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Yorodumi- PDB-2egt: Crystal Structure of Hypothetical protein (AQ1549) from Aquifex a... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2egt | ||||||
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Title | Crystal Structure of Hypothetical protein (AQ1549) from Aquifex aeolicus | ||||||
Components | Hypothetical protein AQ_1549 | ||||||
Keywords | STRUCTURAL GENOMICS / UNKNOWN FUNCTION / Hypothetical protein / Osmatically induced protein / NPPSFA / National Project on Protein Structural and Functional Analyses / RIKEN Structural Genomics/Proteomics Initiative / RSGI | ||||||
Function / homology | Function and homology information N-terminal domain of TfIIb - #50 / OsmC/Ohr family / OsmC/Ohr superfamily / OsmC-like protein / N-terminal domain of TfIIb / K homology (KH) domain / Other non-globular / GMP Synthetase; Chain A, domain 3 / Special / K homology domain-like, alpha/beta ...N-terminal domain of TfIIb - #50 / OsmC/Ohr family / OsmC/Ohr superfamily / OsmC-like protein / N-terminal domain of TfIIb / K homology (KH) domain / Other non-globular / GMP Synthetase; Chain A, domain 3 / Special / K homology domain-like, alpha/beta / 2-Layer Sandwich / Alpha Beta Similarity search - Domain/homology | ||||||
Biological species | Aquifex aeolicus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å | ||||||
Authors | Niwa, H. / Kumarevel, T.S. / Kuramitsu, S. / Yokoyama, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI) | ||||||
Citation | Journal: To be Published Title: Crystal Structure of Hypothetical protein (AQ1549) from Aquifex aeolicus Authors: Niwa, H. / Kumarevel, T.S. / Kuramitsu, S. / Yokoyama, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2egt.cif.gz | 40.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2egt.ent.gz | 27.4 KB | Display | PDB format |
PDBx/mmJSON format | 2egt.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2egt_validation.pdf.gz | 413.1 KB | Display | wwPDB validaton report |
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Full document | 2egt_full_validation.pdf.gz | 414.1 KB | Display | |
Data in XML | 2egt_validation.xml.gz | 7.7 KB | Display | |
Data in CIF | 2egt_validation.cif.gz | 10 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/eg/2egt ftp://data.pdbj.org/pub/pdb/validation_reports/eg/2egt | HTTPS FTP |
-Related structure data
Related structure data | 2e8cS S: Starting model for refinement |
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Similar structure data | |
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: 15037.618 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Aquifex aeolicus (bacteria) / Strain: VF5 / Plasmid: pET21a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)CodonPlus-RIL-X / References: UniProt: O67503 |
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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: 2.47 Å3/Da / Density % sol: 50.17 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 9.5 Details: 0.1M CHES, 40% MPD, pH 9.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL26B2 / Wavelength: 0.97944 Å |
Detector | Type: RIGAKU JUPITER 210 / Detector: CCD / Date: May 26, 2006 |
Radiation | Monochromator: Si / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97944 Å / Relative weight: 1 |
Reflection | Resolution: 2→50 Å / Num. all: 10922 / Num. obs: 10922 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 19.7 % / Biso Wilson estimate: 16.9 Å2 / Rmerge(I) obs: 0.066 |
Reflection shell | Resolution: 2→2.07 Å / Redundancy: 20.4 % / Rmerge(I) obs: 0.422 / Num. unique all: 1058 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2E8C Resolution: 2→41.92 Å / Rfactor Rfree error: 0.008 / Data cutoff high absF: 1932963.77 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 58.5994 Å2 / ksol: 0.370241 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 27.5 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2→41.92 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2→2.13 Å / Rfactor Rfree error: 0.022 / Total num. of bins used: 6
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Xplor file |
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