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Yorodumi- PDB-4cxq: Mycobaterium tuberculosis transaminase BioA complexed with substr... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4cxq | |||||||||
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Title | Mycobaterium tuberculosis transaminase BioA complexed with substrate KAPA | |||||||||
Components | ADENOSYLMETHIONINE-8-AMINO-7-OXONONANOATE AMINOTRANSFERASE | |||||||||
Keywords | TRANSFERASE / TRANSAMINASE / TUBERCULOSIS | |||||||||
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 / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å | |||||||||
Authors | Dai, R. / Wilson, D.J. / Geders, T.W. / Aldrich, C.C. / Finzel, B.C. | |||||||||
Citation | Journal: Chembiochem / Year: 2014 Title: Inhibition of Mycobacterium Tuberculosis Transaminase Bioa by Aryl Hydrazines and Hydrazides. Authors: Dai, R. / Wilson, D.J. / Geders, T.W. / 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 | 4cxq.cif.gz | 188.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4cxq.ent.gz | 149 KB | Display | PDB format |
PDBx/mmJSON format | 4cxq.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4cxq_validation.pdf.gz | 491.3 KB | Display | wwPDB validaton report |
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Full document | 4cxq_full_validation.pdf.gz | 499.4 KB | Display | |
Data in XML | 4cxq_validation.xml.gz | 37.2 KB | Display | |
Data in CIF | 4cxq_validation.cif.gz | 54.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/cx/4cxq ftp://data.pdbj.org/pub/pdb/validation_reports/cx/4cxq | HTTPS FTP |
-Related structure data
Related structure data | 4cxrC 4mqpC 4mqqC 4mqrC 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 (bacteria) / Production host: ESCHERICHIA COLI (E. coli) References: UniProt: P0A4X6, UniProt: P9WQ81*PLUS, adenosylmethionine-8-amino-7-oxononanoate transaminase |
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-Non-polymers , 5 types, 535 molecules
#2: Chemical | #3: Chemical | #4: Chemical | #5: Chemical | #6: 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: 43.78 % / Description: NONE |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: VAPOR DIFFUSION, HANGING DROP PROTEIN: 25 MM HEPES, 50 MM NACL, 0.1 MM TCEP RESERVOIR:10% PEG 8000, 0.1M MAGNESIUM CHLORIDE, 0.1M HEPES CRYO: 15% PEG 400 IN RESERVOIR SOLUTION, VAPOR ...Details: VAPOR DIFFUSION, HANGING DROP PROTEIN: 25 MM HEPES, 50 MM NACL, 0.1 MM TCEP RESERVOIR:10% PEG 8000, 0.1M MAGNESIUM CHLORIDE, 0.1M HEPES CRYO: 15% PEG 400 IN RESERVOIR SOLUTION, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 293K, PH 7.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1 |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 16, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→98.9 Å / Num. obs: 79062 / % possible obs: 98.9 % / Observed criterion σ(I): 2 / Redundancy: 6.5 % / Biso Wilson estimate: 19.6 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 16.6 |
Reflection shell | Resolution: 1.8→1.81 Å / Redundancy: 6.5 % / Rmerge(I) obs: 0.43 / Mean I/σ(I) obs: 4 / % possible all: 98.3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 3TFT Resolution: 1.8→40.55 Å / SU ML: 0.17 / σ(F): 1.35 / Phase error: 18.41 / 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: 1.8→40.55 Å
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Refine LS restraints |
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LS refinement shell |
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