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Yorodumi- PDB-4lr4: Crystal structure of a putative secreted protein (EUBREC_3654) fr... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4lr4 | ||||||
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Title | Crystal structure of a putative secreted protein (EUBREC_3654) from Eubacterium rectale at 2.43 A resolution | ||||||
Components | hypothetical protein | ||||||
Keywords | STRUCTURAL GENOMICS / UNKNOWN FUNCTION / an orphan / two domains protein / N-terminus has a sandwich 10 strands in 2 sheets and jelly-roll fold / C -terminus has galactose-binding domain-like fold / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-BIOLOGY | ||||||
Function / homology | Function and homology information Jelly Rolls - #1420 / Jelly Rolls - #1430 / : / : / Carbohydrate binding module-like / Domain of unknown function (DUF6947) / Jelly Rolls / Sandwich / Mainly Beta Similarity search - Domain/homology | ||||||
Biological species | Eubacterium rectale (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.43 Å | ||||||
Authors | Joint Center for Structural Genomics (JCSG) | ||||||
Citation | Journal: To be published Title: Crystal structure of a hypothetical protein (EUBREC_3654) from Eubacterium rectale at 2.43 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 | 4lr4.cif.gz | 562.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4lr4.ent.gz | 470.2 KB | Display | PDB format |
PDBx/mmJSON format | 4lr4.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4lr4_validation.pdf.gz | 495.2 KB | Display | wwPDB validaton report |
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Full document | 4lr4_full_validation.pdf.gz | 505.6 KB | Display | |
Data in XML | 4lr4_validation.xml.gz | 56.2 KB | Display | |
Data in CIF | 4lr4_validation.cif.gz | 80.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/lr/4lr4 ftp://data.pdbj.org/pub/pdb/validation_reports/lr/4lr4 | HTTPS FTP |
-Related structure data
Similar structure data | |
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Other databases |
-Links
-Assembly
Deposited unit |
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Unit cell |
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-Components
#1: Protein | Mass: 41218.746 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Eubacterium rectale (bacteria) / Strain: ATCC 33656 / VPI 0990 / Gene: EUBREC_3654, RER070207000171 / Plasmid: SpeedET / Production host: Escherichia Coli (E. coli) / Strain (production host): PB1 / References: UniProt: C4ZEB7 #2: Chemical | ChemComp-GOL / #3: Chemical | ChemComp-PO4 / #4: Chemical | ChemComp-CL / #5: Water | ChemComp-HOH / | Sequence details | THE CONSTRUCT (26-394) WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS ...THE CONSTRUCT (26-394) WAS EXPRESSED WITH A PURIFICATI | |
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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: 3.65 Å3/Da / Density % sol: 66.28 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.83 Details: 1.5M ammonium dihydrogen phosphate, 20.0% Glycerol, 0.01M magnesium chloride, 0.1M TRIS pH 7.83, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 0.91837, 0.97864, 0.97805 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 2, 2013 Details: Flat mirror (vertical focusing); single crystal Si(111) bent monochromator (horizontal focusing) | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: single crystal Si(111) bent / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength |
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Reflection | Resolution: 2.43→48.963 Å / Num. obs: 87733 / % possible obs: 98.1 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 52.762 Å2 / Rmerge(I) obs: 0.102 / Net I/σ(I): 9.58 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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: 2.43→48.963 Å / Cor.coef. Fo:Fc: 0.9314 / Cor.coef. Fo:Fc free: 0.9191 / Occupancy max: 1 / Occupancy min: 0.5 / 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. THE MAD PHASES WERE USED AS RESTRAINTS DURING REFINEMENT. 4. PHOSPHATE (PO4), GLYCEROL (GOL), AND CHLORIDE (CL) MODELED WERE PRESENT IN PROTEIN/CYRO CONDITIONS. 5.NCS RESTRAINTS WERE IMPOSED BY AUTOBUSTER'S LSSR PROCEDURE (-AUTONCS). 6. RAMACHANDRAN OUTLIERS (A,D/378, A-D/181) ARE SUPPORTED BY DENSITY.
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Displacement parameters | Biso max: 179.94 Å2 / Biso mean: 52.857 Å2 / Biso min: 20.29 Å2
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Refine analyze | Luzzati coordinate error obs: 0.348 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.43→48.963 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.43→2.49 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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