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Yorodumi- PDB-4ppy: Crystal structure of a putative acylhydrolase (BF3764) from Bacte... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4ppy | ||||||
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Title | Crystal structure of a putative acylhydrolase (BF3764) from Bacteroides fragilis NCTC 9343 at 2.00 A resolution | ||||||
Components | Putative acylhydrolase | ||||||
Keywords | HYDROLASE / PF13472 family / GDSL-like lipase / Structural Genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-BIOLOGY | ||||||
Function / homology | SGNH hydrolase / SGNH hydrolase-type esterase domain / GDSL-like Lipase/Acylhydrolase family / SGNH hydrolase superfamily / hydrolase activity / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta / Putative acylhydrolase Function and homology information | ||||||
Biological species | Bacteroides fragilis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2 Å | ||||||
Authors | Joint Center for Structural Genomics (JCSG) | ||||||
Citation | Journal: To be published Title: Crystal structure of a putative acylhydrolase (BF3764) from Bacteroides fragilis NCTC 9343 at 2.00 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 | 4ppy.cif.gz | 257.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4ppy.ent.gz | 213.2 KB | Display | PDB format |
PDBx/mmJSON format | 4ppy.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/pp/4ppy ftp://data.pdbj.org/pub/pdb/validation_reports/pp/4ppy | 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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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 23509.789 Da / Num. of mol.: 3 / Fragment: UNP residues 27-235 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacteroides fragilis (bacteria) / Strain: ATCC 25285 / NCTC 9343 / Gene: BF9343_3663 / Plasmid: SpeedET / Production host: Escherichia coli (E. coli) / Strain (production host): PB1 / References: UniProt: Q5L8Y8 #2: Water | ChemComp-HOH / | Sequence details | THIS CONSTRUCT (RESIDUES 27-235) WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG ...THIS CONSTRUCT (RESIDUES 27-235) 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: 2.71 Å3/Da / Density % sol: 54.66 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: 0.20M magnesium chloride, 30.00% polyethylene glycol 4000, 0.1M tris hydrochloride pH 8.5, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 0.979106,0.918401,0.979351 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 17, 2013 / Details: KOHZU: Double Crystal Si(111) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: Double Crystal Si(111) / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength |
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Reflection | Resolution: 2→60.686 Å / Num. all: 50307 / Num. obs: 50307 / % possible obs: 98.4 % / Redundancy: 2.1 % / Rsym value: 0.105 / Net I/σ(I): 3.9 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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→60.686 Å / Cor.coef. Fo:Fc: 0.932 / Cor.coef. Fo:Fc free: 0.915 / Occupancy max: 1 / Occupancy min: 0.3 / SU B: 6.33 / SU ML: 0.097 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.174 / ESU R Free: 0.144 Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES Details: 1.HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2.A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN EXPRESSION. THE OCCUPANCY OF THE SE ATOMS IN THE ...Details: 1.HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2.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. 3.ATOM RECORDS CONTAIN SUM OF TLS AND RESIDUAL B FACTORS. ANISOU RECORD CONTAINS SUM OF TLS AND RESIDUAL U FACTORS. 4.WATERS WERE EXCLUDED FROM AUTOMATIC TLS ASSIGNMENT. 5.RAMACHANDRAN OUTLIER AT RESIDUE 112 IN ALL 3 CHAINS IS SUPPORTED BY ELECTRON DENSITY. 6.EXPERIMENTAL PHASES IN THE FORM OF HL COEFFICIENTS WERE USED AS RESTRAINTS DURING CRYSTALLOGRAPHIC REFINEMENT.
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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: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 77.83 Å2 / Biso mean: 19.8906 Å2 / Biso min: 7.91 Å2
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Refinement step | Cycle: LAST / Resolution: 2→60.686 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2→2.052 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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