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Yorodumi- PDB-4wya: Crystal structure of 7,8-diaminopelargonic acid synthase (BioA) f... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4wya | ||||||
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Title | Crystal structure of 7,8-diaminopelargonic acid synthase (BioA) from Mycobacterium tuberculosis, complexed with a fragment hit | ||||||
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 / dethiobiotin synthase activity / biotin biosynthetic process / pyridoxal phosphate binding / cytoplasm Similarity search - Function | ||||||
Biological species | Mycobacterium tuberculosis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.5 Å | ||||||
Authors | Finzel, B.C. / Dai, D. / Geders, T.W. | ||||||
Citation | Journal: J.Med.Chem. / Year: 2015 Title: Fragment-Based Exploration of Binding Site Flexibility in Mycobacterium tuberculosis BioA. Authors: Dai, R. / Geders, T.W. / Liu, F. / Park, S.W. / Schnappinger, D. / Aldrich, C.C. / Finzel, B.C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4wya.cif.gz | 318.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4wya.ent.gz | 257.3 KB | Display | PDB format |
PDBx/mmJSON format | 4wya.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4wya_validation.pdf.gz | 510.8 KB | Display | wwPDB validaton report |
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Full document | 4wya_full_validation.pdf.gz | 542.9 KB | Display | |
Data in XML | 4wya_validation.xml.gz | 60.7 KB | Display | |
Data in CIF | 4wya_validation.cif.gz | 83 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wy/4wya ftp://data.pdbj.org/pub/pdb/validation_reports/wy/4wya | HTTPS FTP |
-Related structure data
Related structure data | 4wycC 4wydC 4wyeC 4wyfC 4wygC 4xewC 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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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 48536.520 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: bioA, Rv1568, MTCY336.35c / Production host: Escherichia coli (E. coli) References: UniProt: P9WQ81, adenosylmethionine-8-amino-7-oxononanoate transaminase #2: Chemical | ChemComp-PLP / #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: 2.17 Å3/Da / Density % sol: 43.4 % |
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Crystal grow | Temperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: Protein: 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, HANGING DROP, temperature 293.15K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU FR-E+ DW / Wavelength: 1.54 Å |
Detector | Type: RIGAKU SATURN 944+ / Detector: CCD / Date: Apr 4, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→29.866 Å / Num. obs: 50047 / % possible obs: 65 % / Redundancy: 1.92 % / Biso Wilson estimate: 38.2 Å2 / Rmerge(I) obs: 0.146 / Χ2: 0.95 / Net I/σ(I): 4.1 / Num. measured all: 136210 / Scaling rejects: 1022 |
Reflection shell | Highest resolution: 2.5 Å |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3TFT Resolution: 2.5→29.866 Å / FOM work R set: 0.6997 / SU ML: 0.43 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 35.91 / 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 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 92.37 Å2 / Biso mean: 43.1 Å2 / Biso min: 21.05 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.5→29.866 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 18
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