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Yorodumi- PDB-8d5d: Structure of Y430F D-ornithine/D-lysine decarboxylase complex wit... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8d5d | ||||||
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Title | Structure of Y430F D-ornithine/D-lysine decarboxylase complex with D-arginine | ||||||
Components | D-ornithine/D-lysine decarboxylase | ||||||
Keywords | LYASE / pyridoxal-5'-phosphate / D-amino acid / decarboxylase / Fold III | ||||||
Function / homology | Function and homology information D-ornithine/D-lysine decarboxylase / diaminopimelate decarboxylase activity / lysine biosynthetic process via diaminopimelate Similarity search - Function | ||||||
Biological species | Salmonella enterica subsp. enterica serovar Typhimurium (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.54 Å | ||||||
Authors | Phillips, R.S. / Nguyen Hoang, K.N. | ||||||
Funding support | United States, 1items
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Citation | Journal: Arch.Biochem.Biophys. / Year: 2022 Title: The Y430F mutant of Salmonella d-ornithine/d-lysine decarboxylase has altered stereospecificity and a putrescine allosteric activation site. Authors: Phillips, R.S. / Nguyen Hoang, K.N. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8d5d.cif.gz | 572.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8d5d.ent.gz | 480.3 KB | Display | PDB format |
PDBx/mmJSON format | 8d5d.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/d5/8d5d ftp://data.pdbj.org/pub/pdb/validation_reports/d5/8d5d | HTTPS FTP |
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-Related structure data
Related structure data | 8d2yC 8d4iC 8d5rC 8d88C 6n2hS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 54046.984 Da / Num. of mol.: 2 / Mutation: Y430F Source method: isolated from a genetically manipulated source Source: (gene. exp.) Salmonella enterica subsp. enterica serovar Typhimurium (bacteria) Gene: dokD, STM2360 / Production host: Escherichia coli BL21(DE3) (bacteria) References: UniProt: Q8ZNC4, D-ornithine/D-lysine decarboxylase |
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-Non-polymers , 5 types, 837 molecules
#2: Chemical | ChemComp-DMS / #3: Chemical | #4: Chemical | #5: Chemical | #6: Water | ChemComp-HOH / | |
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-Details
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: 2.14 Å3/Da / Density % sol: 42.48 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / Details: 0.1 M HEPES, pH 7.5, 0.2 M NaOAc, 20% PEG 4000 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 13, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.54→48.86 Å / Num. obs: 125192 / % possible obs: 96.5 % / Redundancy: 15.1 % / Biso Wilson estimate: 24.53 Å2 / CC1/2: 0.999 / Net I/σ(I): 11.03 |
Reflection shell | Resolution: 1.54→1.595 Å / Mean I/σ(I) obs: 0.53 / Num. unique obs: 9896 / CC1/2: 0.32 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6N2H.pdb Resolution: 1.54→48.86 Å / SU ML: 0.24 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 26.37 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 196.81 Å2 / Biso mean: 40.2441 Å2 / Biso min: 17.33 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.54→48.86 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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