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- PDB-7vqa: Structure of MA1831 from Methanosarcina acetivorans in complex wi... -
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Open data
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Basic information
Entry | Database: PDB / ID: 7vqa | ||||||
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Title | Structure of MA1831 from Methanosarcina acetivorans in complex with dimethylallyl diphosphate. | ||||||
![]() | Di-trans-poly-cis-decaprenylcistransferase | ||||||
![]() | TRANSFERASE / cis-prenyltransferase | ||||||
Function / homology | polyprenol biosynthetic process / Decaprenyl diphosphate synthase-like / Putative undecaprenyl diphosphate synthase / Decaprenyl diphosphate synthase-like superfamily / transferase activity, transferring alkyl or aryl (other than methyl) groups / metal ion binding / DIMETHYLALLYL DIPHOSPHATE / Di-trans-poly-cis-decaprenylcistransferase![]() | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Zhang, L.L. / Chen, C.C. / Liu, W.D. / Huang, J.W. / Zhang, X.W. / Liu, B.B. / Guo, R.T. | ||||||
Funding support | 1items
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![]() | ![]() Title: Structural insights to a bi-functional isoprenyl diphosphate synthase that can catalyze head-to-tail and head-to-middle condensation. Authors: Zhang, L. / Zhang, X. / Min, J. / Liu, B. / Huang, J.W. / Yang, Y. / Liu, W. / Dai, L. / Yang, Y. / Chen, C.C. / Guo, R.T. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 110.3 KB | Display | ![]() |
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PDB format | ![]() | 82.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 7vq9C ![]() 7vqbC ![]() 7vqcC ![]() 7vqdC ![]() 7caqS S: Starting model for refinement C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 25824.670 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Gene: uppS, MA_1831 / Plasmid: pET32a / Production host: ![]() ![]() #2: Chemical | ChemComp-DMA / #3: Chemical | #4: Chemical | ChemComp-SO4 / #5: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.58 Å3/Da / Density % sol: 52.24 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 8 Details: 0.5M ammonium sulfate, 0.1M Tris (pH 8.0), 12% glycerol |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: LIQUID ANODE / Type: BRUKER METALJET / Wavelength: 1.34138 Å |
Detector | Type: Bruker PHOTON III / Detector: PIXEL / Date: Jul 8, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.34138 Å / Relative weight: 1 |
Reflection | Resolution: 1.79→35 Å / Num. obs: 43956 / % possible obs: 99.9 % / Redundancy: 10.9 % / Rmerge(I) obs: 0.051 / Net I/σ(I): 29 |
Reflection shell | Resolution: 1.79→1.89 Å / Redundancy: 6.7 % / Rmerge(I) obs: 0.26 / Num. unique obs: 7297 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 7CAQ Resolution: 1.79→33.45 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.938 / SU B: 2.25 / SU ML: 0.07 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.107 / ESU R Free: 0.113 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||
Displacement parameters | Biso max: 115.02 Å2 / Biso mean: 23.62 Å2 / Biso min: 10.83 Å2
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Refinement step | Cycle: final / Resolution: 1.79→33.45 Å
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LS refinement shell | Resolution: 1.79→1.84 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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