[English] 日本語
Yorodumi- PDB-4z6t: Structure of H200N variant of Homoprotocatechuate 2,3-Dioxygenase... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4z6t | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | Structure of H200N variant of Homoprotocatechuate 2,3-Dioxygenase from B.fuscum in complex with 4-sulfonyl catechol at 1.50 Ang resolution | |||||||||
Components | Homoprotocatechuate 2,3-dioxygenase | |||||||||
Keywords | OXIDOREDUCTASE / Dioxygenase / 2-His-1-carboxylate facial triad / oxygen activation / acid-base catalysis | |||||||||
Function / homology | Function and homology information | |||||||||
Biological species | Brevibacterium fuscum (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å | |||||||||
Authors | Kovaleva, E.G. / Lipscomb, J.D. | |||||||||
Funding support | United Kingdom, United States, 2items
| |||||||||
Citation | Journal: Biochemistry / Year: 2015 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: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 4z6t.cif.gz | 661 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb4z6t.ent.gz | 544.5 KB | Display | PDB format |
PDBx/mmJSON format | 4z6t.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4z6t_validation.pdf.gz | 1.8 MB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 4z6t_full_validation.pdf.gz | 1.8 MB | Display | |
Data in XML | 4z6t_validation.xml.gz | 68.1 KB | Display | |
Data in CIF | 4z6t_validation.cif.gz | 104.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/z6/4z6t ftp://data.pdbj.org/pub/pdb/validation_reports/z6/4z6t | HTTPS FTP |
-Related structure data
Related structure data | 4z6lC 4z6mC 4z6nC 4z6oC 4z6pC 4z6qC 4z6rC 4z6sC 4z6uC 4z6vC 4z6wC 4z6zC 3ojtS C: citing same article (ref.) S: Starting model for refinement |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||||||
Unit cell |
| ||||||||||||
Components on special symmetry positions |
|
-Components
-Protein , 1 types, 4 molecules ABCD
#1: Protein | Mass: 41731.277 Da / Num. of mol.: 4 / Mutation: H200N Source method: isolated from a genetically manipulated source Source: (gene. exp.) Brevibacterium fuscum (bacteria) / Plasmid: pYZW204 / Production host: Escherichia coli (E. coli) / Strain (production host): Jm109 / References: UniProt: Q45135 |
---|
-Non-polymers , 7 types, 1752 molecules
#2: Chemical | ChemComp-FE2 / #3: Chemical | ChemComp-P6G / #4: Chemical | ChemComp-CL / #5: Chemical | ChemComp-CA / | #6: Chemical | #7: Chemical | ChemComp-4SX / | #8: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.37 Å3/Da / Density % sol: 48.18 % |
---|---|
Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: 14% PEG6000, 0.1M calcium acetate, 0.1M Tris-HCl |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.9173 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Oct 14, 2011 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9173 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.5→29.49 Å / Num. all: 248661 / Num. obs: 248661 / % possible obs: 98.6 % / Redundancy: 4.9 % / Rpim(I) all: 0.044 / Rrim(I) all: 0.1 / Rsym value: 0.09 / Net I/av σ(I): 7.5 / Net I/σ(I): 11.6 / Num. measured all: 1212267 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1 / Rejects: _
|
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3OJT Resolution: 1.5→29.49 Å / Cor.coef. Fo:Fc: 0.983 / Cor.coef. Fo:Fc free: 0.969 / WRfactor Rfree: 0.1491 / WRfactor Rwork: 0.1063 / FOM work R set: 0.8971 / SU B: 2.848 / SU ML: 0.045 / SU R Cruickshank DPI: 0.0619 / SU Rfree: 0.0599 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.062 / ESU R Free: 0.06 / 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: 88.23 Å2 / Biso mean: 17.123 Å2 / Biso min: 7.03 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.5→29.49 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 1.5→1.539 Å / Total num. of bins used: 20
|