[English] 日本語
![](img/lk-miru.gif)
- PDB-2hk6: Crystal Structure of B. subtilis ferrochelatase with Iron bound a... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 2hk6 | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal Structure of B. subtilis ferrochelatase with Iron bound at the active site | ||||||
![]() | Ferrochelatase | ||||||
![]() | LYASE / Heme biosynthesis / Iron / Metal-binding / Porphyrin biosynthesis | ||||||
Function / homology | ![]() coproporphyrin ferrochelatase / ferrochelatase activity / heme biosynthetic process / metal ion binding / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Al-Karadaghi, S. / Karlberg, T. | ||||||
![]() | ![]() Title: Amino Acid Residues His183 and Glu264 in Bacillus subtilis Ferrochelatase Direct and Facilitate the Insertion of Metal Ion into Protoporphyrin IX Authors: Hansson, M.D. / Karlberg, T. / Rahardja, M.A. / Al-Karadaghi, S. / Hansson, M. | ||||||
History |
| ||||||
Remark 600 | Heterogen The authors state that the charge state of FE is unknown. |
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 86.1 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 63.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 423.8 KB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 424.7 KB | Display | |
Data in XML | ![]() | 17 KB | Display | |
Data in CIF | ![]() | 26.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2h1vC ![]() 2h1wC ![]() 1dozS S: Starting model for refinement C: citing same article ( |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-
Components
#1: Protein | Mass: 35389.707 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() | ||||
---|---|---|---|---|---|
#2: Chemical | ChemComp-FE / #3: Chemical | #4: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2.04 Å3/Da / Density % sol: 39.72 % |
---|---|
Crystal grow | Temperature: 288 K / Method: vapor diffusion / pH: 8 Details: 25% PEG 2000, 0.2 M MgCl2, 0.1 M Tris-HCl , pH 8.0, VAPOR DIFFUSION, temperature 288K |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MAR CCD 165 mm / Detector: CCD / Date: Jun 8, 2005 |
Radiation | Monochromator: Double crystal monochromator, Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.0605 Å / Relative weight: 1 |
Reflection | Resolution: 1.7→20 Å / Num. obs: 31884 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 11.3 % / Rmerge(I) obs: 0.027 / Rsym value: 0.055 |
Reflection shell | Resolution: 1.7→1.81 Å / % possible all: 95.6 |
-
Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1DOZ Resolution: 1.71→19.64 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.922 / SU B: 2.056 / SU ML: 0.07 / Cross valid method: THROUGHOUT / σ(F): 2 / ESU R: 0.12 / ESU R Free: 0.118 / Stereochemistry target values: MAXIMUM LIKELIHOOD
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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: 15.516 Å2
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.71→19.64 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 1.71→1.754 Å / Total num. of bins used: 20
|