[English] 日本語
![](img/lk-miru.gif)
- PDB-1cbf: THE X-RAY STRUCTURE OF A COBALAMIN BIOSYNTHETIC ENZYME, COBALT PR... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 1cbf | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | THE X-RAY STRUCTURE OF A COBALAMIN BIOSYNTHETIC ENZYME, COBALT PRECORRIN-4 METHYLTRANSFERASE, CBIF | |||||||||
![]() | COBALT-PRECORRIN-4 TRANSMETHYLASE | |||||||||
![]() | METHYLTRANSFERASE / PRECORRIN-4 METHYLTRANSFERASE / METHYLASE / COBALAMIN BIOSYNTHESIS | |||||||||
Function / homology | ![]() cobalt-precorrin-4 methyltransferase / precorrin-4 C11-methyltransferase activity / cobalamin biosynthetic process / methylation Similarity search - Function | |||||||||
Biological species | ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Schubert, H.L. / Raux, E. / Woodcock, S.C. / Wilson, K.S. / Warren, M.J. | |||||||||
![]() | ![]() Title: The X-ray structure of a cobalamin biosynthetic enzyme, cobalt-precorrin-4 methyltransferase. Authors: Schubert, H.L. / Wilson, K.S. / Raux, E. / Woodcock, S.C. / Warren, M.J. #1: ![]() Title: Cobalamin (Vitamin B12) Biosynthesis--Cloning, Expression and Crystallisation of the Bacillus Megaterium S-Adenosyl-L-Methionine-Dependent Cobalt-Precorrin-4 Transmethylase Cbif Authors: Raux, E. / Schubert, H.L. / Woodcock, S.C. / Wilson, K.S. / Warren, M.J. | |||||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 64.3 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 46.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 856.9 KB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 865.8 KB | Display | |
Data in XML | ![]() | 14 KB | Display | |
Data in CIF | ![]() | 19.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 | ![]()
| ||||||||
Unit cell |
|
-
Components
#1: Protein | Mass: 30996.051 Da / Num. of mol.: 1 / Mutation: HIS-TAGGED Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: O87696, precorrin-4 C11-methyltransferase | ||||
---|---|---|---|---|---|
#2: Chemical | #3: Chemical | ChemComp-SAH / | #4: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 3.32 Å3/Da / Density % sol: 63 % | ||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Crystal grow | pH: 7.5 / Details: pH 7.5 | ||||||||||||||||||||||||
Crystal | *PLUS Density % sol: 64 % | ||||||||||||||||||||||||
Crystal grow | *PLUS pH: 5.6 / Method: unknown | ||||||||||||||||||||||||
Components of the solutions | *PLUS
|
-Data collection
Diffraction | Mean temperature: 120 K |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Mar 1, 1997 / Details: PLATINUM COATED TORROIDAL MIRROR |
Radiation | Monochromator: SI(111) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.91 Å / Relative weight: 1 |
Reflection | Resolution: 2.4→20 Å / Num. obs: 16587 / % possible obs: 100 % / Redundancy: 5 % / Rmerge(I) obs: 0.039 / Rsym value: 0.04 / Net I/σ(I): 21.3 |
Reflection shell | Resolution: 2.4→2.44 Å / Redundancy: 5 % / Rmerge(I) obs: 0.122 / Mean I/σ(I) obs: 10 / Rsym value: 0.115 / % possible all: 100 |
Reflection | *PLUS % possible obs: 99.8 % |
Reflection shell | *PLUS % possible obs: 100 % |
-
Processing
Software |
| ||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Details: FREE R VALUE TEST SET SELECTION WAS RANDOM, BUT FRIEDEL MATES ARE KEPT IN SAME SET.
| ||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.4→20 Å
| ||||||||||||||||||||
Software | *PLUS Name: REFMAC / Classification: refinement | ||||||||||||||||||||
Refinement | *PLUS Rfactor obs: 0.204 / Rfactor Rfree: 0.252 | ||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||
Refine LS restraints | *PLUS
|