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Yorodumi- PDB-3r6v: Crystal structure of aspartase from Bacillus sp. YM55-1 with boun... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3r6v | ||||||
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Title | Crystal structure of aspartase from Bacillus sp. YM55-1 with bound L-aspartate | ||||||
Components | Aspartase | ||||||
Keywords | LYASE / aspartase / aspartate ammonia lyase | ||||||
Function / homology | Function and homology information aspartate ammonia-lyase / aspartate ammonia-lyase activity / aspartate metabolic process / tricarboxylic acid cycle / cytosol Similarity search - Function | ||||||
Biological species | Bacillus sp. (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å | ||||||
Authors | Fibriansah, G. / Puthan Veetil, V. / Poelarends, G.J. / Thunnissen, A.-M.W.H. | ||||||
Citation | Journal: Biochemistry / Year: 2011 Title: Structural basis for the catalytic mechanism of aspartate ammonia lyase. Authors: Fibriansah, G. / Veetil, V.P. / Poelarends, G.J. / Thunnissen, A.M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3r6v.cif.gz | 1.3 MB | Display | PDBx/mmCIF format |
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PDB format | pdb3r6v.ent.gz | 1.1 MB | Display | PDB format |
PDBx/mmJSON format | 3r6v.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3r6v_validation.pdf.gz | 499.9 KB | Display | wwPDB validaton report |
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Full document | 3r6v_full_validation.pdf.gz | 537.6 KB | Display | |
Data in XML | 3r6v_validation.xml.gz | 121 KB | Display | |
Data in CIF | 3r6v_validation.cif.gz | 169.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/r6/3r6v ftp://data.pdbj.org/pub/pdb/validation_reports/r6/3r6v | HTTPS FTP |
-Related structure data
Related structure data | 3r6qC 3r6yC 1j3uS 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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2 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: GLU / Beg label comp-ID: GLU / End auth comp-ID: HOH / End label comp-ID: HOH / Refine code: 5 / Auth seq-ID: 400 - 500 / Label seq-ID: 400
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-Components
#1: Protein | Mass: 51694.977 Da / Num. of mol.: 8 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacillus sp. (bacteria) / Strain: YM55-1 / Gene: aspB / Plasmid: pBAD/Myc-His A / Production host: Escherichia coli (E. coli) / Strain (production host): TOP10 / References: UniProt: Q9LCC6, aspartate ammonia-lyase #2: Chemical | ChemComp-CA / #3: Chemical | #4: 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: 3 Å3/Da / Density % sol: 58.99 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 0.25 M NaSCN, 10 mM CaCl2, 0.1 M HEPES, pH 7.0, 20% PEG3350, vapor diffusion, hanging drop, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.9334 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Nov 28, 2009 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: Diamond (111)and Ge (220) crystals / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9334 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.6→141.414 Å / Num. all: 144679 / Num. obs: 144679 / % possible obs: 97.9 % / Redundancy: 2.1 % / Rsym value: 0.108 / Net I/σ(I): 8 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1 / Redundancy: 2.1 %
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1J3U Resolution: 2.6→39.73 Å / Cor.coef. Fo:Fc: 0.935 / Cor.coef. Fo:Fc free: 0.887 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 24.306 / SU ML: 0.228 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.306 / 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: 1.4 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 131.35 Å2 / Biso mean: 34.5829 Å2 / Biso min: 3.22 Å2
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Refinement step | Cycle: LAST / Resolution: 2.6→39.73 Å
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Refine LS restraints |
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Refine LS restraints NCS | Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION
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LS refinement shell | Resolution: 2.6→2.667 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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