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Yorodumi- PDB-3f67: Crystal Structure of Putative Dienelactone Hydrolase from Klebsie... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3f67 | ||||||
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Title | Crystal Structure of Putative Dienelactone Hydrolase from Klebsiella pneumoniae subsp. pneumoniae MGH 78578 | ||||||
Components | Putative dienelactone hydrolase | ||||||
Keywords | HYDROLASE / alpha-beta-alpha sandwich / Structural Genomics / PSI-2 / Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Klebsiella pneumoniae subsp. pneumoniae MGH 78578 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.74 Å | ||||||
Authors | Kim, Y. / Li, H. / Bearden, J. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG) | ||||||
Citation | Journal: To be Published Title: Crystal Structure of Putative Dienelactone Hydrolase from Klebsiella pneumoniae subsp. pneumoniae MGH 78578 Authors: Kim, Y. / Li, H. / Bearden, J. / Joachimiak, A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3f67.cif.gz | 71.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3f67.ent.gz | 52.9 KB | Display | PDB format |
PDBx/mmJSON format | 3f67.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/f6/3f67 ftp://data.pdbj.org/pub/pdb/validation_reports/f6/3f67 | 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: 26833.744 Da / Num. of mol.: 1 / Fragment: residues 28-265 Source method: isolated from a genetically manipulated source Details: N-terminal fusion of maltose-binding protein (removed in situ) and N-terminal His-tag which is removed during the purification Source: (gene. exp.) Klebsiella pneumoniae subsp. pneumoniae MGH 78578 (bacteria) Strain: ATCC 700721; MGH 78578 / Gene: KPN78578_42700, KPN_04326, ysgA / Plasmid: pMCSG19 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 magic References: UniProt: A6TGL0, Hydrolases; Acting on ester bonds; Carboxylic-ester hydrolases | ||||
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#2: Chemical | ChemComp-EDO / | ||||
#3: Chemical | #4: Chemical | ChemComp-ACY / | #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.82 Å3/Da / Density % sol: 56.46 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7 Details: 0.2M Li2SO4 0.1 M Tris pH 7.0 1.0 M K/Na tartrate, VAPOR DIFFUSION, SITTING DROP, temperature 289K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.9792 Å |
Detector | Type: SBC-3 / Detector: CCD / Date: Oct 5, 2008 / Details: mirrors |
Radiation | Monochromator: double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9792 Å / Relative weight: 1 |
Reflection | Resolution: 1.74→47.85 Å / Num. all: 31820 / Num. obs: 31820 / % possible obs: 99.8 % / Observed criterion σ(I): 0 / Redundancy: 14 % / Biso Wilson estimate: 24.19 Å2 / Rmerge(I) obs: 0.109 / Net I/σ(I): 7.6 |
Reflection shell | Resolution: 1.74→1.78 Å / Redundancy: 10.3 % / Rmerge(I) obs: 0.866 / Mean I/σ(I) obs: 2.4 / Num. unique all: 1583 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 1.74→47.85 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.952 / SU B: 4.054 / SU ML: 0.059 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.103 / ESU R Free: 0.1 Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
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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: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 19.911 Å2
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Refinement step | Cycle: LAST / Resolution: 1.74→47.85 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.744→1.789 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Origin x: 53.1541 Å / Origin y: 26.6225 Å / Origin z: 7.8597 Å
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