+Open data
-Basic information
Entry | Database: PDB / ID: 6bws | ||||||
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Title | Crystal structure of Efga from Methylobacterium extorquens | ||||||
Components | Glycolate utilization protein | ||||||
Keywords | UNKNOWN FUNCTION / enhanced formaldehyde growth | ||||||
Function / homology | Haem-degrading domain / Corrinoid adenosyltransferase PduO/GlcC-like / Corrinoid adenosyltransferase PduO/GlcC-like superfamily / Haem degrading protein HbpS-like / Beta-Lactamase / 2-Layer Sandwich / Alpha Beta / Glycolate utilization protein Function and homology information | ||||||
Biological species | Methylobacterium extorquens (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.65 Å | ||||||
Authors | Shamoo, Y. / Davlieva, M. | ||||||
Citation | Journal: To Be Published Title: Crystal structure of Efga from Methylobacterium extorquens Authors: Shamoo, Y. / Davlieva, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6bws.cif.gz | 119.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6bws.ent.gz | 92.1 KB | Display | PDB format |
PDBx/mmJSON format | 6bws.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bw/6bws ftp://data.pdbj.org/pub/pdb/validation_reports/bw/6bws | HTTPS FTP |
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-Related structure data
Related structure data | 2a2lS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 16962.027 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Methylobacterium extorquens (bacteria) / Gene: BV511_11735 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A1P8QPB5 #2: 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 Å3/Da / Density % sol: 38.62 % |
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Crystal grow | Temperature: 283.15 K / Method: vapor diffusion, sitting drop / Details: 0.2 M Potassium fluoride, 2.2 m Ammonium sulfate |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.97857 Å |
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Dec 4, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97857 Å / Relative weight: 1 |
Reflection | Resolution: 1.65→50 Å / Num. obs: 62866 / % possible obs: 94.7 % / Redundancy: 12.9 % / Biso Wilson estimate: 15.46 Å2 / Rmerge(I) obs: 0.136 / Net I/σ(I): 4.2 |
Reflection shell | Resolution: 1.65→1.68 Å / Redundancy: 12.5 % / Rmerge(I) obs: 0.991 / % possible all: 95.6 |
-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2A2L Resolution: 1.65→42.47 Å / SU ML: 0.19 / Cross valid method: THROUGHOUT / σ(F): 1.37 / Phase error: 28.33 / 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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 18.98 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.65→42.47 Å
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Refine LS restraints |
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LS refinement shell |
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