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Yorodumi- PDB-1vaj: Crystal Structure of Uncharacterized Protein PH0010 From Pyrococc... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1vaj | ||||||
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Title | Crystal Structure of Uncharacterized Protein PH0010 From Pyrococcus horikoshii | ||||||
Components | Hypothetical protein PH0010 | ||||||
Keywords | STRUCTURAL GENOMICS / UNKNOWN FUNCTION / alpha + beta fold | ||||||
Function / homology | Function and homology information Hypothetical protein ph0010; domain 2 / Hypothetical protein ph0010; domain 1 / AMMECR1 domain / Uncharacterised protein family MJ0810 / AMMECR1 / AMMECR1, N-terminal / AmmeMemoRadiSam system protein A / AMMECR1 domain superfamily / AMMECR1 / AMMECR1 domain profile. ...Hypothetical protein ph0010; domain 2 / Hypothetical protein ph0010; domain 1 / AMMECR1 domain / Uncharacterised protein family MJ0810 / AMMECR1 / AMMECR1, N-terminal / AmmeMemoRadiSam system protein A / AMMECR1 domain superfamily / AMMECR1 / AMMECR1 domain profile. / Glycoprotein, Type 4 Pilin / Dna Ligase; domain 1 / 2-Layer Sandwich / Alpha Beta Similarity search - Domain/homology | ||||||
Biological species | Pyrococcus horikoshii (archaea) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.82 Å | ||||||
Authors | Tajika, Y. / Sakai, N. / Tamura, T. / Yao, M. / Watanabe, N. / Tanaka, I. | ||||||
Citation | Journal: Proteins / Year: 2005 Title: Crystal structure of PH0010 from Pyrococcus horikoshii, which is highly homologous to human AMMECR 1C-terminal region Authors: Tajika, Y. / Sakai, N. / Tamura, T. / Yao, M. / Watanabe, N. / Tanaka, I. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1vaj.cif.gz | 56.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1vaj.ent.gz | 40.9 KB | Display | PDB format |
PDBx/mmJSON format | 1vaj.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1vaj_validation.pdf.gz | 369 KB | Display | wwPDB validaton report |
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Full document | 1vaj_full_validation.pdf.gz | 370.9 KB | Display | |
Data in XML | 1vaj_validation.xml.gz | 5.6 KB | Display | |
Data in CIF | 1vaj_validation.cif.gz | 8.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/va/1vaj ftp://data.pdbj.org/pub/pdb/validation_reports/va/1vaj | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 24862.168 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pyrococcus horikoshii (archaea) / Gene: PH0010 / Plasmid: pET-26b(+) / Production host: Escherichia coli (E. coli) Strain (production host): BL21-codonplus(DE3)-RIL (Stratagene) References: UniProt: O57770 |
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#2: 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: 2.46 Å3/Da / Density % sol: 50 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.9 Details: PEG 8000, magnesium chloride, pH 7.9, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NW12A / Wavelength: 0.9742, 0.9785, 0.9600 | ||||||||||||
Detector | Detector: CCD / Date: Dec 21, 2003 | ||||||||||||
Radiation | Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||
Radiation wavelength |
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Reflection | Resolution: 1.82→38.63 Å / Num. obs: 19449 / % possible obs: 95.7 % / Observed criterion σ(I): -3 / Redundancy: 5.4 % / Biso Wilson estimate: 26.5 Å2 / Rmerge(I) obs: 0.071 / Net I/σ(I): 10.6 | ||||||||||||
Reflection shell | Resolution: 1.82→1.89 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.336 / % possible all: 77.2 |
-Processing
Software |
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Refinement | Method to determine structure: MAD / Resolution: 1.82→10 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Displacement parameters | Biso mean: 20.24 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.82→10 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.82→1.88 Å / Total num. of bins used: 10
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Xplor file | Serial no: 1 / Param file: protein_rep.param / Topol file: protein.top |