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Yorodumi- PDB-3tz6: Crystal structure of Aspartate semialdehyde dehydrogenase Complex... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3tz6 | ||||||
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Title | Crystal structure of Aspartate semialdehyde dehydrogenase Complexed With inhibitor SMCS (CYS) And Phosphate From Mycobacterium tuberculosis H37Rv | ||||||
Components | Aspartate-semialdehyde dehydrogenase | ||||||
Keywords | OXIDOREDUCTASE / ASADH / ASD / ASA / DEHYDROGENASE / AMINO-ACID BIOSYNTHESIS / DIAMINOPIMELATE BIOSYNTHESIS / LYSINE BIOSYNTHESIS / SMCS | ||||||
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 / MOLECULAR REPLACEMENT / Resolution: 1.95 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 | 3tz6.cif.gz | 87.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3tz6.ent.gz | 67.2 KB | Display | PDB format |
PDBx/mmJSON format | 3tz6.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3tz6_validation.pdf.gz | 460.9 KB | Display | wwPDB validaton report |
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Full document | 3tz6_full_validation.pdf.gz | 462.3 KB | Display | |
Data in XML | 3tz6_validation.xml.gz | 18.8 KB | Display | |
Data in CIF | 3tz6_validation.cif.gz | 28.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/tz/3tz6 ftp://data.pdbj.org/pub/pdb/validation_reports/tz/3tz6 | HTTPS FTP |
-Related structure data
Related structure data | 3vosC 3llg 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: 36133.848 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: PQE30 / 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 | ChemComp-CYS / | ||||
#3: Chemical | #4: Chemical | ChemComp-SO4 / #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: 5.26 Å3/Da / Density % sol: 76.45 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion / pH: 5 Details: 100MM CITRIC ACID, 1.6M AMMONIUM SULFATE, pH 5.0, VAPOR DIFFUSION, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 |
Detector | Type: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Mar 14, 2010 / Details: MIRRORS |
Radiation | Monochromator: MIRRORS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.95→50 Å / Num. obs: 58288 / % possible obs: 99.4 % / Redundancy: 5.7 % / Biso Wilson estimate: 27.43 Å2 / Rmerge(I) obs: 0.075 / Rsym value: 0.075 / Net I/σ(I): 19.59 |
Reflection shell | Resolution: 1.95→2.02 Å / Redundancy: 4.9 % / Rmerge(I) obs: 0.728 / Mean I/σ(I) obs: 2.21 / Rsym value: 0.728 / % possible all: 99.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3LLG 3llg Resolution: 1.95→29.2 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.954 / SU B: 2.499 / SU ML: 0.069 / Cross valid method: THROUGHOUT / σ(F): 1.33 / ESU R: 0.1 / ESU R Free: 0.098 / 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: 1.2 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 31.13 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.95→29.2 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.951→2.001 Å / Total num. of bins used: 20
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