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Yorodumi- PDB-4fdw: Crystal structure of a putative cell surface protein (BACOVA_0156... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4fdw | ||||||
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Title | Crystal structure of a putative cell surface protein (BACOVA_01565) from Bacteroides ovatus ATCC 8483 at 2.05 A resolution | ||||||
Components | leucine rich hypothetical protein | ||||||
Keywords | STRUCTURAL GENOMICS / UNKNOWN FUNCTION / putative cell surface protein / Big3 domain / LRR domain / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-BIOLOGY | ||||||
Function / homology | Function and homology information Immunoglobulin-like - #3630 / Bacterial Ig-like domain (group 3) / Ig-like domain, bacterial type / BspA type Leucine rich repeat region / BspA type Leucine rich repeat region (6 copies) / Leucine-rich repeat, LRR (right-handed beta-alpha superhelix) / Ribonuclease Inhibitor / Alpha-Beta Horseshoe / Leucine-rich repeat domain superfamily / Immunoglobulin-like ...Immunoglobulin-like - #3630 / Bacterial Ig-like domain (group 3) / Ig-like domain, bacterial type / BspA type Leucine rich repeat region / BspA type Leucine rich repeat region (6 copies) / Leucine-rich repeat, LRR (right-handed beta-alpha superhelix) / Ribonuclease Inhibitor / Alpha-Beta Horseshoe / Leucine-rich repeat domain superfamily / Immunoglobulin-like / Sandwich / Mainly Beta / Alpha Beta Similarity search - Domain/homology | ||||||
Biological species | Bacteroides ovatus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.05 Å | ||||||
Authors | Joint Center for Structural Genomics (JCSG) | ||||||
Citation | Journal: To be published Title: Crystal structure of a leucine rich hypothetical protein (BACOVA_01565) from Bacteroides ovatus ATCC 8483 at 2.05 A resolution Authors: Joint Center for Structural Genomics (JCSG) | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4fdw.cif.gz | 174.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4fdw.ent.gz | 135.9 KB | Display | PDB format |
PDBx/mmJSON format | 4fdw.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4fdw_validation.pdf.gz | 421.2 KB | Display | wwPDB validaton report |
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Full document | 4fdw_full_validation.pdf.gz | 422.8 KB | Display | |
Data in XML | 4fdw_validation.xml.gz | 17.8 KB | Display | |
Data in CIF | 4fdw_validation.cif.gz | 26.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fd/4fdw ftp://data.pdbj.org/pub/pdb/validation_reports/fd/4fdw | HTTPS FTP |
-Related structure data
Related structure data | 4fd0S 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: 44400.906 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacteroides ovatus (bacteria) / Strain: ATCC 8483 / Gene: BACOVA_01565 / Plasmid: SpeedET / Production host: Escherichia Coli (E. coli) / Strain (production host): PB1 / References: UniProt: A7LUR6 | ||||||
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#2: Chemical | ChemComp-CD / #3: Chemical | ChemComp-CL / #4: Water | ChemComp-HOH / | Sequence details | THE CONSTRUCT (RESIDUES 29-428) WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG ...THE CONSTRUCT (RESIDUES 29-428) WAS EXPRESSED WITH A PURIFICATI | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.8 Å3/Da / Density % sol: 56.11 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4.6 Details: 0.1M Cadmium Chloride, 30.0% polyethylene glycol 400, 0.1M sodium acetate pH 4.6, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.9793 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 29, 2012 Details: Rhodium-coated vertical and horizontal focusing mirrors; liquid-nitrogen cooled double crystal Si(111) monochromator | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9793 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.05→45.8 Å / Num. obs: 31501 / % possible obs: 95.1 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 30.151 Å2 / Rmerge(I) obs: 0.068 / Net I/σ(I): 8.5 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 4fd0 Resolution: 2.05→45.8 Å / Cor.coef. Fo:Fc: 0.9345 / Cor.coef. Fo:Fc free: 0.9274 / Occupancy max: 1 / Occupancy min: 0.3 / Cross valid method: THROUGHOUT / σ(F): 0 Details: 1. A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN EXPRESSION. THE OCCUPANCY OF THE SE ATOMS IN THE MSE RESIDUES WAS REDUCED TO 0.75 FOR THE REDUCED ...Details: 1. A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN EXPRESSION. THE OCCUPANCY OF THE SE ATOMS IN THE MSE RESIDUES WAS REDUCED TO 0.75 FOR THE REDUCED SCATTERING POWER DUE TO PARTIAL S-MET INCORPORATION. 2. ATOM RECORD CONTAINS SUM OF TLS AND RESIDUAL B FACTORS. ANISOU RECORD CONTAINS SUM OF TLS AND RESIDUAL U FACTORS. 3. CD AND CL MODELED WERE PRESENT IN THE CRYSTALLIZATION CONDITION.
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Displacement parameters | Biso max: 101 Å2 / Biso mean: 37.8138 Å2 / Biso min: 16.04 Å2
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Refine analyze | Luzzati coordinate error obs: 0.251 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.05→45.8 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.05→2.12 Å / Total num. of bins used: 16
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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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