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Yorodumi- PDB-4fs7: Crystal structure of a leucine-rich repeat protein (BACOVA_04585)... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4fs7 | ||||||
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Title | Crystal structure of a leucine-rich repeat protein (BACOVA_04585) from Bacteroides ovatus ATCC 8483 at 1.19 A resolution | ||||||
Components | Uncharacterized protein | ||||||
Keywords | PROTEIN BINDING / leucine-rich repeats / extracellular protein / Structural Genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-BIOLOGY | ||||||
Function / homology | 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 / Alpha Beta / Uncharacterized protein Function and homology information | ||||||
Biological species | Bacteroides ovatus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.19 Å | ||||||
Authors | Joint Center for Structural Genomics (JCSG) | ||||||
Citation | Journal: To be published Title: Crystal structure of a hypothetical leucine rich repeat protein (BACOVA_04585) from Bacteroides ovatus ATCC 8483 at 1.19 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 | 4fs7.cif.gz | 194.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4fs7.ent.gz | 156.6 KB | Display | PDB format |
PDBx/mmJSON format | 4fs7.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fs/4fs7 ftp://data.pdbj.org/pub/pdb/validation_reports/fs/4fs7 | HTTPS FTP |
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-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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-Components
#1: Protein | Mass: 44304.445 Da / Num. of mol.: 1 / Fragment: UNP residues 22-414 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacteroides ovatus (bacteria) / Gene: BACOVA_04585 / Plasmid: SpeedET / Production host: Escherichia coli (E. coli) / Strain (production host): PB1 / References: UniProt: A7M397 | ||||
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#2: Chemical | #3: Water | ChemComp-HOH / | Sequence details | THE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH ...THE CONSTRUCT 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: 2.1 Å3/Da / Density % sol: 41.5 % |
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Crystal grow | Temperature: 293 K Details: 0.200M sodium fluoride 20.00% polyethylene glycol 3350, 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: BL9-2 / Wavelength: 0.91837,0.97949,0.97915 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: MAR MAR325 / Detector: CCD / Date: Jan 11, 2012 / Details: DOUBLE CRYSTAL MONOCHROMATOR | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: DOUBLE CRYSTAL / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength |
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Reflection | Resolution: 1.19→29.278 Å / Num. obs: 119592 / % possible obs: 97.8 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 10.858 Å2 / Rmerge F obs: 0.165 / Rmerge(I) obs: 0.048 / Rrim(I) all: 0.061 / Net I/σ(I): 9.11 / Num. measured all: 430225 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Phasing
Phasing | Method: MAD |
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-Processing
Software |
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Refinement | Method to determine structure: MAD / Resolution: 1.19→29.278 Å / Cor.coef. Fo:Fc: 0.98 / Cor.coef. Fo:Fc free: 0.974 / Occupancy max: 1 / Occupancy min: 0.2 / SU B: 1.204 / SU ML: 0.024 / Cross valid method: THROUGHOUT Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. ATOM RECORD CONTAINS SUM OF TLS AND RESIDUAL B FACTORS. ANISOU RECORD CONTAINS SUM OF TLS AND RESIDUAL U FACTORS. 3. A MET-INHIBITION ...Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. ATOM RECORD CONTAINS SUM OF TLS AND RESIDUAL B FACTORS. ANISOU RECORD CONTAINS SUM OF TLS AND RESIDUAL U FACTORS. 3. 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 TO ACCOUNT FOR THE REDUCED SCATTERING POWER DUE TO PARTIAL S-MET INCORPORATION. 4. ETHYLENE GLYCOL (EDO) USED AS A CRYOPROTECTANT HAS BEEN MODELED INTO THE STRUCTURE. 5. AN UNEXPLAINED DIFFEREANCE ELECTRON DENSITY NEAR TYR314 WAS NOT MODELED.
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Solvent computation | Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 18.38 Å2
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Refinement step | Cycle: LAST / Resolution: 1.19→29.278 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.19→1.221 Å
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