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Yorodumi- PDB-4xjo: Crystal structure of 7,8-diaminopelargonic acid synthase (BioA) f... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4xjo | |||||||||
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Title | Crystal structure of 7,8-diaminopelargonic acid synthase (BioA) from Mycobacterium tuberculosis, complexed with an inhibitor optimized from HTS lead | |||||||||
Components | Adenosylmethionine-8-amino-7-oxononanoate aminotransferase | |||||||||
Keywords | transferase/transferase inhibitor / Inhibitor Complex Transaminase PLP / transferase-transferase inhibitor complex | |||||||||
Function / homology | Function and homology information adenosylmethionine-8-amino-7-oxononanoate transaminase / adenosylmethionine-8-amino-7-oxononanoate transaminase activity / biotin biosynthetic process / pyridoxal phosphate binding / cytoplasm Similarity search - Function | |||||||||
Biological species | Mycobacterium tuberculosis (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å | |||||||||
Authors | Finzel, B.C. / Dai, R. | |||||||||
Citation | Journal: J. Med. Chem. / Year: 2017 Title: Structure-Based Optimization of Pyridoxal 5'-Phosphate-Dependent Transaminase Enzyme (BioA) Inhibitors that Target Biotin Biosynthesis in Mycobacterium tuberculosis. Authors: Liu, F. / Dawadi, S. / Maize, K.M. / Dai, R. / Park, S.W. / Schnappinger, D. / Finzel, B.C. / Aldrich, C.C. #1: Journal: THESIS, UNIVERSITY OF MINNESOTA / Year: 2015 Title: FRAGMENT BASED INHIBITOR DESIGN OF MYCOBACTERIUM TUBERCULOSIS BIOA (HTTP://HDL.HANDLE.NET/11299/171084) Authors: Dai, R. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4xjo.cif.gz | 192.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4xjo.ent.gz | 148.9 KB | Display | PDB format |
PDBx/mmJSON format | 4xjo.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xj/4xjo ftp://data.pdbj.org/pub/pdb/validation_reports/xj/4xjo | HTTPS FTP |
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-Related structure data
Related structure data | 4xjpC 5kgsC 5kgtC 3tftS 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
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 48536.520 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv) (bacteria) Strain: ATCC 25618 / H37Rv / Gene: bioA, Rv1568, MTCY336.35c / Production host: Escherichia coli (E. coli) References: UniProt: P9WQ81, adenosylmethionine-8-amino-7-oxononanoate transaminase |
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-Non-polymers , 6 types, 661 molecules
#2: Chemical | #3: Chemical | #4: Chemical | ChemComp-EDO / | #5: Chemical | ChemComp-SO4 / | #6: Chemical | ChemComp-CL / | #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: 2.19 Å3/Da / Density % sol: 43.71 % |
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Crystal grow | Temperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 25 mM HEPES pH 7.5, 50 mM NaCl, 0.1 mM TCEP Reservoir:10% PEG 8000, 0.1M magnesium chloride, 0.1M HEPES pH 7.5 Cryo: 15% PEG 400 in reservoir solution, VAPOR DIFFUSION |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1 Å | |||||||||||||||||||||
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 21, 2014 | |||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 | |||||||||||||||||||||
Reflection | Resolution: 1.5→101.628 Å / Num. obs: 136219 / % possible obs: 99.5 % / Redundancy: 6.4 % / Rmerge(I) obs: 0.082 / Net I/σ(I): 14 / Num. measured all: 878235 | |||||||||||||||||||||
Reflection shell | Diffraction-ID: 1 / Rejects: _
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3TFT Resolution: 1.5→101.628 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.948 / SU B: 1.195 / SU ML: 0.046 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.077 / ESU R Free: 0.074 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES : REFINED INDIVIDUALLY
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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 max: 48.08 Å2 / Biso mean: 15.528 Å2 / Biso min: 7.21 Å2
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Refinement step | Cycle: final / Resolution: 1.5→101.628 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.5→1.539 Å / Total num. of bins used: 20
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