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- PDB-5yzj: Crystal structure of human Archease mutant D51A -

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Basic information

Entry
Database: PDB / ID: 5yzj
TitleCrystal structure of human Archease mutant D51A
ComponentsProtein archease
KeywordsCHAPERONE / Mutant of human Archase D51A
Function / homologyArchease / Archease domain / Archease domain superfamily / Archease protein family (MTH1598/TM1083) / tRNA processing / metal ion binding / Protein archease
Function and homology information
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.79 Å
AuthorsDuan, S.Y. / LI, J.X.
Funding support China, 1items
OrganizationGrant numberCountry
China
CitationJournal: To Be Published
Title: Structural and mechanistic insights into hArchease mutant D51A
Authors: Duan, S.Y. / Li, J.X.
History
DepositionDec 15, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 2, 2019Provider: repository / Type: Initial release
Revision 1.1Nov 22, 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: Protein archease
B: Protein archease


Theoretical massNumber of molelcules
Total (without water)43,5872
Polymers43,5872
Non-polymers00
Water28816
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4570 Å2
ΔGint-12 kcal/mol
Surface area15600 Å2
MethodPISA
Unit cell
Length a, b, c (Å)48.465, 59.587, 132.756
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Protein archease / cDNA FLJ75987 / highly similar to Homo sapiens zinc finger and BTB domain containing 8 opposite ...cDNA FLJ75987 / highly similar to Homo sapiens zinc finger and BTB domain containing 8 opposite strand (ZBTB8OS) / mRNA


Mass: 21793.312 Da / Num. of mol.: 2 / Mutation: D51A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ZBTB8OS / Plasmid: pET28b(+) / Production host: Escherichia coli (E. coli) / References: UniProt: A8K0B5
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 16 / 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: 2.2 Å3/Da / Density % sol: 44.06 %
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 30% PEG 400, 100mM HEPES/Sodium hydroxide pH 7.5, 200mM Magnesium chloride

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.9792 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: May 16, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.79→50 Å / Num. obs: 10143 / % possible obs: 99.9 % / Redundancy: 13.6 % / Net I/σ(I): 34.748
Reflection shellResolution: 2.79→2.84 Å

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Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5YZ1

5yz1


Resolution: 2.79→36.18 Å / Cross valid method: THROUGHOUT
RfactorNum. reflection% reflection
Rfree0.2456 482 -
Rwork0.1769 --
obs-10102 99.5 %
Refinement stepCycle: LAST / Resolution: 2.79→36.18 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2608 0 0 16 2624

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