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- PDB-2xwp: ANAEROBIC COBALT CHELATASE (CbiK) FROM SALMONELLA TYPHIMURIUM IN ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 2xwp | ||||||
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Title | ANAEROBIC COBALT CHELATASE (CbiK) FROM SALMONELLA TYPHIMURIUM IN COMPLEX WITH METALATED TETRAPYRROLE | ||||||
![]() | SIROHYDROCHLORIN COBALTOCHELATASE | ||||||
![]() | LYASE / BETA-ALPHA-BETA / COBALAMIN BIOSYNTHESIS / METAL-BINDING / PARALLEL BETA SHEET | ||||||
Function / homology | ![]() sirohydrochlorin cobaltochelatase / anaerobic cobalamin biosynthetic process / sirohydrochlorin cobaltochelatase activity / tetrapyrrole binding / porphyrin-containing compound biosynthetic process / cobalt ion binding Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Ladakis, D. / Brindley, A.A. / Deery, E. / Warren, M.J. / Pickersgill, R.W. | ||||||
![]() | ![]() Title: Evolution in a Family of Chelatases Facilitated by the Introduction of Active Site Asymmetry and Protein Oligomerization. Authors: Romao, C.V. / Ladakis, D. / Lobo, S.A. / Carrondo, M.A. / Brindley, A.A. / Deery, E. / Matias, P.M. / Pickersgill, R.W. / Saraiva, L.M. / Warren, M.J. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 72.5 KB | Display | ![]() |
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PDB format | ![]() | 52.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 918.6 KB | Display | ![]() |
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Full document | ![]() | 926.5 KB | Display | |
Data in XML | ![]() | 15.3 KB | Display | |
Data in CIF | ![]() | 21.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2xvxC ![]() 2xvzC ![]() 2xwqC ![]() 2xwsC ![]() 1qgoS S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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Unit cell |
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Components on special symmetry positions |
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Components
#1: Protein | Mass: 29273.678 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: Q05592, sirohydrochlorin cobaltochelatase |
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#2: Chemical | ChemComp-SIR / |
#3: Chemical | ChemComp-GOL / |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.66 Å3/Da / Density % sol: 54 % / Description: NONE |
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Details: MIRRORS |
Radiation | Monochromator: SILICON / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.978 Å / Relative weight: 1 |
Reflection | Resolution: 2→47.9 Å / Num. obs: 176900 / % possible obs: 99.4 % / Observed criterion σ(I): 0 / Redundancy: 8 % / Biso Wilson estimate: 23.9 Å2 / Rmerge(I) obs: 0.12 / Net I/σ(I): 10.4 |
Reflection shell | Resolution: 2→2.11 Å / Redundancy: 6.5 % / Rmerge(I) obs: 0.7 / Mean I/σ(I) obs: 2.6 / % possible all: 97.4 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1QGO Resolution: 1.9→44.77 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.923 / SU B: 3.592 / SU ML: 0.104 / Cross valid method: THROUGHOUT / ESU R: 0.147 / ESU R Free: 0.143 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.U VALUES REFINED INDIVIDUALLY.
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 26.762 Å2
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Refinement step | Cycle: LAST / Resolution: 1.9→44.77 Å
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Refine LS restraints |
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