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- PDB-6xp7: Nucleoside Diphosphate Kinase from Aspergillus fumgiatus Af293 bo... -

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Basic information

Entry
Database: PDB / ID: 6xp7
TitleNucleoside Diphosphate Kinase from Aspergillus fumgiatus Af293 bound to ADP
ComponentsNucleoside diphosphate kinaseNucleoside-diphosphate kinase
KeywordsTRANSFERASE / Nucleoside diphosphate kinase / phosphotransferase / kinase
Function / homology
Function and homology information


nucleoside-diphosphate kinase / CTP biosynthetic process / UTP biosynthetic process / GTP biosynthetic process / nucleoside diphosphate kinase activity / phosphorylation / 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
ADENOSINE-5'-DIPHOSPHATE / Nucleoside diphosphate kinase
Similarity search - Component
Biological speciesAspergillus fumigatus Af293 (mold)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.2 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 8, 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,4526
Polymers54,1703
Non-polymers1,2823
Water13,854769
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)110,90312
Polymers108,3406
Non-polymers2,5636
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area20440 Å2
ΔGint-116 kcal/mol
Surface area32570 Å2
MethodPISA
Unit cell
Length a, b, c (Å)53.050, 71.810, 118.850
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-403-

HOH

21A-549-

HOH

31B-535-

HOH

41C-483-

HOH

51C-523-

HOH

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Components

#1: Protein Nucleoside diphosphate kinase / 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-ADP / ADENOSINE-5'-DIPHOSPHATE / Adenosine diphosphate


Mass: 427.201 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: ADP, energy-carrying molecule*YM
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 769 / 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: 2.09 Å3/Da / Density % sol: 41.14 %
Crystal growTemperature: 289.15 K / Method: vapor diffusion, hanging drop / Details: 21% PEG 3350, 0.25 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: 0.9537 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: 2.2→45.782 Å / Num. obs: 23387 / % possible obs: 98.6 % / Redundancy: 12 % / CC1/2: 0.998 / Rmerge(I) obs: 0.105 / Rpim(I) all: 0.03 / Rrim(I) all: 0.109 / Net I/σ(I): 19.1
Reflection shell

Diffraction-ID: 1 / Redundancy: 11.1 %

Resolution (Å)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
2.2-2.270.2822128519260.960.0830.2949.895.4
9.07-45.780.03644294000.9980.0110.03830.899.4

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
PHENIX1.16_3549refinement
Aimless0.7.2data scaling
PHASER2.8.2phasing
PDB_EXTRACT3.25data extraction
iMOSFLM7.0.072data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6XP4

6xp4


Resolution: 2.2→45.782 Å / SU ML: 0.24 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 23.07 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2382 1115 4.78 %
Rwork0.1821 22210 -
obs0.1848 23325 98.15 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 55.45 Å2 / Biso mean: 16.5429 Å2 / Biso min: 6.06 Å2
Refinement stepCycle: final / Resolution: 2.2→45.782 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3525 0 81 769 4375
Biso mean--19.26 22.22 -
Num. residues----456
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.2-2.30010.36951370.2861262995
2.3001-2.42140.26811300.2256269497
2.4214-2.57310.28621390.2102270698
2.5731-2.77170.24411510.1938275499
2.7717-3.05060.25511460.182276299
3.0506-3.49190.23881300.1627281999
3.4919-4.39890.19291390.1443285599
4.3989-45.7820.1741430.1555299199

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