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation5.68 Å47.82 Å
Translation5.68 Å47.82 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: 2.3→47.817 Å / SU ML: 0.31 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 27.44 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2503 2606 5.01 %
Rwork0.1936 49434 -
obs0.1965 52040 99.78 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 80.9 Å2 / Biso mean: 35.7865 Å2 / Biso min: 13.97 Å2
Refinement stepCycle: final / Resolution: 2.3→47.817 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7116 0 175 1167 8458
Biso mean--50.46 41.89 -
Num. residues----922
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.3-2.34180.30921160.26672581100
2.3418-2.38690.32391280.26742576100
2.3869-2.43560.34531560.26052545100
2.4356-2.48850.33411210.24592600100
2.4885-2.54640.32151480.25972521100
2.5464-2.61010.29391380.23662584100
2.6101-2.68070.30821400.2382568100
2.6807-2.75950.32691430.2382568100
2.7595-2.84860.36571420.23772573100
2.8486-2.95040.26491390.23792566100
2.9504-3.06850.27211520.2183257399
3.0685-3.20810.26991340.21532582100
3.2081-3.37720.29041450.20542607100
3.3772-3.58880.25451170.1872615100
3.5888-3.86570.21431360.17622613100
3.8657-4.25460.20281310.15432628100
4.2546-4.86970.17221220.14392682100
4.8697-6.13320.22721520.15712660100
6.1332-47.8170.18121460.1597279299

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