[English] 日本語
Yorodumi- PDB-2xvx: Cobalt chelatase CbiK (periplasmatic) from Desulvobrio vulgaris H... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2xvx | ||||||
---|---|---|---|---|---|---|---|
Title | Cobalt chelatase CbiK (periplasmatic) from Desulvobrio vulgaris Hildenborough (Native) | ||||||
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: 1.9 Å | ||||||
Authors | Romao, C.V. / Lobo, S.A.L. / Carrondo, M.A. / Saraiva, L.M. / Matias, P.M. | ||||||
Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2011 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.L. / Carrondo, M.A. / Brindley, A.A. / Deery, E. / Matias, P.M. / Pickersgill, R.W. / Saraiva, L.M. / Warren, M.J. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 2xvx.cif.gz | 74 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb2xvx.ent.gz | 55 KB | Display | PDB format |
PDBx/mmJSON format | 2xvx.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xv/2xvx ftp://data.pdbj.org/pub/pdb/validation_reports/xv/2xvx | HTTPS FTP |
---|
-Related structure data
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
| ||||||||
Components on special symmetry positions |
|
-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 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 GOLD (DE3) References: UniProt: Q72EC8, sirohydrochlorin cobaltochelatase |
---|
-Non-polymers , 7 types, 236 molecules
#2: Chemical | ChemComp-HEM / | ||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|
#3: Chemical | ChemComp-SO4 / #4: Chemical | ChemComp-GOL / #5: Chemical | ChemComp-CO2 / | #6: Chemical | ChemComp-CL / | #7: Chemical | ChemComp-NA / | #8: Water | ChemComp-HOH / | |
-Details
Sequence details | THE SEQUENCE ON THE DATABASE HAS A SIGNAL PEPTIDE, THE SEQUENCE OF THE STRUCTURE PRESENTED STARTS ...THE SEQUENCE ON THE DATABASE HAS A SIGNAL PEPTIDE, THE SEQUENCE OF THE STRUCTURE PRESENTED STARTS ON RESIDUE 29 |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 3.6 Å3/Da / Density % sol: 66.2 % / Description: NONE |
---|---|
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 2UL OF CRYSTALLIZATION SOLUTION. |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.934 |
Detector | Type: ADSC CCD / Detector: CCD / Date: Apr 20, 2007 / Details: MIRRORS |
Radiation | Monochromator: SI (111) / 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→42.8 Å / Num. obs: 35365 / % possible obs: 99.9 % / Observed criterion σ(I): 0 / Redundancy: 28 % / Biso Wilson estimate: 25.5 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 7.6 |
Reflection shell | Resolution: 1.9→2 Å / Redundancy: 20.3 % / Rmerge(I) obs: 0.83 / Mean I/σ(I) obs: 0.9 / % possible all: 99.2 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: MODEL OBTAINED WITH THE PROTEIN CO- CRYSTALLIZED WITH COBALT. Resolution: 1.9→85.6 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.95 / SU B: 2.276 / SU ML: 0.067 / Cross valid method: THROUGHOUT / ESU R: 0.105 / ESU R Free: 0.102 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.THE SIDE-CHAINS OF THE AMINO ACID RESIDUES- GLU22, GLU23, ARG25, LYS30, ARG36, LYS51, MET52, LYS110, GLU184, GLU225 WERE MODELLED WITH 0.5 ...Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.THE SIDE-CHAINS OF THE AMINO ACID RESIDUES- GLU22, GLU23, ARG25, LYS30, ARG36, LYS51, MET52, LYS110, GLU184, GLU225 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, SER138, ARG173, ARG236, GLU239, HIS245.
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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: 29.552 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.9→85.6 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
|