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Yorodumi- PDB-4iyj: Crystal structure of a putative acylhydrolase (BACUNI_03406) from... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4iyj | ||||||
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Title | Crystal structure of a putative acylhydrolase (BACUNI_03406) from Bacteroides uniformis ATCC 8492 at 1.37 A resolution | ||||||
Components | GDSL-like protein | ||||||
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 / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta / Unknown ligand / GDSL-like protein Function and homology information | ||||||
Biological species | Bacteroides uniformis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.37 Å | ||||||
Authors | Joint Center for Structural Genomics (JCSG) | ||||||
Citation | Journal: To be published Title: Crystal structure of a putative acylhydrolase (BACUNI_03406) from Bacteroides uniformis ATCC 8492 at 1.37 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 | 4iyj.cif.gz | 203.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4iyj.ent.gz | 168 KB | Display | PDB format |
PDBx/mmJSON format | 4iyj.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4iyj_validation.pdf.gz | 437.7 KB | Display | wwPDB validaton report |
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Full document | 4iyj_full_validation.pdf.gz | 439.4 KB | Display | |
Data in XML | 4iyj_validation.xml.gz | 24.2 KB | Display | |
Data in CIF | 4iyj_validation.cif.gz | 38.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/iy/4iyj ftp://data.pdbj.org/pub/pdb/validation_reports/iy/4iyj | 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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-Components
#1: Protein | Mass: 23819.223 Da / Num. of mol.: 2 / Fragment: UNP residues 18-228 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacteroides uniformis (bacteria) / Plasmid: SpeedE5T / Production host: Escherichia coli (E. coli) / Strain (production host): PB1 / References: UniProt: A7V743 #2: Chemical | Num. of mol.: 2 / Source method: obtained synthetically #3: Chemical | #4: Chemical | ChemComp-GOL / | #5: Water | ChemComp-HOH / | Sequence details | THIS CONSTRUCT (RESIDUES 18-228) WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG ...THIS CONSTRUCT (RESIDUES 18-228) 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: 2.32 Å3/Da / Density % sol: 46.95 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 10.00% 2-propanol, 20.00% polyethylene glycol 4000, 0.1M HEPES pH 7.5, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 0.918401,0.979415 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 21, 2012 / 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: 1.37→29.552 Å / Num. all: 93097 / Num. obs: 93097 / % possible obs: 99.4 % / Redundancy: 3.5 % / Rsym value: 0.093 / Net I/σ(I): 7.2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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: 1.37→29.552 Å / Cor.coef. Fo:Fc: 0.977 / Cor.coef. Fo:Fc free: 0.964 / Occupancy max: 1 / Occupancy min: 0.33 / SU B: 1.766 / SU ML: 0.032 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.053 / ESU R Free: 0.052 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. CHLORIDE (CL) AND GLYCEROL (GOL) FROM THE CRYSTALLIZATION/CRYO CONDITIONS HAVE BEEN MODELED INTO THE STRUCTURE. 4.UNKNOWN LIGANDS (UNL) HAVE BEEN MODELED INTO THE PUTATIVE ACTIVE SITE.IDENTIFICATION OF THE PUTATIVE ACTIVE SITE IS BASED ON ElECTRON DENSITY AND STRUCTURAL COMPARISONS WITH SIMILAR PROTEINS OF KNOWN FUNCTION. 5.THE SIDECHAINS OF GLU B177,ASP B193,GLU A211, AND GLU B33 SHOW ELEVATED NEGATIVE DIFFERENCE DENSITY. THE OCCUPANCIES OF THE SIDECHAIN ATOMS WERE NOT ADJUSTED IN THESE REGIONS OF APPARENT RADIATION DAMAGE.
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 57.44 Å2 / Biso mean: 18.4822 Å2 / Biso min: 3.46 Å2
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Refinement step | Cycle: LAST / Resolution: 1.37→29.552 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.37→1.406 Å / Total num. of bins used: 20
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