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Yorodumi- PDB-5t25: Kinetic, Spectral and Structural Characterization of the Slow Bin... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5t25 | ||||||
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Title | Kinetic, Spectral and Structural Characterization of the Slow Binding Inhibitor Acetopyruvate with Dihydrodipicolinate Synthase from Escherichia coli. | ||||||
Components | 4-hydroxy-tetrahydrodipicolinate synthase | ||||||
Keywords | HYDROLASE / Dihydrodipicolinate Synthase / Kinetics / Acetopyruvate modification | ||||||
Function / homology | Function and homology information 4-hydroxy-tetrahydrodipicolinate synthase / 4-hydroxy-tetrahydrodipicolinate synthase activity / diaminopimelate biosynthetic process / lysine biosynthetic process via diaminopimelate / cytoplasm Similarity search - Function | ||||||
Biological species | Escherichia coli O8 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.991 Å | ||||||
Authors | Chooback, L. / Thomas, L.M. / Karsten, W.E. / Fleming, C.D. / Seabourn, P. | ||||||
Funding support | United States, 1items
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Citation | Journal: To Be Published Title: Kinetic, Spectral and Structural Characterization of the Slow Binding Inhibitor Acetopyruvate with Dihydrodipicolinate Synthase from Escherichia coli. Authors: Chooback, L. / Thomas, L.M. / Karsten, W.E. / Fleming, C.D. / Seabourn, P. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5t25.cif.gz | 139.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5t25.ent.gz | 106.5 KB | Display | PDB format |
PDBx/mmJSON format | 5t25.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5t25_validation.pdf.gz | 444.8 KB | Display | wwPDB validaton report |
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Full document | 5t25_full_validation.pdf.gz | 447.9 KB | Display | |
Data in XML | 5t25_validation.xml.gz | 30.2 KB | Display | |
Data in CIF | 5t25_validation.cif.gz | 45.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/t2/5t25 ftp://data.pdbj.org/pub/pdb/validation_reports/t2/5t25 | HTTPS FTP |
-Related structure data
Related structure data | 5t26C 1yxcS C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 31554.160 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli O8 (strain IAI1) (bacteria) Strain: IAI1 / Gene: dapA, ECIAI1_2529 / Production host: Escherichia coli (E. coli) References: UniProt: B7M7I1, 4-hydroxy-tetrahydrodipicolinate synthase #2: Chemical | #3: Chemical | ChemComp-NA / #4: Water | ChemComp-HOH / | |
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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: 2.43 Å3/Da / Density % sol: 49.45 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.1 Details: 20% PEG3350 200mM Sodium Tartarate 14.7 mM HEPES pH 7.1 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.54178 Å |
Detector | Type: DECTRIS PILATUS 200K / Detector: PIXEL / Date: Jul 10, 2015 / Details: VeriMaxHF |
Radiation | Monochromator: Multilayer optics / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54178 Å / Relative weight: 1 |
Reflection | Resolution: 2→81 Å / Num. obs: 193325 / % possible obs: 100 % / Redundancy: 4.5 % / Net I/σ(I): 9.8 |
Reflection shell | Resolution: 2→2.03 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.54 / Mean I/σ(I) obs: 1.911 / CC1/2: 0.809 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1yxc Resolution: 1.991→26.806 Å / SU ML: 0.2 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 20.09 / 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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.991→26.806 Å
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Refine LS restraints |
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LS refinement shell |
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