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Yorodumi- PDB-4xu2: Mycobacterium tuberculosis biotin ligase complexed with bisubstra... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4xu2 | ||||||
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Title | Mycobacterium tuberculosis biotin ligase complexed with bisubstrate inhibitor 87 with a 3'deoxy ribose | ||||||
Components | Bifunctional ligase/repressor BirA | ||||||
Keywords | LIGASE/LIGASE INHIBITOR / biotin-protein ligase / bisubstrate inhibitor / LIGASE-LIGASE INHIBITOR COMPLEX | ||||||
Function / homology | Function and homology information biotin-[biotin carboxyl-carrier protein] ligase / biotin--[biotin carboxyl-carrier protein] ligase activity / biotin binding / protein modification process / positive regulation of cell population proliferation / protein homodimerization activity / protein-containing complex / ATP binding / cytoplasm Similarity search - Function | ||||||
Biological species | Mycobacterium tuberculosis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.85002844216 Å | ||||||
Authors | De la Mora-Rey, T. / Finzel, B.C. | ||||||
Funding support | United States, 1items
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Citation | Journal: J.Med.Chem. / Year: 2015 Title: Targeting Mycobacterium tuberculosis Biotin Protein Ligase (MtBPL) with Nucleoside-Based Bisubstrate Adenylation Inhibitors. Authors: Bockman, M.R. / Kalinda, A.S. / Petrelli, R. / De la Mora-Rey, T. / Tiwari, D. / Liu, F. / Dawadi, S. / Nandakumar, M. / Rhee, K.Y. / Schnappinger, D. / Finzel, B.C. / Aldrich, C.C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4xu2.cif.gz | 151.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4xu2.ent.gz | 94.7 KB | Display | PDB format |
PDBx/mmJSON format | 4xu2.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4xu2_validation.pdf.gz | 1.1 MB | Display | wwPDB validaton report |
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Full document | 4xu2_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | 4xu2_validation.xml.gz | 26.4 KB | Display | |
Data in CIF | 4xu2_validation.cif.gz | 38.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xu/4xu2 ftp://data.pdbj.org/pub/pdb/validation_reports/xu/4xu2 | HTTPS FTP |
-Related structure data
Related structure data | 4xtvC 4xtwC 4xtxC 4xtyC 4xtzC 4xu0C 4xu1C 4xu3C 3ruxS 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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2 |
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Unit cell |
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Details | The biological unit is a monomer |
-Components
#1: Protein | Mass: 28534.428 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) Gene: birA, CH81_03124, CH82_03406, CH84_03412, CH85_03111, CH87_01691, CH88_02592, CO60_3782, ER17_17395, FF22_02902, FI98_01129, IQ38_01820, IQ39_01720, IQ40_01775, IQ41_01700, IQ42_01770, IQ43_ ...Gene: birA, CH81_03124, CH82_03406, CH84_03412, CH85_03111, CH87_01691, CH88_02592, CO60_3782, ER17_17395, FF22_02902, FI98_01129, IQ38_01820, IQ39_01720, IQ40_01775, IQ41_01700, IQ42_01770, IQ43_01710, IQ44_01750, IQ45_01765, IQ46_01705, IQ47_01735, IQ48_01770, IU12_01860, IU13_01785, IU14_01730, IU16_01770, IU17_01745, IU18_01730, IU19_01775, IU20_01750, IU22_01755, IU23_01750, IU24_01735, IZ84_17515, JE53_17495, LJ70_17695, T209_01770 Plasmid: pET28b / Production host: Escherichia coli (E. coli) / Strain (production host): MACH I References: UniProt: A0A045H8W3, UniProt: I6YFP0*PLUS, biotin-[biotin carboxyl-carrier protein] ligase #2: Chemical | #3: 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: 2.22 Å3/Da / Density % sol: 44.69 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: 17-24% PEG2000 MME, 100 mM Tris, pH 8.5, 100 mM triethylamine N-oxide |
-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: Mar 16, 2013 |
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.85→115.61 Å / Num. obs: 44260 / % possible obs: 100 % / Redundancy: 6.4 % / Biso Wilson estimate: 21.2388518081 Å2 / Rsym value: 0.055 / Net I/σ(I): 21.9 |
Reflection shell | Resolution: 1.85→1.856 Å / Redundancy: 6.4 % / Rmerge(I) obs: 0.334 / Mean I/σ(I) obs: 5.2 / % possible all: 99.8 |
-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 3RUX Resolution: 1.85002844216→36.3668016401 Å / SU ML: 0.198193004874 / Cross valid method: FREE R-VALUE / σ(F): 1.35504501685 / Phase error: 21.6073895711
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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 mean: 24.5055983662 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.85002844216→36.3668016401 Å
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Refine LS restraints |
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LS refinement shell |
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