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Yorodumi- PDB-3f6g: Crystal structure of the regulatory domain of LiCMS in complexed ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3f6g | ||||||
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Title | Crystal structure of the regulatory domain of LiCMS in complexed with isoleucine - type II | ||||||
Components | Alpha-isopropylmalate synthase | ||||||
Keywords | TRANSFERASE / LiCMSC / allosteric regulation / feedback inhibition / selectivity / specificity / Acyltransferase | ||||||
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 / SYNCHROTRON / MAD / Resolution: 2 Å | ||||||
Authors | Zhang, P. / Ma, J. / Zhao, G. / Ding, J. | ||||||
Citation | Journal: Biochem.J. / Year: 2009 Title: Molecular basis of the inhibitor selectivity and insights into the feedback inhibition mechanism of citramalate synthase from Leptospira interrogans Authors: Zhang, P. / Ma, J. / 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 | 3f6g.cif.gz | 90.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3f6g.ent.gz | 66.5 KB | Display | PDB format |
PDBx/mmJSON format | 3f6g.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/f6/3f6g ftp://data.pdbj.org/pub/pdb/validation_reports/f6/3f6g | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 14238.300 Da / Num. of mol.: 2 / Fragment: Regulatory domain, UNP residues 390-516 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, EC: 2.3.1.182 #2: Chemical | #3: Chemical | #4: Chemical | ChemComp-SO4 / #5: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 2 |
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-Sample preparation
Crystal | Density Matthews: 2.11 Å3/Da / Density % sol: 41.62 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8 Details: 0.1M Tris-HCl, pH8.0, 1.6M (NH4)2SO4, VAPOR DIFFUSION, HANGING DROP, temperature 277K |
-Data collection
Diffraction |
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Diffraction source |
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Detector |
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Radiation |
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Radiation wavelength |
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Reflection | Resolution: 2→20 Å / Num. obs: 15916 / Redundancy: 3.8 % / Rmerge(I) obs: 0.076 | ||||||||||||||||||
Reflection shell | Resolution: 2→2.07 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.327 / Num. unique all: 5456 |
-Processing
Software |
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Refinement | Method to determine structure: MAD / Resolution: 2→20 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.924 / Occupancy max: 1 / Occupancy min: 0.5 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.201 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 90.46 Å2 / Biso mean: 33.646 Å2 / Biso min: 14.4 Å2
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Refinement step | Cycle: LAST / Resolution: 2→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2→2.051 Å / Total num. of bins used: 20
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