[English] 日本語
Yorodumi- PDB-7ms8: Crystal structure of Y103F mutant of Cg10062 with a covalent inte... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7ms8 | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of Y103F mutant of Cg10062 with a covalent intermediate of the hydration of acetylenecarboxylic acid | ||||||
Components | 4-oxalocrotonate tautomerase | ||||||
Keywords | ISOMERASE / tautomerase | ||||||
Function / homology | Tautomerase, cis-CaaD-like / Putative oxalocrotonate tautomerase enzyme / Tautomerase/MIF superfamily / 3-HYDROXY-PROPANOIC ACID / 4-oxalocrotonate tautomerase Function and homology information | ||||||
Biological species | Corynebacterium glutamicum (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å | ||||||
Authors | Nayebi, G.H. / Geiger, J.H. / Draths, K. | ||||||
Citation | Journal: Biochemistry / Year: 2021 Title: Cg10062 Catalysis Forges a Link between Acetylenecarboxylic Acid and Bacterial Metabolism. Authors: Mathes Hewage, A. / Nayebi Gavgani, H. / Chi, D. / Qiu, B. / Geiger, J.H. / Draths, K. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 7ms8.cif.gz | 55.7 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb7ms8.ent.gz | 32.2 KB | Display | PDB format |
PDBx/mmJSON format | 7ms8.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7ms8_validation.pdf.gz | 755.7 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 7ms8_full_validation.pdf.gz | 757.2 KB | Display | |
Data in XML | 7ms8_validation.xml.gz | 8.6 KB | Display | |
Data in CIF | 7ms8_validation.cif.gz | 10.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ms/7ms8 ftp://data.pdbj.org/pub/pdb/validation_reports/ms/7ms8 | HTTPS FTP |
-Related structure data
Related structure data | 7ms0SC 7ms1C 7ms3C 7ms9C S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 19022.250 Da / Num. of mol.: 1 / Mutation: Y103F Source method: isolated from a genetically manipulated source Source: (gene. exp.) Corynebacterium glutamicum (bacteria) Gene: APT58_00490, AUO95_07180, CS176_0056, FM102_14895, KaCgl_17770, KbCgl_30240 Production host: Escherichia coli BL21(DE3) (bacteria) References: UniProt: A0A0S2T163, 2-hydroxymuconate tautomerase |
---|---|
#2: Chemical | ChemComp-3OH / |
#3: Water | ChemComp-HOH / |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 6.91 Å3/Da / Density % sol: 82.21 % |
---|---|
Crystal grow | Temperature: 300 K / Method: vapor diffusion, hanging drop / pH: 8 Details: 100 mM magnesium acetate tetrahydrate, 10% w/v PEG3350 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 1 Å |
Detector | Type: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Jun 2, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→33.65 Å / Num. obs: 19222 / % possible obs: 99.84 % / Redundancy: 10.4 % / Biso Wilson estimate: 56.68 Å2 / Rmerge(I) obs: 0.103 / Rpim(I) all: 0.033 / Rrim(I) all: 0.108 / Net I/σ(I): 15.6 |
Reflection shell | Resolution: 2.5→2.59 Å / Num. unique obs: 1895 / Rpim(I) all: 0.482 |
-Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 7MS0 Resolution: 2.5→33.65 Å / SU ML: 0.3241 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 24.4747 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 61.7 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.5→33.65 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
|