[English] 日本語
![](img/lk-miru.gif)
- PDB-4z6m: Structure of H200Q variant of Homoprotocatechuate 2,3-Dioxygenase... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 4z6m | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | Structure of H200Q variant of Homoprotocatechuate 2,3-Dioxygenase from B.fuscum at 1.35 Ang resolution | |||||||||
![]() | Homoprotocatechuate 2,3-dioxygenase | |||||||||
![]() | OXIDOREDUCTASE / Dioxygenase / 2-His-1-carboxylate facial triad / oxygen activation / acid-base catalysis | |||||||||
Function / homology | ![]() | |||||||||
Biological species | ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Kovaleva, E.G. / Lipscomb, J.D. | |||||||||
Funding support | ![]() ![]()
| |||||||||
![]() | ![]() Title: Structural Basis for Substrate and Oxygen Activation in Homoprotocatechuate 2,3-Dioxygenase: Roles of Conserved Active Site Histidine 200. Authors: Kovaleva, E.G. / Rogers, M.S. / Lipscomb, J.D. | |||||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 666.7 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 548.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 439.2 KB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 443.8 KB | Display | |
Data in XML | ![]() | 68.4 KB | Display | |
Data in CIF | ![]() | 107.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4z6lC ![]() 4z6nC ![]() 4z6oC ![]() 4z6pC ![]() 4z6qC ![]() 4z6rC ![]() 4z6sC ![]() 4z6tC ![]() 4z6uC ![]() 4z6vC ![]() 4z6wC ![]() 4z6zC ![]() 3ojtS C: citing same article ( S: Starting model for refinement |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-
Components
#1: Protein | Mass: 41745.305 Da / Num. of mol.: 4 / Mutation: H200Q Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Chemical | ChemComp-FE2 / #3: Chemical | ChemComp-CL / #4: Chemical | ChemComp-CA / | #5: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2.42 Å3/Da / Density % sol: 49.26 % |
---|---|
Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.4 / Details: 14% PEG6000, 0.1M calcium chloride, 0.1M MES |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Diffraction source | Source: ![]() ![]() ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Nov 14, 2008 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.35→48.094 Å / Num. all: 338753 / Num. obs: 338753 / % possible obs: 96.1 % / Redundancy: 5.2 % / Rpim(I) all: 0.045 / Rrim(I) all: 0.104 / Rsym value: 0.094 / Net I/av σ(I): 5.84 / Net I/σ(I): 11.3 / Num. measured all: 1766318 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1 / Rejects: _
|
-
Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: 3OJT Resolution: 1.35→48.09 Å / Cor.coef. Fo:Fc: 0.982 / Cor.coef. Fo:Fc free: 0.975 / WRfactor Rfree: 0.1341 / WRfactor Rwork: 0.1064 / FOM work R set: 0.9274 / SU B: 1.504 / SU ML: 0.027 / SU R Cruickshank DPI: 0.0418 / SU Rfree: 0.0406 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.042 / ESU R Free: 0.041 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 74.2 Å2 / Biso mean: 12.958 Å2 / Biso min: 4.76 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.35→48.09 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 1.35→1.385 Å / Total num. of bins used: 20
|