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Yorodumi- PDB-3qgu: L,L-Diaminopimelate aminotransferase from Chlamydomonas reinhardtii -
+Open data
-Basic information
Entry | Database: PDB / ID: 3qgu | ||||||
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Title | L,L-Diaminopimelate aminotransferase from Chlamydomonas reinhardtii | ||||||
Components | LL-diaminopimelate aminotransferase | ||||||
Keywords | TRANSFERASE / L-lysine / L / L-diaminopimelate aminotransferase / pyridoxal-5'-phosphate / Chamydomonas reinhardtii | ||||||
Function / homology | Function and homology information transaminase activity / biosynthetic process / pyridoxal phosphate binding Similarity search - Function | ||||||
Biological species | Chlamydomonas reinhardtii (plant) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.55 Å | ||||||
Authors | Dobson, R.C.J. / Giron, I. / Hudson, A.O. | ||||||
Citation | Journal: Plos One / Year: 2011 Title: L,L-Diaminopimelate Aminotransferase from Chlamydomonas reinhardtii: A Target for Algaecide Development Authors: Dobson, R.C.J. / Giron, I. / Hudson, A.O. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3qgu.cif.gz | 360.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3qgu.ent.gz | 292.6 KB | Display | PDB format |
PDBx/mmJSON format | 3qgu.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3qgu_validation.pdf.gz | 469.4 KB | Display | wwPDB validaton report |
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Full document | 3qgu_full_validation.pdf.gz | 481.7 KB | Display | |
Data in XML | 3qgu_validation.xml.gz | 40.9 KB | Display | |
Data in CIF | 3qgu_validation.cif.gz | 62.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qg/3qgu ftp://data.pdbj.org/pub/pdb/validation_reports/qg/3qgu | HTTPS FTP |
-Related structure data
Related structure data | 2z20S 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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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: SER / Beg label comp-ID: SER / End auth comp-ID: GLU / End label comp-ID: GLU / Refine code: 3 / Auth seq-ID: 105 - 110 / Label seq-ID: 105 - 110
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-Components
#1: Protein | Mass: 48905.090 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Chlamydomonas reinhardtii (plant) / Gene: DPA1 / Plasmid: pET30a / Production host: Escherichia coli (E. coli) References: UniProt: A8IW39, LL-diaminopimelate aminotransferase #2: Chemical | ChemComp-SO4 / #3: Chemical | #4: Chemical | #5: 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: 2.25 Å3/Da / Density % sol: 45.37 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.5 Details: 200mM lithium sulfate, 25%(w/v) polyethylene glycol 3350, 100mM Bis-Tris propane, 0.02%(w/v) sodium azide, pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 110 K |
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Diffraction source | Source: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 1, 2010 |
Radiation | Monochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.55→50 Å / Num. all: 126116 / Num. obs: 122383 / % possible obs: 97.04 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 |
Reflection shell | Resolution: 1.55→1.59 Å / % possible all: 99 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2Z20 Resolution: 1.55→50 Å / Cor.coef. Fo:Fc: 0.976 / Cor.coef. Fo:Fc free: 0.961 / SU B: 2.468 / SU ML: 0.04 / Cross valid method: THROUGHOUT / ESU R Free: 0.065 / 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: 18.862 Å2
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Refinement step | Cycle: LAST / Resolution: 1.55→50 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: 1.55→1.59 Å / Total num. of bins used: 20
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