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Yorodumi- PDB-3h5j: LeuD_1-168 small subunit of isopropylmalate isomerase (Rv2987c) f... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3h5j | ||||||
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Title | LeuD_1-168 small subunit of isopropylmalate isomerase (Rv2987c) from mycobacterium tuberculosis | ||||||
Components | 3-isopropylmalate dehydratase small subunit | ||||||
Keywords | LYASE / Leucine biosynthesis / isopropylmalate isomerase / LeuD / M.tuberculosis / Amino-acid biosynthesis / Branched-chain amino acid biosynthesis | ||||||
Function / homology | Function and homology information 3-isopropylmalate dehydratase complex / 3-isopropylmalate dehydratase / 3-isopropylmalate dehydratase activity / L-leucine biosynthetic process / plasma membrane Similarity search - Function | ||||||
Biological species | Mycobacterium tuberculosis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.2 Å | ||||||
Authors | Manikandan, K. / Geerlof, A. / Weiss, M.S. | ||||||
Citation | Journal: Proteins / Year: 2011 Title: Structural studies on the enzyme complex isopropylmalate isomerase (LeuCD) from Mycobacterium tuberculosis Authors: Manikandan, K. / Geerlof, A. / Zozulya, A.V. / Svergun, D.I. / Weiss, M.S. #1: Journal: Acta Crystallogr.,Sect.F / Year: 2009 Title: Cloning, expression, purification, crystallization and preliminary X-ray diffraction analysis of the small subunit of isopropylmalate isomerase (Rv2987c) from Mycobacterium tuberculosis Authors: Manikandan, K. / Geerlof, A. / Schuldt, L. / Mueller-Dieckmann, C. / Weiss, M.S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3h5j.cif.gz | 167.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3h5j.ent.gz | 131.9 KB | Display | PDB format |
PDBx/mmJSON format | 3h5j.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/h5/3h5j ftp://data.pdbj.org/pub/pdb/validation_reports/h5/3h5j | HTTPS FTP |
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-Related structure data
Related structure data | 3h5eSC 3h5hC 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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2 |
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Unit cell |
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Details | AS THE STRUCTURE REPRESENTS ONLY A PART OF A SUBUNIT OF AN ENZYME COMPLEX, THE ASSEMBLIES DESCRIBED IN REMARK350 IS NOT RELEVANT TO THE REAL BIOLOGICAL ASSEMBLIES |
-Components
#1: Protein | Mass: 18644.068 Da / Num. of mol.: 2 / Fragment: LeuD, residues 1-168 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Strain: H37Rv / Gene: Rv2987c / Plasmid: pETM11 / Production host: Escherichia coli (E. coli) References: UniProt: P65277, UniProt: P9WK95*PLUS, 3-isopropylmalate dehydratase #2: Chemical | ChemComp-EDO / #3: Chemical | ChemComp-SO4 / | #4: Water | ChemComp-HOH / | Sequence details | THE SER 1A WAS INTRODUCED | |
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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: 1.98 Å3/Da / Density % sol: 37.95 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion / pH: 8.5 Details: 0.2M lithium sulfate, 0.1M Tris-HCl pH 8.5, 20%(w/v) PEG 3350, VAPOR DIFFUSION, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X12 / Wavelength: 1 Å |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Oct 22, 2008 |
Radiation | Monochromator: Double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.2→99 Å / Num. all: 90248 / Num. obs: 90248 / % possible obs: 99.5 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 4 % / Rmerge(I) obs: 0.065 / Net I/σ(I): 20.7 |
Reflection shell | Resolution: 1.2→1.22 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.296 / Mean I/σ(I) obs: 3.8 / % possible all: 91.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 3H5E Resolution: 1.2→13.42 Å / Num. parameters: 28335 / Num. restraintsaints: 35073 / Cross valid method: FREE R / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Refine analyze | Num. disordered residues: 24 / Occupancy sum hydrogen: 2546.15 / Occupancy sum non hydrogen: 3024.55 | |||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.2→13.42 Å
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Refine LS restraints |
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