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Yorodumi- PDB-2pzz: 2.2 A resolution crystal structure of UPF0201 protein from Methan... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2pzz | ||||||
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Title | 2.2 A resolution crystal structure of UPF0201 protein from Methanococcus jannaschii | ||||||
Components | UPF0201 protein MJ1564 | ||||||
Keywords | STRUCTURAL GENOMICS / UNKNOWN FUNCTION / UPF0201 / MJ1564 / 10077a3 / Methanococcus jannaschii / PSI2 / NYSGXRC / Protein Structure Initiative / New York SGX Research Center for Structural Genomics | ||||||
Function / homology | Uncharacterised protein family UPF0201 / RNA binding / 50s Ribosomal Protein L5; Chain: A, / Ribosomal protein L5 / Ribosomal protein L5 domain superfamily / 2-Layer Sandwich / Alpha Beta / UPF0201 protein MJ1564 Function and homology information | ||||||
Biological species | Methanocaldococcus jannaschii DSM 2661 (archaea) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.2 Å | ||||||
Authors | Rao, K.N. / Burley, S.K. / Swaminathan, S. / New York SGX Research Center for Structural Genomics (NYSGXRC) | ||||||
Citation | Journal: Plos One / Year: 2008 Title: UPF201 archaeal specific family members reveal structural similarity to RNA-binding proteins but low likelihood for RNA-binding function. Authors: Rao, K.N. / Burley, S.K. / Swaminathan, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2pzz.cif.gz | 103.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2pzz.ent.gz | 85.7 KB | Display | PDB format |
PDBx/mmJSON format | 2pzz.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2pzz_validation.pdf.gz | 456.5 KB | Display | wwPDB validaton report |
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Full document | 2pzz_full_validation.pdf.gz | 470.3 KB | Display | |
Data in XML | 2pzz_validation.xml.gz | 21 KB | Display | |
Data in CIF | 2pzz_validation.cif.gz | 28.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/pz/2pzz ftp://data.pdbj.org/pub/pdb/validation_reports/pz/2pzz | HTTPS FTP |
-Related structure data
Related structure data | 2nrqC 2nwuC 2ogkC C: citing same article (ref.) |
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Similar structure data | |
Other databases |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 16896.023 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Methanocaldococcus jannaschii DSM 2661 (archaea) Species: Methanocaldococcus jannaschii / Strain: DSM 2661, JAL-1, JCM 10045, NBRC 100440 / Gene: MJ1564 / Plasmid: pSGX3(BC) / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q58959 #2: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 2 |
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-Sample preparation
Crystal | Density Matthews: 2.29 Å3/Da / Density % sol: 46.28 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: Ammonium acetate, HEPES Buffer, PEG3350, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X12C / Wavelength: 0.9793 Å |
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: May 1, 2007 / Details: Mirrors |
Radiation | Monochromator: Si III / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9793 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→50 Å / Num. all: 30128 / Num. obs: 30128 / % possible obs: 98.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.2 % / Biso Wilson estimate: 25.7 Å2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 14.6 |
Reflection shell | Resolution: 2.2→2.28 Å / Redundancy: 5.3 % / Rmerge(I) obs: 0.278 / Mean I/σ(I) obs: 2.4 / Num. unique all: 2775 / % possible all: 90.9 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 2.2→47.23 Å / Rfactor Rfree error: 0.01 / Data cutoff high absF: 120713.55 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber Details: Residues listed as missing in Remark 465 are due to lack of electron density. Residues with missing atoms listed in Remark 470 are due to lack of electron density for side chains and modeled as alanines.
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 45.4452 Å2 / ksol: 0.364126 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 46.4 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.2→47.23 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.2→2.34 Å / Rfactor Rfree error: 0.028 / Total num. of bins used: 6
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Xplor file |
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