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Yorodumi- PDB-2w6l: The crystal structure at 1.7 A resolution of CobE, a protein from... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2w6l | ||||||
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Title | The crystal structure at 1.7 A resolution of CobE, a protein from the cobalamin (vitamin B12) biosynthetic pathway | ||||||
Components | COBE | ||||||
Keywords | BIOSYNTHETIC PROTEIN / PSEUDOMONAS AERUGINOSA / COBE / COBALAMIN / PRECORRIN / NOVEL FOLD / VITAMIN B12 | ||||||
Function / homology | CobE/GbiG C-terminal domain / CobE/GbiG C-terminal domain / CobE/GbiG C-terminal domain superfamily / Cobalamin synthesis G C-terminus / cobalamin biosynthetic process / Nucleotidyltransferase; domain 5 / 2-Layer Sandwich / Alpha Beta / CobE/GbiG C-terminal domain-containing protein Function and homology information | ||||||
Biological species | PSEUDOMONAS AERUGINOSA (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.89 Å | ||||||
Authors | Vevodova, J. / Smith, D. / McGoldrick, H. / Deery, E. / Murzin, A.G. / Warren, M.J. / Wilson, K.S. | ||||||
Citation | Journal: To be Published Title: The Crystal Structure at 1.7 A Resolution of Cobe, a Protein from the Cobalamin (Vitamin B12) Biosynthetic Pathway Authors: Vevodova, J. / Smith, D. / Mcgoldrick, H. / Deery, E. / Murzin, A.G. / Warren, M.J. / Wilson, K.S. | ||||||
History |
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Remark 700 | SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2w6l.cif.gz | 40.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2w6l.ent.gz | 28.6 KB | Display | PDB format |
PDBx/mmJSON format | 2w6l.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/w6/2w6l ftp://data.pdbj.org/pub/pdb/validation_reports/w6/2w6l | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 15090.366 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) PSEUDOMONAS AERUGINOSA (bacteria) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9HZQ0 | ||||
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#2: Chemical | #3: Chemical | #4: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 1.9 Å3/Da / Density % sol: 35 % / Description: NONE |
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Crystal grow | Details: 0.1 MES PH 6.9, 2M AMMONIUM SULPHATE, 5% DIOXANE |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.934 |
Detector | Type: ADSC CCD / Detector: CCD |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.934 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→50 Å / Num. obs: 9752 / % possible obs: 98.3 % / Observed criterion σ(I): 2 / Redundancy: 7 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 26.8 |
Reflection shell | Resolution: 1.89→1.93 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.34 / Mean I/σ(I) obs: 6.4 / % possible all: 73 |
-Processing
Software |
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Refinement | Method to determine structure: MAD Starting model: NONE Resolution: 1.89→43.69 Å / Cor.coef. Fo:Fc: 0.942 / Cor.coef. Fo:Fc free: 0.925 / SU B: 3.742 / SU ML: 0.116 / Cross valid method: THROUGHOUT / ESU R: 0.203 / ESU R Free: 0.185 / 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: 32.6 Å2
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Refinement step | Cycle: LAST / Resolution: 1.89→43.69 Å
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Refine LS restraints |
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