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Yorodumi- PDB-3be3: Crystal structure of a protein belonging to pfam DUF1653 from Bor... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3be3 | ||||||
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Title | Crystal structure of a protein belonging to pfam DUF1653 from Bordetella bronchiseptica | ||||||
Components | Uncharacterized protein | ||||||
Keywords | STRUCTURAL GENOMICS / UNKNOWN FUNCTION / 10206d / pfam DUF1653 / PSI-2 / Protein Structure Initiative / New York SGX Research Center for Structural Genomics / NYSGXRC | ||||||
Function / homology | DUF1653-like domain / DUF1653-like domain / DUF1653-like domain superfamily / Protein of unknown function (DUF1653) / SH3 type barrels. / Roll / Mainly Beta / DUF1653 domain-containing protein / DUF1653 domain-containing protein Function and homology information | ||||||
Biological species | Bordetella bronchiseptica RB50 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.04 Å | ||||||
Authors | Tyagi, R. / Eswaramoorthy, S. / Burley, S.K. / Swaminathan, S. / New York SGX Research Center for Structural Genomics (NYSGXRC) | ||||||
Citation | Journal: To be Published Title: Crystal structure of a protein belonging to pfam DUF1653 from Bordetella bronchiseptica. Authors: Tyagi, R. / Eswaramoorthy, S. / 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 | 3be3.cif.gz | 43.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3be3.ent.gz | 33.7 KB | Display | PDB format |
PDBx/mmJSON format | 3be3.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3be3_validation.pdf.gz | 449 KB | Display | wwPDB validaton report |
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Full document | 3be3_full_validation.pdf.gz | 450 KB | Display | |
Data in XML | 3be3_validation.xml.gz | 9.8 KB | Display | |
Data in CIF | 3be3_validation.cif.gz | 12.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/be/3be3 ftp://data.pdbj.org/pub/pdb/validation_reports/be/3be3 | HTTPS FTP |
-Related structure data
Similar structure data | |
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Other databases |
-Links
-Assembly
Deposited unit |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 10521.347 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bordetella bronchiseptica RB50 (bacteria) Species: Bordetella bronchiseptica / Strain: RB50, NCTC 13252 / Gene: 81430067, BB4950 / Plasmid: pSGX3-BC / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q7WDN8, UniProt: A0A0H3LS10*PLUS #2: Chemical | #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.2 Å3/Da / Density % sol: 43.97 % |
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Crystal grow | Temperature: 294 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 0.1 M HEPES pH 7.5, 2.0 M Ammonium sulfate, VAPOR DIFFUSION, SITTING DROP, temperature 294K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X12C / Wavelength: 0.979 Å |
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Nov 13, 2007 / Details: Mirrors |
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 2.04→50 Å / Num. all: 12048 / Num. obs: 12048 / % possible obs: 100 % / Observed criterion σ(I): 0 / Redundancy: 21.6 % / Biso Wilson estimate: 9.5 Å2 / Rmerge(I) obs: 0.087 / Net I/σ(I): 12.2 |
Reflection shell | Resolution: 2.04→2.11 Å / Redundancy: 19.3 % / Rmerge(I) obs: 0.304 / Mean I/σ(I) obs: 2.1 / Num. unique all: 1185 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 2.04→44.58 Å / Rfactor Rfree error: 0.012 / Data cutoff high absF: 130435.42 / 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: 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: 39.7621 Å2 / ksol: 0.37786 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 21.4 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.04→44.58 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.04→2.17 Å / Rfactor Rfree error: 0.029 / Total num. of bins used: 6
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Xplor file |
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