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Yorodumi- PDB-2a5z: Crystal Structure of Protein of Unknown Function SO2946 from Shew... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2a5z | ||||||
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Title | Crystal Structure of Protein of Unknown Function SO2946 from Shewanella oneidensis MR-1 | ||||||
Components | hypothetical protein SO2946 | ||||||
Keywords | STRUCTURAL GENOMICS / UNKNOWN FUNCTION / Shewanella oneidensis MR-1 / hypothetical protein / SO2946 / PSI / Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG | ||||||
Function / homology | Jelly Rolls - #200 / Concanavalin A-like lectin/glucanase domain superfamily / Jelly Rolls / Sandwich / Mainly Beta / metal ion binding / Lambda phage protein with carbohydrate-binding module Function and homology information | ||||||
Biological species | Shewanella oneidensis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.015 Å | ||||||
Authors | Nocek, B. / Bigelow, L. / Abdullah, J. / Collart, F. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG) | ||||||
Citation | Journal: J.STRUCT.FUNCT.GENOM. / Year: 2008 Title: Structure of SO2946 orphan from Shewanella oneidensis shows "jelly-roll" fold with carbohydrate-binding module. Authors: Nocek, B. / Bigelow, L. / Abdullah, J. / Joachimiak, A. | ||||||
History |
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Remark 300 | BIOMOLECULE: 1 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 3 CHAIN(S) ...BIOMOLECULE: 1 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 3 CHAIN(S). SEE REMARK 350 FOR INFORMATION ON GENERATING THE BIOLOGICAL MOLECULE(S). HOWEVER AUTHORS STATE, 'NO BIOLOGICAL INFORMATION IS AVAILABLE TO CONFIRM THIS'. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2a5z.cif.gz | 152.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2a5z.ent.gz | 127.2 KB | Display | PDB format |
PDBx/mmJSON format | 2a5z.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2a5z_validation.pdf.gz | 440.7 KB | Display | wwPDB validaton report |
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Full document | 2a5z_full_validation.pdf.gz | 445 KB | Display | |
Data in XML | 2a5z_validation.xml.gz | 31.5 KB | Display | |
Data in CIF | 2a5z_validation.cif.gz | 46.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/a5/2a5z ftp://data.pdbj.org/pub/pdb/validation_reports/a5/2a5z | HTTPS FTP |
-Related structure data
Similar structure data | |
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Other databases |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Details | This protein exist as a homotrimer. |
-Components
#1: Protein | Mass: 27879.520 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Shewanella oneidensis (bacteria) / Strain: MR-1 / Gene: SO2946 / Plasmid: pET15b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q8ED25 #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: 2.11 Å3/Da / Density % sol: 40.98 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7 Details: Peg 3350, 0.2 Mgcl2, pH 7, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.9794 Å |
Detector | Type: SBC-1 / Detector: CCD / Date: Jun 29, 2005 / Details: mirrors |
Radiation | Monochromator: Si 111channel / Protocol: SAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9794 Å / Relative weight: 1 |
Reflection | Resolution: 2→50 Å / Num. all: 45439 / Num. obs: 45258 / % possible obs: 99.6 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Rmerge(I) obs: 0.12 |
Reflection shell | Resolution: 2→2.09 Å / % possible all: 99.5 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 2.015→50 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.938 / SU B: 7.071 / SU ML: 0.105 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.191 / ESU R Free: 0.155 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 22.378 Å2
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Refinement step | Cycle: LAST / Resolution: 2.015→50 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.015→2.068 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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