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Yorodumi- PDB-1yqe: Crystal Structure of Conserved Protein of Unknown Function AF0625 -
+Open data
-Basic information
Entry | Database: PDB / ID: 1yqe | ||||||
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Title | Crystal Structure of Conserved Protein of Unknown Function AF0625 | ||||||
Components | Hypothetical UPF0204 protein AF0625 | ||||||
Keywords | STRUCTURAL GENOMICS / UNKNOWN FUNCTION / AF0625 / Sulfur SAD / PSI / Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG | ||||||
Function / homology | Function and homology information D-aminoacyl-tRNA deacylase activity / D-aminoacyl-tRNA deacylase / D-amino acid catabolic process / zinc ion binding Similarity search - Function | ||||||
Biological species | Archaeoglobus fulgidus (archaea) | ||||||
Method | X-RAY DIFFRACTION / SAD / Resolution: 1.83 Å | ||||||
Authors | Liu, Y. / Skarina, T. / Dong, A. / Kudritskam, M. / Savchenko, A. / Pai, E.F. / Edwards, A. / Midwest Center for Structural Genomics (MCSG) | ||||||
Citation | Journal: To be Published Title: Crystal Structure of Conserved Hypothetical Protein AF0625 Authors: Liu, Y. / Skarina, T. / Dong, A. / Kudritskam, M. / Savchenko, A. / Pai, E.F. / Edwards, A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1yqe.cif.gz | 73.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1yqe.ent.gz | 54.1 KB | Display | PDB format |
PDBx/mmJSON format | 1yqe.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1yqe_validation.pdf.gz | 445.3 KB | Display | wwPDB validaton report |
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Full document | 1yqe_full_validation.pdf.gz | 447.1 KB | Display | |
Data in XML | 1yqe_validation.xml.gz | 15 KB | Display | |
Data in CIF | 1yqe_validation.cif.gz | 21.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/yq/1yqe ftp://data.pdbj.org/pub/pdb/validation_reports/yq/1yqe | HTTPS FTP |
-Related structure data
Similar structure data | |
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Other databases |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 31973.205 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Archaeoglobus fulgidus (archaea) / Gene: gi|2649994 / Plasmid: pET15b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / Keywords: chain A / References: UniProt: O29630 |
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#2: Chemical | ChemComp-POP / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.08 Å3/Da / Density % sol: 40.31 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 3.5 Details: PEG3350, pH 3.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU FR-C / Wavelength: 1.5418 / Wavelength: 1.5418 Å |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Jan 4, 2005 / Details: xenocs multilayer confocal mirror |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.83→80 Å / Num. all: 24272 / Num. obs: 22078 / % possible obs: 91 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 8.5 % / Biso Wilson estimate: 18.6 Å2 / Rmerge(I) obs: 0.031 / Rsym value: 0.031 / Net I/σ(I): 17.4 |
Reflection shell | Resolution: 1.83→1.86 Å / Redundancy: 4.9 % / Rmerge(I) obs: 0.448 / Mean I/σ(I) obs: 3.26 / Num. unique all: 808 / Rsym value: 0.448 / % possible all: 69.5 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 1.83→25.04 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 542777.94 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber / Details: O v8.0 was also used in refinement
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 48.8674 Å2 / ksol: 0.37799 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 25.3 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.83→25.04 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.83→1.94 Å / Rfactor Rfree error: 0.033 / Total num. of bins used: 6
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Xplor file |
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