[English] 日本語
Yorodumi- PDB-8epz: Crystal structure of Fe-S cluster-dependent dehydratase from Para... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8epz | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of Fe-S cluster-dependent dehydratase from Paralcaligenes ureilyticus in complex with Mn | ||||||
Components | Dihydroxyacid dehydratase | ||||||
Keywords | LYASE / Fe-S dehydratase / sugar-acid dehydratase / ilvD/EDD family / DHAD | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Paralcaligenes ureilyticus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å | ||||||
Authors | Bayaraa, T. / Lonhienne, T. / Guddat, L.W. | ||||||
Funding support | Australia, 1items
| ||||||
Citation | Journal: To Be Published Title: Crystal structure of Fe-S cluster-dependent dehydratase from Paralcaligenes ureilyticus in complex with Mg Authors: Bayaraa, T. / Lonhienne, T. / Guddat, L.W. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 8epz.cif.gz | 224.4 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb8epz.ent.gz | 177.8 KB | Display | PDB format |
PDBx/mmJSON format | 8epz.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ep/8epz ftp://data.pdbj.org/pub/pdb/validation_reports/ep/8epz | HTTPS FTP |
---|
-Related structure data
Related structure data | 8ej0SC S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 62651.746 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Paralcaligenes ureilyticus (bacteria) / Gene: EDC26_11947 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A4R3LQ44 |
---|
-Non-polymers , 5 types, 78 molecules
#2: Chemical | #3: Chemical | #4: Chemical | #5: Chemical | ChemComp-BCT / | #6: Water | ChemComp-HOH / | |
---|
-Details
Has ligand of interest | Y |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 1.99 Å3/Da / Density % sol: 38.34 % |
---|---|
Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / Details: 0.2 M succinic acid, 15% PEG 3350 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX1 / Wavelength: 0.954 Å |
Detector | Type: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Apr 21, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.954 Å / Relative weight: 1 |
Reflection | Resolution: 2.6→48.107 Å / Num. obs: 44640 / % possible obs: 98.8 % / Redundancy: 5.3 % / Rmerge(I) obs: 0.108 / Rpim(I) all: 0.046 / Net I/σ(I): 9.1 |
Reflection shell | Resolution: 2.6→2.987 Å / Rmerge(I) obs: 0.747 / Mean I/σ(I) obs: 1.9 / Num. unique obs: 3904 / Rpim(I) all: 0.316 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 8EJ0 Resolution: 2.6→48.107 Å / SU ML: 0.3 / Cross valid method: THROUGHOUT / σ(F): 1.38 / Phase error: 32.35 / Stereochemistry target values: ML
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 107.05 Å2 / Biso mean: 61.2977 Å2 / Biso min: 30 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.6→48.107 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0
|