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Yorodumi- PDB-3udu: Crystal structure of putative 3-isopropylmalate dehydrogenase fro... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3udu | ||||||
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Title | Crystal structure of putative 3-isopropylmalate dehydrogenase from Campylobacter jejuni | ||||||
Components | 3-isopropylmalate dehydrogenase | ||||||
Keywords | OXIDOREDUCTASE / Structural Genomics / Center for Structural Genomics of Infectious Diseases / CSGID / putative isopropylmalate 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 / MIR / Resolution: 1.85 Å | ||||||
Authors | Tkaczuk, K.L. / Chruszcz, M. / Grimshaw, S. / Onopriyenko, O. / 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 3-isopropylmalate dehydrogenase from Campylobacter jejuni Authors: Tkaczuk, K.L. / Chruszcz, M. / Grimshaw, S. / Onopriyenko, O. / 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 | 3udu.cif.gz | 572.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3udu.ent.gz | 468.7 KB | Display | PDB format |
PDBx/mmJSON format | 3udu.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3udu_validation.pdf.gz | 493.8 KB | Display | wwPDB validaton report |
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Full document | 3udu_full_validation.pdf.gz | 509 KB | Display | |
Data in XML | 3udu_validation.xml.gz | 113.7 KB | Display | |
Data in CIF | 3udu_validation.cif.gz | 162.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ud/3udu ftp://data.pdbj.org/pub/pdb/validation_reports/ud/3udu | HTTPS FTP |
-Related structure data
Related structure data | 1cm7S S: Starting model for refinement |
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Similar structure data | |
Other databases |
-Links
-Assembly
Deposited unit |
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2 |
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3 |
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4 |
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Unit cell |
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-Components
#1: Protein | Mass: 39649.438 Da / Num. of mol.: 8 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 #2: Chemical | ChemComp-EDO / #3: Chemical | ChemComp-CL / | #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: 2.17 Å3/Da / Density % sol: 43.39 % |
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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: 0.9793 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 19, 2010 |
Radiation | Monochromator: Si 111 channel / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9793 Å / Relative weight: 1 |
Reflection | Resolution: 1.85→50 Å / Num. all: 213853 / Num. obs: 213853 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 2.5 % / Biso Wilson estimate: 30.7 Å2 / Rmerge(I) obs: 0.093 / Rsym value: 0.093 / Net I/σ(I): 18.2 |
Reflection shell | Resolution: 1.85→1.88 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.554 / Mean I/σ(I) obs: 2 / Num. unique all: 10781 / Rsym value: 0.554 / % possible all: 94.7 |
-Processing
Software |
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Refinement | Method to determine structure: MIR Starting model: PDB ENTRY 1CM7 Resolution: 1.85→50 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.946 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R Free: 0.154 / 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: 24.991 Å2
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Refinement step | Cycle: LAST / Resolution: 1.85→50 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.85→1.898 Å / Total num. of bins used: 20
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