+Open data
-Basic information
Entry | Database: PDB / ID: 5yzl | ||||||
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Title | Crystal structure of human Archease D178A | ||||||
Components | Protein archease | ||||||
Keywords | CHAPERONE / a cofactor of RTCB | ||||||
Function / homology | Archease / Archease domain / Archease domain superfamily / Archease protein family (MTH1598/TM1083) / tRNA-splicing ligase complex / tRNA splicing, via endonucleolytic cleavage and ligation / metal ion binding / Protein archease Function and homology information | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.4 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 human Archease mutant D178A 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 | 5yzl.cif.gz | 76.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5yzl.ent.gz | 57 KB | Display | PDB format |
PDBx/mmJSON format | 5yzl.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/yz/5yzl ftp://data.pdbj.org/pub/pdb/validation_reports/yz/5yzl | HTTPS FTP |
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-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: D178A 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: 2.22 Å3/Da / Density % sol: 44.53 % |
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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: BL19U1 / Wavelength: 1.0688 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 19, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.0688 Å / Relative weight: 1 |
Reflection | Resolution: 3.4→50 Å / Num. obs: 5767 / % possible obs: 98.6 % / Redundancy: 10.5 % / Net I/σ(I): 2 |
Reflection shell | Resolution: 3.4→3.46 Å |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5YZ1 Resolution: 3.4→45.73 Å / Cross valid method: THROUGHOUT
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Refinement step | Cycle: LAST / Resolution: 3.4→45.73 Å
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