+Open data
-Basic information
Entry | Database: PDB / ID: 5yzj | ||||||
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Title | Crystal structure of human Archease mutant D51A | ||||||
Components | Protein archease | ||||||
Keywords | CHAPERONE / Mutant of human Archase D51A | ||||||
Function / homology | Archease / Archease domain / Archease domain superfamily / Archease protein family (MTH1598/TM1083) / tRNA processing / metal ion binding / Protein archease Function and homology information | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.79 Å | ||||||
Authors | Duan, S.Y. / LI, J.X. | ||||||
Funding support | China, 1items
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Citation | Journal: To Be Published Title: Structural and mechanistic insights into hArchease mutant D51A Authors: Duan, S.Y. / Li, J.X. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5yzj.cif.gz | 77.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5yzj.ent.gz | 57.4 KB | Display | PDB format |
PDBx/mmJSON format | 5yzj.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5yzj_validation.pdf.gz | 437.1 KB | Display | wwPDB validaton report |
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Full document | 5yzj_full_validation.pdf.gz | 440.8 KB | Display | |
Data in XML | 5yzj_validation.xml.gz | 13.5 KB | Display | |
Data in CIF | 5yzj_validation.cif.gz | 17.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/yz/5yzj ftp://data.pdbj.org/pub/pdb/validation_reports/yz/5yzj | HTTPS FTP |
-Related structure data
Related structure data | 5yz1S S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | 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 / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.2 Å3/Da / Density % sol: 44.06 % |
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Crystal grow | Temperature: 290 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 30% PEG 400, 100mM HEPES/Sodium hydroxide pH 7.5, 200mM Magnesium chloride |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.9792 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: May 16, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9792 Å / Relative weight: 1 |
Reflection | Resolution: 2.79→50 Å / Num. obs: 10143 / % possible obs: 99.9 % / Redundancy: 13.6 % / Net I/σ(I): 34.748 |
Reflection shell | Resolution: 2.79→2.84 Å |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5YZ1 Resolution: 2.79→36.18 Å / Cross valid method: THROUGHOUT
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Refinement step | Cycle: LAST / Resolution: 2.79→36.18 Å
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