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Yorodumi- PDB-6ien: Substrate/product bound Argininosuccinate lyase from Mycobacteriu... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6ien | |||||||||
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Title | Substrate/product bound Argininosuccinate lyase from Mycobacterium tuberculosis | |||||||||
Components | Argininosuccinate lyase | |||||||||
Keywords | LYASE / arginine biosynthesis / tetramer / aspartase/fumarase / concerted movement | |||||||||
Function / homology | Function and homology information argininosuccinate lyase / argininosuccinate lyase activity / arginine biosynthetic process via ornithine / peptidoglycan-based cell wall / cytosol Similarity search - Function | |||||||||
Biological species | Mycobacterium tuberculosis (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.7 Å | |||||||||
Authors | Paul, A. / Mishra, A. / Surolia, A. / Vijayan, M. | |||||||||
Citation | Journal: IUBMB Life / Year: 2019 Title: Structural studies on M. tuberculosis argininosuccinate lyase and its liganded complex: Insights into catalytic mechanism. Authors: Paul, A. / Mishra, A. / Surolia, A. / Vijayan, M. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6ien.cif.gz | 329.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6ien.ent.gz | 268.2 KB | Display | PDB format |
PDBx/mmJSON format | 6ien.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ie/6ien ftp://data.pdbj.org/pub/pdb/validation_reports/ie/6ien | 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
-Protein , 1 types, 4 molecules ABCD
#1: Protein | Mass: 49828.156 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv) (bacteria) Strain: ATCC 25618 / H37Rv / Gene: argH, Rv1659, MTCY06H11.24 / Plasmid: pET22b(+) / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P9WPY7, argininosuccinate lyase |
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-Non-polymers , 6 types, 304 molecules
#2: Chemical | #3: Chemical | ChemComp-FUM / | #4: Chemical | ChemComp-EDO / #5: Chemical | ChemComp-PEG / | #6: Chemical | ChemComp-ARG / | #7: Water | ChemComp-HOH / | |
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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: 2.73 Å3/Da / Density % sol: 54.95 % |
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Crystal grow | Temperature: 295 K / Method: microbatch / Details: 2.1M DL-malic acid pH 7.0, 10% v/v ethylene glycol |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: BRUKER AXS MICROSTAR / Wavelength: 1.54 Å |
Detector | Type: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Jan 30, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54 Å / Relative weight: 1 |
Reflection | Resolution: 2.7→25.86 Å / Num. obs: 60527 / % possible obs: 99.9 % / Redundancy: 5.2 % / Rmerge(I) obs: 0.257 / Net I/σ(I): 4.4 |
Reflection shell | Resolution: 2.7→2.85 Å / Rmerge(I) obs: 0.812 / Mean I/σ(I) obs: 1.9 / Num. unique obs: 8743 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.7→25.86 Å / Cor.coef. Fo:Fc: 0.928 / Cor.coef. Fo:Fc free: 0.903 / SU B: 15.353 / SU ML: 0.314 / Cross valid method: THROUGHOUT / ESU R: 1.252 / ESU R Free: 0.389 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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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: 25.291 Å2
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Refinement step | Cycle: 1 / Resolution: 2.7→25.86 Å
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