+Open data
-Basic information
Entry | Database: PDB / ID: 2ea9 | ||||||
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Title | Crystal structure of a hypothetical protein JW2626 from E.coli | ||||||
Components | Hypothetical protein yfjZ | ||||||
Keywords | STRUCTURAL GENOMICS / UNKNOWN FUNCTION / Escherichia coli / JW2626 / hypothetical protein / NPPSFA / National Project on Protein Structural and Functional Analyses / RIKEN Structural Genomics/Proteomics Initiative / RSGI | ||||||
Function / homology | Antitoxin CbeA / Antitoxin CbeA superfamily / CbeA_antitoxin, type IV, cytoskeleton bundling-enhancing factor A / positive regulation of cytoskeleton organization / PAS domain / Beta-Lactamase / 2-Layer Sandwich / Alpha Beta / Antitoxin YfjZ Function and homology information | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å | ||||||
Authors | Okazaki, N. / Kuramitsu, S. / Yamamoto, M. / Yokoyama, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI) | ||||||
Citation | Journal: To be Published Title: Crystal structure of a hypothetical protein JW2626 from E.coli Authors: Okazaki, N. / Kuramitsu, S. / Yamamoto, M. / Yokoyama, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2ea9.cif.gz | 33.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2ea9.ent.gz | 21.7 KB | Display | PDB format |
PDBx/mmJSON format | 2ea9.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ea/2ea9 ftp://data.pdbj.org/pub/pdb/validation_reports/ea/2ea9 | HTTPS FTP |
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-Related structure data
Related structure data | 2h28S 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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Details | The biological assembly is a monomer. |
-Components
#1: Protein | Mass: 11749.244 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Description: E.coli Cell Free Protein Synthesis / References: UniProt: P52141 |
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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: 2.35 Å3/Da / Density % sol: 47.74 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7 Details: 0.1M HEPES, 1.0M Succinic acid, 1.0% PEG MME 2000, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 291K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL26B2 / Wavelength: 0.97915 Å |
Detector | Type: RIGAKU JUPITER 210 / Detector: CCD / Date: Oct 12, 2006 / Details: mirrors |
Radiation | Monochromator: Bending Magnet / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97915 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→50 Å / Num. obs: 6091 / % possible obs: 97.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5 % / Biso Wilson estimate: 18.6 Å2 / Rmerge(I) obs: 0.075 / Net I/σ(I): 12.5 |
Reflection shell | Resolution: 2.1→2.18 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.325 / Mean I/σ(I) obs: 3.4 / Num. unique all: 503 / % possible all: 81.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ID 2H28 Resolution: 2.1→28.76 Å / Rfactor Rfree error: 0.015 / Data cutoff high absF: 760666.92 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 54.4968 Å2 / ksol: 0.386536 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 31.8 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.1→28.76 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.1→2.23 Å / Rfactor Rfree error: 0.047 / Total num. of bins used: 6
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Xplor file |
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