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Yorodumi- PDB-7ms1: Crystal structure of H28A mutant of Cg10062 with a covalent inter... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7ms1 | ||||||
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Title | Crystal structure of H28A mutant of Cg10062 with a covalent intermediate of the hydration of acetylenecarboxylic acid | ||||||
Components | 4-oxalocrotonate tautomerase | ||||||
Keywords | HYDROLASE / 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: 2.95 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 |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7ms1.cif.gz | 78.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7ms1.ent.gz | 55.5 KB | Display | PDB format |
PDBx/mmJSON format | 7ms1.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7ms1_validation.pdf.gz | 695.1 KB | Display | wwPDB validaton report |
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Full document | 7ms1_full_validation.pdf.gz | 702.7 KB | Display | |
Data in XML | 7ms1_validation.xml.gz | 13.8 KB | Display | |
Data in CIF | 7ms1_validation.cif.gz | 17.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ms/7ms1 ftp://data.pdbj.org/pub/pdb/validation_reports/ms/7ms1 | HTTPS FTP |
-Related structure data
Related structure data | 7ms0SC 7ms3C 7ms8C 7ms9C S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 18971.182 Da / Num. of mol.: 2 / Mutation: H28A 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: Chemical | ChemComp-3OH / | #3: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.54 Å3/Da / Density % sol: 65.3 % |
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Crystal grow | Temperature: 300 K / Method: vapor diffusion, hanging drop / pH: 5.6 Details: 50 mM ammonium acetate, 25 mM sodium citrate tribasic dihydrate, pH 5.6, 7.5% w/v PEG4000 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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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: 2.95→35.42 Å / Num. obs: 11335 / % possible obs: 96.45 % / Redundancy: 5.9 % / Rmerge(I) obs: 0.163 / Rpim(I) all: 0.071 / Rrim(I) all: 0.179 / Net I/σ(I): 11.3 |
Reflection shell | Resolution: 2.95→3.06 Å / Redundancy: 5.7 % / Rmerge(I) obs: 1 / Num. unique obs: 1112 / Χ2: 0.516 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 7MS0 Resolution: 2.95→35.42 Å / Cross valid method: FREE R-VALUE Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Refinement step | Cycle: LAST / Resolution: 2.95→35.42 Å
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Refine LS restraints |
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