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Yorodumi- PDB-3bli: Crystal structure of the catalytic domain of LiCMS in complexed w... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3bli | |||||||||
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Title | Crystal structure of the catalytic domain of LiCMS in complexed with pyruvate and acetyl-CoA | |||||||||
Components | Citramalate synthase from Leptospira interrogans | |||||||||
Keywords | TRANSFERASE / TIM barrel / LiCMSN / substrate specificity / Acyltransferase / Amino-acid biosynthesis / Branched-chain amino acid biosynthesis / Leucine biosynthesis | |||||||||
Function / homology | Function and homology information (R)-citramalate synthase / (R)-citramalate synthase activity / 2-isopropylmalate synthase activity / L-leucine biosynthetic process / isoleucine biosynthetic process / lyase activity / metal ion binding Similarity search - Function | |||||||||
Biological species | Leptospira interrogans (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.5 Å | |||||||||
Authors | Zhang, P. / Ma, J. | |||||||||
Citation | Journal: Biochem.J. / Year: 2008 Title: Molecular basis of the substrate specificity and the catalytic mechanism of citramalate synthase from Leptospira interrogans Authors: Ma, J. / Zhang, P. / Zhang, Z. / Zha, M. / Xu, H. / Zhao, G. / Ding, J. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3bli.cif.gz | 79.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3bli.ent.gz | 57.6 KB | Display | PDB format |
PDBx/mmJSON format | 3bli.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3bli_validation.pdf.gz | 753.2 KB | Display | wwPDB validaton report |
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Full document | 3bli_full_validation.pdf.gz | 766.2 KB | Display | |
Data in XML | 3bli_validation.xml.gz | 16.2 KB | Display | |
Data in CIF | 3bli_validation.cif.gz | 21.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bl/3bli ftp://data.pdbj.org/pub/pdb/validation_reports/bl/3bli | HTTPS FTP |
-Related structure data
Related structure data | 3bleSC 3blfC 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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Unit cell |
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-Components
#1: Protein | Mass: 37605.523 Da / Num. of mol.: 1 / Fragment: UNP residues 1-325 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Leptospira interrogans (bacteria) / Strain: 56601 / Gene: cimA / Plasmid: pET28b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q8F3Q1, 2-isopropylmalate synthase |
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#2: Chemical | ChemComp-ZN / |
#3: Chemical | ChemComp-ACO / |
#4: Chemical | ChemComp-PYR / |
#5: 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: 3.21 Å3/Da / Density % sol: 61.66 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion / pH: 7.5 Details: 0.1M HEPES, 2.0M Sodium malonate, pH7.5, vapor diffusion, temperature 293K, VAPOR DIFFUSION |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU ULTRAX 18 / Wavelength: 1.5418 Å |
Detector | Detector: IMAGE PLATE |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→19.95 Å / Num. all: 17171 / Num. obs: 16591 / % possible obs: 96.6 % / Redundancy: 8.4 % / Rmerge(I) obs: 0.104 |
-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 3BLE Resolution: 2.5→19.29 Å / σ(F): 0
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Solvent computation | Bsol: 53.691 Å2 | ||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 43.534 Å2
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Refinement step | Cycle: LAST / Resolution: 2.5→19.29 Å
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Xplor file |
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