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Yorodumi- PDB-2xvy: Cobalt chelatase CbiK (periplasmic) from Desulvobrio vulgaris Hil... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2xvy | ||||||
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Title | Cobalt chelatase CbiK (periplasmic) from Desulvobrio vulgaris Hildenborough (co-crystallised with cobalt and SHC) | ||||||
Components | CHELATASE, PUTATIVE | ||||||
Keywords | METAL BINDING PROTEIN | ||||||
Function / homology | Function and homology information sirohydrochlorin ferrochelatase / sirohydrochlorin ferrochelatase activity / sirohydrochlorin cobaltochelatase / anaerobic cobalamin biosynthetic process / sirohydrochlorin cobaltochelatase activity / cobalt ion binding / protein tetramerization / periplasmic space / heme binding Similarity search - Function | ||||||
Biological species | DESULFOVIBRIO VULGARIS (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å | ||||||
Authors | Romao, C.V. / Lobo, S.A.L. / Carrondo, M.A. / Saraiva, L.M. / Matias, P.M. | ||||||
Citation | Journal: Environ. Microbiol. / Year: 2017 Title: Desulfovibrio vulgaris CbiK(P) cobaltochelatase: evolution of a haem binding protein orchestrated by the incorporation of two histidine residues. Authors: Lobo, S.A. / Videira, M.A. / Pacheco, I. / Wass, M.N. / Warren, M.J. / Teixeira, M. / Matias, P.M. / Romao, C.V. / Saraiva, L.M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2xvy.cif.gz | 76.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2xvy.ent.gz | 55.5 KB | Display | PDB format |
PDBx/mmJSON format | 2xvy.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xv/2xvy ftp://data.pdbj.org/pub/pdb/validation_reports/xv/2xvy | HTTPS FTP |
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-Related structure data
Related structure data | 2xvzS S: Starting model for refinement |
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Similar structure data |
-Links
-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
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 28767.809 Da / Num. of mol.: 1 / Fragment: RESIDUES 29-297 Source method: isolated from a genetically manipulated source Source: (gene. exp.) DESULFOVIBRIO VULGARIS (bacteria) / Strain: HILDENBOROUGH / Plasmid: PET-28 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) References: UniProt: Q72EC8, sirohydrochlorin cobaltochelatase |
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-Non-polymers , 7 types, 256 molecules
#2: Chemical | ChemComp-HEM / | ||||||||
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#3: Chemical | ChemComp-CO / | ||||||||
#4: Chemical | ChemComp-SO4 / #5: Chemical | ChemComp-GOL / #6: Chemical | ChemComp-PER / | #7: Chemical | #8: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.6 Å3/Da / Density % sol: 65.9 % / Description: NONE |
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Crystal grow | pH: 8.5 Details: CRYSTALLIZATION SOLUTION: 100MM TRIS-HCL PH8.5, 2M AMMONIUM SULFATE. THE DROP WAS MADE BY ADDING 1UL OF PROTEIN PLUS 1.8UL OF CRYSTALLIZATION SOLUTION AND 0.2UL OF 2MM SIROHYDROCHLORIN AND 0. ...Details: CRYSTALLIZATION SOLUTION: 100MM TRIS-HCL PH8.5, 2M AMMONIUM SULFATE. THE DROP WAS MADE BY ADDING 1UL OF PROTEIN PLUS 1.8UL OF CRYSTALLIZATION SOLUTION AND 0.2UL OF 2MM SIROHYDROCHLORIN AND 0.2UL OF COBALT CHLORIDE IN AEROBIC CONDITIONS. |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 1.0332 |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Jul 12, 2007 Details: COLLIMATING RHODIUM COATED MIRROR (BEFORE MONOCHROMATOR) AND FOCUSSING TOROIDAL RHODIUM COATED MIRROR (AFTER MONOCHROMATOR) |
Radiation | Monochromator: SI 111 CHANNEL-CUT CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.0332 Å / Relative weight: 1 |
Reflection | Resolution: 1.7→49.24 Å / Num. obs: 46830 / % possible obs: 96.7 % / Observed criterion σ(I): 0 / Redundancy: 5.4 % / Biso Wilson estimate: 30.5 Å2 / Rmerge(I) obs: 0.04 / Net I/σ(I): 20.8 |
Reflection shell | Resolution: 1.7→1.81 Å / Redundancy: 4.4 % / Rmerge(I) obs: 0.46 / Mean I/σ(I) obs: 2.9 / % possible all: 84.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2XVZ Resolution: 1.7→85.44 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.962 / SU B: 1.518 / SU ML: 0.05 / Cross valid method: THROUGHOUT / ESU R: 0.079 / ESU R Free: 0.076 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. THE SIDE-CHAINS OF THE AMINO ACID RESIDUES- GLU22, GLU23, LYS51, MET52, GLU93, LYS110, ARG218 WERE MODELLED WITH 0.5 OF OCCUPANCY DUE TO ...Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. THE SIDE-CHAINS OF THE AMINO ACID RESIDUES- GLU22, GLU23, LYS51, MET52, GLU93, LYS110, ARG218 WERE MODELLED WITH 0.5 OF OCCUPANCY DUE TO THE LACK OF ELECTRON DENSITY PROBABLY DUE TO DISORDER. THE FOLLOWING AMINO ACID RESIDUES WERE MODELLED WITH DOUBLE CONFORMATION- MET31, ARG34, GLU133, ARG173, VAL198, LEU206, LEU209, ASP227, ARG236.
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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: 25.875 Å2
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Refinement step | Cycle: LAST / Resolution: 1.7→85.44 Å
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Refine LS restraints |
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