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Yorodumi- PDB-3vos: Crystal structure of Aspartate semialdehyde dehydrogenase Complex... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3vos | |||||||||
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Title | Crystal structure of Aspartate semialdehyde dehydrogenase Complexed With glycerol and sulfate From Mycobacterium tuberculosis H37Rv | |||||||||
Components | Aspartate-semialdehyde dehydrogenase | |||||||||
Keywords | OXIDOREDUCTASE / DEHYDROGENASE / AMINO-ACID BIOSYNTHESIS / LYSINE BIOSYNTHESIS | |||||||||
Function / homology | Function and homology information aspartate-semialdehyde dehydrogenase / aspartate-semialdehyde dehydrogenase activity / 'de novo' L-methionine biosynthetic process / threonine biosynthetic process / cell wall / diaminopimelate biosynthetic process / isoleucine biosynthetic process / lysine biosynthetic process via diaminopimelate / peptidoglycan-based cell wall / NAD binding ...aspartate-semialdehyde dehydrogenase / aspartate-semialdehyde dehydrogenase activity / 'de novo' L-methionine biosynthetic process / threonine biosynthetic process / cell wall / diaminopimelate biosynthetic process / isoleucine biosynthetic process / lysine biosynthetic process via diaminopimelate / peptidoglycan-based cell wall / NAD binding / NADP binding / protein dimerization activity / plasma membrane Similarity search - Function | |||||||||
Biological species | Mycobacterium tuberculosis (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.18 Å | |||||||||
Authors | Vyas, R. / Tewari, R. / Weiss, M.S. / Karthikeyan, S. | |||||||||
Citation | Journal: Acta Crystallogr.,Sect.D / Year: 2012 Title: Structures of ternary complexes of aspartate-semialdehyde dehydrogenase (Rv3708c) from Mycobacterium tuberculosis H37Rv Authors: Vyas, R. / Tewari, R. / Weiss, M.S. / Karthikeyan, S. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3vos.cif.gz | 85.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3vos.ent.gz | 65 KB | Display | PDB format |
PDBx/mmJSON format | 3vos.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3vos_validation.pdf.gz | 450.5 KB | Display | wwPDB validaton report |
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Full document | 3vos_full_validation.pdf.gz | 451.1 KB | Display | |
Data in XML | 3vos_validation.xml.gz | 17.8 KB | Display | |
Data in CIF | 3vos_validation.cif.gz | 26.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/vo/3vos ftp://data.pdbj.org/pub/pdb/validation_reports/vo/3vos | HTTPS FTP |
-Related structure data
Related structure data | 3tz6C 2gyyS C: citing same article (ref.) S: Starting model for refinement |
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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 on special symmetry positions |
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-Components
#1: Protein | Mass: 38114.008 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Strain: h37rv / Gene: asd, MT3811, MTV025.056c, Rv3708c / Plasmid: pQE-30 / Production host: Escherichia coli (E. coli) / Strain (production host): M15 References: UniProt: P0A542, UniProt: P9WNX5*PLUS, aspartate-semialdehyde dehydrogenase | ||||
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#2: Chemical | #3: Chemical | ChemComp-SO4 / #4: 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: 5.24 Å3/Da / Density % sol: 76.5 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5 Details: 100MM CITRIC ACID, 1.6M AMSO4, pH 5.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 1.067 Å |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Sep 10, 2007 / Details: Mirrors |
Radiation | Monochromator: Mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.067 Å / Relative weight: 1 |
Reflection | Resolution: 2.18→99 Å / Num. all: 43078 / Num. obs: 43078 / % possible obs: 99.9 % / Observed criterion σ(F): 2.18 / Observed criterion σ(I): -3 / Redundancy: 8.2 % / Biso Wilson estimate: 32.1 Å2 / Rmerge(I) obs: 0.154 / Rsym value: 0.154 / Net I/σ(I): 14.1 |
Reflection shell | Resolution: 2.18→2.22 Å / % possible obs: 100 % / Redundancy: 8.2 % / Rmerge(I) obs: 0.953 / Mean I/σ(I) obs: 2.2 / Rsym value: 0.953 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2GYY Resolution: 2.18→32.42 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.952 / SU B: 3.014 / SU ML: 0.076 / Cross valid method: THROUGHOUT / ESU R: 0.125 / ESU R Free: 0.114 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
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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: MASK | |||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 30.848 Å2 | |||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.18→32.42 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.18→2.237 Å / Total num. of bins used: 20
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