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Yorodumi- PDB-3h5h: LeuD_1-186 small subunit of isopropylmalate isomerase (Rv2987c) f... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3h5h | ||||||
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Title | LeuD_1-186 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: 2.5 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 | 3h5h.cif.gz | 77.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3h5h.ent.gz | 57.7 KB | Display | PDB format |
PDBx/mmJSON format | 3h5h.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/h5/3h5h ftp://data.pdbj.org/pub/pdb/validation_reports/h5/3h5h | HTTPS FTP |
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-Related structure data
Related structure data | 3h5eSC 3h5jC 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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2 |
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Unit cell |
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Components on special symmetry positions |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Ens-ID: 1 / Refine code: 2
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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: 20632.318 Da / Num. of mol.: 2 / Fragment: LeuD, residues 1-186 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: 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: 1.9 Å3/Da / Density % sol: 35.41 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion / pH: 7 Details: 0.1M NaCl, 0.1M Hepes pH 7.0, 1.2M Ammonium sulphate, VAPOR DIFFUSION, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.873 Å |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Dec 11, 2008 |
Radiation | Monochromator: Crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.873 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→51 Å / Num. all: 10727 / Num. obs: 10727 / % possible obs: 98.9 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 4.6 % / Biso Wilson estimate: 37.4 Å2 / Rmerge(I) obs: 0.171 / Net I/σ(I): 7.6 |
Reflection shell | Resolution: 2.5→2.56 Å / Redundancy: 4.2 % / Rmerge(I) obs: 0.447 / Mean I/σ(I) obs: 2.2 / % possible all: 92.3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 3H5E Resolution: 2.5→30 Å / Cor.coef. Fo:Fc: 0.903 / Cor.coef. Fo:Fc free: 0.843 / SU B: 13.29 / SU ML: 0.295 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.348 / 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 mean: 19 Å2
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Refinement step | Cycle: LAST / Resolution: 2.5→30 Å
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Refine LS restraints |
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Refine LS restraints NCS | Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION
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LS refinement shell | Resolution: 2.5→2.565 Å / Total num. of bins used: 20
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