+Open data
-Basic information
Entry | Database: PDB / ID: 4kt8 | |||||||||
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Title | The complex structure of Rv3378c-Y51FY90F with substrate, TPP | |||||||||
Components | Diterpene synthase | |||||||||
Keywords | HYDROLASE / Diterpene synthase | |||||||||
Function / homology | Function and homology information adenosine tuberculosinyltransferase / (13S)-vitexifolin A synthase activity / tuberculosinol biosynthetic process / diterpenoid biosynthetic process / transferase activity, transferring alkyl or aryl (other than methyl) groups / response to host immune response / phosphatase activity Similarity search - Function | |||||||||
Biological species | Mycobacterium tuberculosis (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å | |||||||||
Authors | Chan, H.C. / Feng, X. / Ko, T.P. / Huang, C.H. / Hu, Y. / Zheng, Y. / Bogue, S. / Nakano, C. / Hoshino, T. / Zhang, L. ...Chan, H.C. / Feng, X. / Ko, T.P. / Huang, C.H. / Hu, Y. / Zheng, Y. / Bogue, S. / Nakano, C. / Hoshino, T. / Zhang, L. / Lv, P. / Liu, W. / Crick, D.C. / Liang, P.H. / Wang, A.H. / Oldfield, E. / Guo, R.T. | |||||||||
Citation | Journal: J.Am.Chem.Soc. / Year: 2014 Title: Structure and inhibition of tuberculosinol synthase and decaprenyl diphosphate synthase from Mycobacterium tuberculosis. Authors: Chan, H.C. / Feng, X. / Ko, T.P. / Huang, C.H. / Hu, Y. / Zheng, Y. / Bogue, S. / Nakano, C. / Hoshino, T. / Zhang, L. / Lv, P. / Liu, W. / Crick, D.C. / Liang, P.H. / Wang, A.H. / Oldfield, E. / Guo, R.T. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4kt8.cif.gz | 74.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4kt8.ent.gz | 55.1 KB | Display | PDB format |
PDBx/mmJSON format | 4kt8.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4kt8_validation.pdf.gz | 691.8 KB | Display | wwPDB validaton report |
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Full document | 4kt8_full_validation.pdf.gz | 697.2 KB | Display | |
Data in XML | 4kt8_validation.xml.gz | 14.1 KB | Display | |
Data in CIF | 4kt8_validation.cif.gz | 18.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/kt/4kt8 ftp://data.pdbj.org/pub/pdb/validation_reports/kt/4kt8 | HTTPS FTP |
-Related structure data
Related structure data | 3wqkC 3wqlC 3wqmC 3wqnC 4oncC 3vx5 3vx9 3vxa 3w3i S: Starting model for refinement C: citing same article (ref.) |
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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: 34039.484 Da / Num. of mol.: 1 / Mutation: Y51F, Y90F Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Strain: H37Rv / Gene: Rv3378c, MT3488 / Plasmid: pET32a Xa/LIC / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 trx B References: UniProt: O50407, UniProt: P9WJ61*PLUS, EC: 3.1.7.9, EC: 3.1.7.8 | ||||
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#2: Chemical | #3: Chemical | ChemComp-9AX / ( | #4: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.77 Å3/Da / Density % sol: 55.58 % |
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSRRC / Beamline: BL13C1 / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: May 3, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.4→25 Å / Num. obs: 15419 / % possible obs: 99.7 % / Redundancy: 10.3 % / Rmerge(I) obs: 0.065 |
Reflection shell | Resolution: 2.4→2.5 Å / Redundancy: 10.6 % / Rmerge(I) obs: 0.397 / Mean I/σ(I) obs: 6.4 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3VX5 3vx5 Resolution: 2.4→25 Å / σ(F): 2 / Stereochemistry target values: Engh & Huber
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Refinement step | Cycle: LAST / Resolution: 2.4→25 Å
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LS refinement shell | Resolution: 2.4→2.5 Å /
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