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Yorodumi- PDB-4rsh: Structure of a putative lipolytic protein of G-D-S-L family from ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4rsh | ||||||
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Title | Structure of a putative lipolytic protein of G-D-S-L family from Desulfitobacterium hafniense DCB-2 | ||||||
Components | Lipolytic protein G-D-S-L family | ||||||
Keywords | STRUCTURAL GENOMICS / UNKNOWN FUNCTION / PSI-Biology / Midwest Center for Structural Genomics / MCSG | ||||||
Function / homology | SGNH hydrolase / SGNH hydrolase-type esterase domain / GDSL-like Lipase/Acylhydrolase family / SGNH hydrolase superfamily / membrane => GO:0016020 / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta / Lipolytic protein G-D-S-L family Function and homology information | ||||||
Biological species | Desulfitobacterium hafniense DCB-2 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.19 Å | ||||||
Authors | Filippova, E.V. / Wawrzak, Z. / Minasov, G. / Kiryukhina, O. / Endres, M. / Joachimiak, A. / Anderson, W.F. / Midwest Center for Structural Genomics (MCSG) | ||||||
Citation | Journal: To be Published Title: Structure of a putative lipolytic protein of G-D-S-L family from Desulfitobacterium hafniense DCB-2 Authors: Filippova, E.V. / Wawrzak, Z. / Minasov, G. / Kiryukhina, O. / Endres, M. / Joachimiak, A. / Anderson, W.F. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4rsh.cif.gz | 216.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4rsh.ent.gz | 184.3 KB | Display | PDB format |
PDBx/mmJSON format | 4rsh.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4rsh_validation.pdf.gz | 434.9 KB | Display | wwPDB validaton report |
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Full document | 4rsh_full_validation.pdf.gz | 438.9 KB | Display | |
Data in XML | 4rsh_validation.xml.gz | 23.4 KB | Display | |
Data in CIF | 4rsh_validation.cif.gz | 34 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/rs/4rsh ftp://data.pdbj.org/pub/pdb/validation_reports/rs/4rsh | 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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Noncrystallographic symmetry (NCS) | NCS oper:
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-Components
#1: Protein | Mass: 19994.062 Da / Num. of mol.: 3 / Fragment: residues 53-228 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Desulfitobacterium hafniense DCB-2 (bacteria) Strain: DCB-2 / Gene: ACL22416, Dhaf_4411 / Plasmid: pMCSG68 / Production host: Escherichia coli (E. coli) / Strain (production host): BL-21 (DE3) magic / References: UniProt: B8FVL4 #2: Chemical | #3: Water | ChemComp-HOH / | |
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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: 2.34 Å3/Da / Density % sol: 47.44 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop Details: 0.1 M Potassium Thiocyanate, 30% PEG MME 2000, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jul 21, 2014 / Details: beryllium lenses |
Radiation | Monochromator: C(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97872 Å / Relative weight: 1 |
Reflection | Resolution: 2.19→85.65 Å / Num. all: 29332 / Num. obs: 29332 / % possible obs: 98.9 % / Observed criterion σ(I): -3 / Redundancy: 13.6 % / Rmerge(I) obs: 0.199 / Net I/σ(I): 13.6 |
Reflection shell | Resolution: 2.19→2.4 Å / Redundancy: 11.1 % / Rmerge(I) obs: 0.84 / Mean I/σ(I) obs: 3 / % possible all: 95.6 |
-Processing
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Refinement | Method to determine structure: SAD / Resolution: 2.19→30 Å / Cor.coef. Fo:Fc: 0.927 / Cor.coef. Fo:Fc free: 0.86 / SU B: 15.54 / SU ML: 0.198 / Isotropic thermal model: ISOTROPIC / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.297 / ESU R Free: 0.242 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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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: 23.771 Å2
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Refinement step | Cycle: LAST / Resolution: 2.19→30 Å
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