+Open data
-Basic information
Entry | Database: PDB / ID: 6ge8 | ||||||
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Title | Crystal structure of Mycobacterium tuberculosis BioA | ||||||
Components | Adenosylmethionine-8-amino-7-oxononanoate aminotransferase | ||||||
Keywords | BIOSYNTHETIC PROTEIN / BioA / PLP / Hydrazine / Biotin / mycobacterium tuberculosis / transaminase | ||||||
Function / homology | Aspartate Aminotransferase, domain 1 / Aspartate Aminotransferase, domain 1 / Aspartate Aminotransferase; domain 2 / Type I PLP-dependent aspartate aminotransferase-like (Major domain) / Alpha-Beta Complex / 3-Layer(aba) Sandwich / Alpha Beta / Chem-EWE / : Function and homology information | ||||||
Biological species | Mycobacterium tuberculosis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.869 Å | ||||||
Authors | Ekstrom, A. / Campopiano, D.J. / Marles-Wright, J. | ||||||
Citation | Journal: To Be Published Title: Crystal structure of Mycobacterium tuberculosis BioA Authors: Marles-Wright, J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6ge8.cif.gz | 472.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6ge8.ent.gz | 393.4 KB | Display | PDB format |
PDBx/mmJSON format | 6ge8.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6ge8_validation.pdf.gz | 1.1 MB | Display | wwPDB validaton report |
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Full document | 6ge8_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | 6ge8_validation.xml.gz | 34.9 KB | Display | |
Data in CIF | 6ge8_validation.cif.gz | 51.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ge/6ge8 ftp://data.pdbj.org/pub/pdb/validation_reports/ge/6ge8 | HTTPS FTP |
-Related structure data
Related structure data | 3bv0S 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
#1: Protein | Mass: 48536.520 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Gene: bioA, RN08_1757 / Plasmid: pET28a / Production host: Escherichia coli BL21(DE3) (bacteria) References: UniProt: A0A120IWN6, adenosylmethionine-8-amino-7-oxononanoate transaminase #2: Chemical | #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: 2.18 Å3/Da / Density % sol: 43.53 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: mtBioA was dialysed against fresh PLP (50 uM), desalted (25 mM HEPES pH 7.5, 50 mM NaCl) and concentrated to 10 mg/mL. Wells consisted of 100 mM HEPES pH 7.5, 100 mM MgCl2, and 5 mM small ...Details: mtBioA was dialysed against fresh PLP (50 uM), desalted (25 mM HEPES pH 7.5, 50 mM NaCl) and concentrated to 10 mg/mL. Wells consisted of 100 mM HEPES pH 7.5, 100 mM MgCl2, and 5 mM small molecule ligand, and rows 1-6 of the plate contained a range of 9-14% w/v PEG 8000 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9762 Å |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Oct 16, 2017 |
Radiation | Monochromator: Double Crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9762 Å / Relative weight: 1 |
Reflection | Resolution: 1.869→29.85 Å / Num. obs: 71080 / % possible obs: 99.85 % / Redundancy: 11.4 % / CC1/2: 0.998 / Rmerge(I) obs: 0.1332 / Rpim(I) all: 0.04124 / Rrim(I) all: 0.1396 / Net I/σ(I): 12.41 |
Reflection shell | Resolution: 1.869→1.936 Å / Redundancy: 11.2 % / Rmerge(I) obs: 1.393 / Mean I/σ(I) obs: 1.44 / Num. unique obs: 6947 / CC1/2: 0.579 / Rpim(I) all: 0.4321 / Rrim(I) all: 1.461 / % possible all: 99.67 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3BV0 Resolution: 1.869→29.85 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 19.82 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.869→29.85 Å
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Refine LS restraints |
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LS refinement shell |
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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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