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Yorodumi- PDB-3udo: Crystal structure of putative isopropylamlate dehydrogenase from ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3udo | ||||||
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Title | Crystal structure of putative isopropylamlate dehydrogenase from Campylobacter jejuni | ||||||
Components | 3-isopropylmalate dehydrogenase | ||||||
Keywords | OXIDOREDUCTASE / Structural Genomics / Center for Structural Genomics of Infectious Diseases / CSGID / putative isopropylamlate dehydrogenase | ||||||
Function / homology | Function and homology information 3-isopropylmalate dehydrogenase / 3-isopropylmalate dehydrogenase activity / L-leucine biosynthetic process / NAD binding / magnesium ion binding / cytoplasm Similarity search - Function | ||||||
Biological species | Campylobacter jejuni (Campylobacter) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.3 Å | ||||||
Authors | Tkaczuk, K.L. / Chruszcz, M. / Blus, B.J. / Onopriyenko, O. / Grimshaw, S. / Savchenko, A. / Anderson, W.F. / Minor, W. / Center for Structural Genomics of Infectious Diseases (CSGID) | ||||||
Citation | Journal: To be Published Title: Crystal structure of putative isopropylamlate dehydrogenase from Campylobacter jejuni Authors: Tkaczuk, K.L. / Chruszcz, M. / Blus, B.J. / Onopriyenko, O. / Grimshaw, S. / Savchenko, A. / Anderson, W.F. / Minor, W. / Center for Structural Genomics of Infectious Diseases (CSGID) | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3udo.cif.gz | 148.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3udo.ent.gz | 123.5 KB | Display | PDB format |
PDBx/mmJSON format | 3udo.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ud/3udo ftp://data.pdbj.org/pub/pdb/validation_reports/ud/3udo | HTTPS FTP |
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-Related structure data
Similar structure data | |
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Other databases |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 40024.594 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Campylobacter jejuni (Campylobacter) / Gene: leuB, Cj1718c / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-CodonPlus(DE3)-RIL References: UniProt: Q9PLW0, 3-isopropylmalate dehydrogenase | ||||
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#2: Chemical | #3: Chemical | ChemComp-SO4 / #4: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.86 Å3/Da / Density % sol: 57.02 % |
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Crystal grow | Temperature: 297 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 25%PEG3350, 0.2M Na Chloride, 0.1MHEPES, pH 7, VAPOR DIFFUSION, HANGING DROP, temperature 297K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9772 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 6, 2011 |
Radiation | Monochromator: Si 111 channel / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9772 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→50 Å / Num. all: 21382 / Num. obs: 21382 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 7.8 % / Biso Wilson estimate: 57.9 Å2 / Rmerge(I) obs: 0.063 / Rsym value: 0.063 / Net I/σ(I): 40.9 |
Reflection shell | Resolution: 2.3→2.34 Å / Redundancy: 7.8 % / Rmerge(I) obs: 0.595 / Mean I/σ(I) obs: 3.7 / Num. unique all: 1051 / Rsym value: 0.595 / % possible all: 99.1 |
-Processing
Software |
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Refinement | Method to determine structure: SAD Starting model: none Resolution: 2.3→50 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.955 / SU B: 12.271 / SU ML: 0.142 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R Free: 0.191 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 54.211 Å2
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Refinement step | Cycle: LAST / Resolution: 2.3→50 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.303→2.362 Å / Total num. of bins used: 20
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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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