+Open data
-Basic information
Entry | Database: PDB / ID: 8f8f | ||||||
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Title | The structure of Rv2173 from M. tuberculosis (APO form) | ||||||
Components | (2E,6E)-farnesyl diphosphate synthase | ||||||
Keywords | TRANSFERASE / Rv2173 / M. tuberculosis / Isoprenyl diphosphate synthase | ||||||
Function / homology | Function and homology information geranyl diphosphate biosynthetic process / dimethylallyltranstransferase / (2E,6E)-farnesyl diphosphate synthase / geranyltranstransferase activity / prenyltransferase activity / dimethylallyltranstransferase activity / isoprenoid biosynthetic process / metal ion binding Similarity search - Function | ||||||
Biological species | Mycobacterium tuberculosis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å | ||||||
Authors | Johnston, J.M. / Allison, T.M. / Titterington, J. | ||||||
Funding support | New Zealand, 1items
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Citation | Journal: To be Published Title: The structure of Rv2173 from M. tuberculosis in APO-, IPP-, and DMAP-bound forms. Authors: Johnston, J.M. / Allison, T.M. / Titterington, J. / Beasley, C.P.H. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8f8f.cif.gz | 152.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8f8f.ent.gz | 117.7 KB | Display | PDB format |
PDBx/mmJSON format | 8f8f.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/f8/8f8f ftp://data.pdbj.org/pub/pdb/validation_reports/f8/8f8f | HTTPS FTP |
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-Related structure data
Related structure data | 8f8kC 8f8lC C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 42057.738 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Gene: idsA2, Rv2173 / Production host: Escherichia coli BL21(DE3) (bacteria) References: UniProt: O53507, (2E,6E)-farnesyl diphosphate synthase, dimethylallyltranstransferase #2: Chemical | ChemComp-GOL / #3: Chemical | ChemComp-MG / | #4: Water | ChemComp-HOH / | Has ligand of interest | N | |
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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: 3.09 Å3/Da / Density % sol: 60.17 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion Details: 0.1 M Bicine-Tris, pH 8.3, 10% PEG4000, 24% glycerol, 0.03 M DC mix (Ca2+/Mg2+ mix) |
-Data collection
Diffraction | Mean temperature: 77 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9537 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 1, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9537 Å / Relative weight: 1 |
Reflection | Resolution: 2→19.76 Å / Num. obs: 71090 / % possible obs: 99.9 % / Redundancy: 14.6 % / CC1/2: 0.999 / Rmerge(I) obs: 0.124 / Rpim(I) all: 0.033 / Rrim(I) all: 0.128 / Χ2: 1.07 / Net I/σ(I): 17.8 / Num. measured all: 1039648 |
Reflection shell | Resolution: 2→2.04 Å / % possible obs: 100 % / Redundancy: 14.9 % / Rmerge(I) obs: 3.25 / Num. measured all: 66769 / Num. unique obs: 4495 / CC1/2: 0.384 / Rpim(I) all: 0.865 / Rrim(I) all: 3.364 / Χ2: 0.97 / Net I/σ(I) obs: 1.2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→19.76 Å / SU ML: 0.31 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 27.47 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2→19.76 Å
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Refine LS restraints |
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LS refinement shell |
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