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Yorodumi- PDB-5cml: Crystal structure of the Esterase domain from Rhodothermus marinu... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5cml | ||||||
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Title | Crystal structure of the Esterase domain from Rhodothermus marinus Rmar_1206 protein | ||||||
Components | OsmC family protein | ||||||
Keywords | HYDROLASE / Serine Esterase OsmC Thermophile | ||||||
Function / homology | Function and homology information OsmC/Ohr family / OsmC/Ohr superfamily / OsmC-like protein / Serine aminopeptidase, S33 / Serine aminopeptidase, S33 / Alpha/Beta hydrolase fold, catalytic domain / K homology domain-like, alpha/beta / Alpha/Beta hydrolase fold / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta Similarity search - Domain/homology | ||||||
Biological species | Rhodothermus marinus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.56 Å | ||||||
Authors | Marles-Wright, J. / Wardrope, C. / Jensen, M.-B.V. / Horsfall, L.E. / Togneri, P.D. / Rosser, S.J. | ||||||
Funding support | United Kingdom, 1items
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Citation | Journal: Plos One / Year: 2016 Title: Characterisation of a New Family of Carboxyl Esterases with an OsmC Domain. Authors: Jensen, M.V. / Horsfall, L.E. / Wardrope, C. / Togneri, P.D. / Marles-Wright, J. / Rosser, S.J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5cml.cif.gz | 276.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5cml.ent.gz | 227.5 KB | Display | PDB format |
PDBx/mmJSON format | 5cml.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5cml_validation.pdf.gz | 447.8 KB | Display | wwPDB validaton report |
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Full document | 5cml_full_validation.pdf.gz | 452.7 KB | Display | |
Data in XML | 5cml_validation.xml.gz | 20.9 KB | Display | |
Data in CIF | 5cml_validation.cif.gz | 30.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/cm/5cml ftp://data.pdbj.org/pub/pdb/validation_reports/cm/5cml | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 29018.025 Da / Num. of mol.: 2 / Fragment: UNP residues 1-255 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rhodothermus marinus (bacteria) / Gene: Rmar_1206 / Plasmid: pDest17 / Production host: Escherichia coli (E. coli) / Strain (production host): AI / References: UniProt: D0MHY8 #2: Chemical | #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.15 Å3/Da / Density % sol: 42.85 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 5 Details: Protein at 15 mg/ml was crystallized by sitting drop vapour diffusion with 100 nl drops of protein supplemented with 100 nl of mother liquor comprising 0.2 M ammonium citrate dibasic, pH 5. ...Details: Protein at 15 mg/ml was crystallized by sitting drop vapour diffusion with 100 nl drops of protein supplemented with 100 nl of mother liquor comprising 0.2 M ammonium citrate dibasic, pH 5.0, 20 % w/v PEG 3350 (Hampton PEG/Ion HT96 screen D12), drops were equilibrated against 70 ul of mother liquor for one month before crystals appeared. |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.9795 Å |
Detector | Type: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Jul 25, 2013 |
Radiation | Monochromator: Single Crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 |
Reflection | Resolution: 1.56→44.62 Å / Num. all: 255878 / Num. obs: 69888 / % possible obs: 99.09 % / Redundancy: 3.7 % / Rmerge(I) obs: 0.044 / Net I/σ(I): 13.91 |
Reflection shell | Resolution: 1.56→1.612 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.725 / Mean I/σ(I) obs: 1.88 / % possible all: 98.48 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2FUK, 3TRD, 3PF9 Resolution: 1.56→44.62 Å / SU ML: 0.17 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 19.5 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.56→44.62 Å
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Refine LS restraints |
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LS refinement shell |
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