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- PDB-5yz1: Crystal structure of human Archease -

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Basic information

Entry
Database: PDB / ID: 5yz1
TitleCrystal structure of human Archease
ComponentsProtein archease
KeywordsCHAPERONE / key cofacor / human RTCB
Function / homologyArchease / Archease domain / Archease domain superfamily / Archease protein family (MTH1598/TM1083) / tRNA processing / metal ion binding / DI(HYDROXYETHYL)ETHER / Protein archease
Function and homology information
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.97 Å
AuthorsDuan, S.Y. / Li, J.X.
Funding support China, 1items
OrganizationGrant numberCountry
China
CitationJournal: Int.J.Biochem.Cell Biol. / Year: 2020
Title: Crystal structure of human archease, a key cofactor of tRNA splicing ligase complex.
Authors: Duan, S. / Gao, W. / Chen, Z. / Li, Z. / Li, S. / Gan, J. / Chen, X. / Li, J.
History
DepositionDec 11, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 2, 2019Provider: repository / Type: Initial release
Revision 1.1Jul 15, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Nov 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,9495
Polymers43,6752
Non-polymers2743
Water1,928107
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, SEC-MALS for absolute molar mass and size measurement
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5120 Å2
ΔGint-10 kcal/mol
Surface area16030 Å2
MethodPISA
Unit cell
Length a, b, c (Å)46.201, 55.844, 133.261
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: 21837.322 Da / Num. of mol.: 2
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: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 107 / 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: 1.97 Å3/Da / Density % sol: 37.5 %
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop / pH: 5 / Details: 20% PEG 6000, 100mM sodium citrate pH5.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.9778 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 19, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9778 Å / Relative weight: 1
ReflectionResolution: 1.961→50 Å / Num. obs: 24285 / % possible obs: 96.1 % / Redundancy: 11.5 % / Net I/σ(I): 19.778
Reflection shellResolution: 1.98→2.01 Å

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Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
HKL-3000data reduction
HKL-3000data scaling
MLPHAREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4N2P

4n2p


Resolution: 1.97→42.8 Å / Cross valid method: THROUGHOUT
RfactorNum. reflection% reflection
Rfree0.23395 1255 -
Rwork0.1839 --
obs-22975 96.6 %
Refinement stepCycle: LAST / Resolution: 1.97→42.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2625 0 18 107 2750

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