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Yorodumi- PDB-5oi1: Crystal structure of Mycolicibacterium hassiacum glucosylglycerat... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5oi1 | |||||||||
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Title | Crystal structure of Mycolicibacterium hassiacum glucosylglycerate hydrolase (MhGgH) D182A variant in complex with serine and glycerol | |||||||||
Components | Hydrolase | |||||||||
Keywords | HYDROLASE / Mycobacterium | |||||||||
Function / homology | Function and homology information glucosylglycerate hydrolase / glucosylglycerate hydrolase activity / Glc3Man9GlcNAc2 oligosaccharide glucosidase activity / oligosaccharide metabolic process / protein N-linked glycosylation Similarity search - Function | |||||||||
Biological species | Mycobacterium hassiacum | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 Å | |||||||||
Authors | Cereija, T.B. / Macedo-Ribeiro, S. / Pereira, P.J.B. | |||||||||
Funding support | Portugal, 2items
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Citation | Journal: Iucrj / Year: 2019 Title: The structural characterization of a glucosylglycerate hydrolase provides insights into the molecular mechanism of mycobacterial recovery from nitrogen starvation. Authors: Cereija, T.B. / Alarico, S. / Lourenco, E.C. / Manso, J.A. / Ventura, M.R. / Empadinhas, N. / Macedo-Ribeiro, S. / Pereira, P.J.B. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5oi1.cif.gz | 400.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5oi1.ent.gz | 328.9 KB | Display | PDB format |
PDBx/mmJSON format | 5oi1.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5oi1_validation.pdf.gz | 463.1 KB | Display | wwPDB validaton report |
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Full document | 5oi1_full_validation.pdf.gz | 469.1 KB | Display | |
Data in XML | 5oi1_validation.xml.gz | 40.8 KB | Display | |
Data in CIF | 5oi1_validation.cif.gz | 61.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/oi/5oi1 ftp://data.pdbj.org/pub/pdb/validation_reports/oi/5oi1 | HTTPS FTP |
-Related structure data
Related structure data | 5ohcC 5ohzSC 5oi0C 5oieC 5oivC 5oiwC 5oj4C 5ojuC 5ojvC 5ontC 5onzC 5oo2C 6q5tC S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data | |
Experimental dataset #1 | Data reference: 10.15785/SBGRID/468 / Data set type: diffraction image data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 50913.484 Da / Num. of mol.: 2 / Mutation: D182A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mycobacterium hassiacum (strain DSM 44199 / CIP 105218 / JCM 12690 / 3849) (bacteria) Gene: C731_0006 / Production host: Escherichia coli (E. coli) / References: UniProt: K5BDL0 #2: Chemical | ChemComp-GOL / #3: Chemical | #4: 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: 2.94 Å3/Da / Density % sol: 58.23 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop Details: Tris-Bicine pH 8.5, amino acids, PEG 4000, glycerol |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-3 / Wavelength: 0.9677 Å |
Detector | Type: DECTRIS EIGER X 4M / Detector: PIXEL / Date: Oct 29, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9677 Å / Relative weight: 1 |
Reflection | Resolution: 1.75→42.23 Å / Num. obs: 119738 / % possible obs: 98.8 % / Redundancy: 4.9 % / CC1/2: 0.998 / Rmerge(I) obs: 0.07 / Rpim(I) all: 0.035 / Rrim(I) all: 0.079 / Net I/σ(I): 11.6 |
Reflection shell | Resolution: 1.75→1.78 Å / Redundancy: 5 % / Rmerge(I) obs: 0.987 / Mean I/σ(I) obs: 1.6 / CC1/2: 0.579 / Rpim(I) all: 0.48 / Rrim(I) all: 1.102 / % possible all: 99.3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5OHZ Resolution: 1.75→40.007 Å / SU ML: 0.16 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 17.02 / 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: 1.75→40.007 Å
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Refine LS restraints |
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LS refinement shell |
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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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