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Yorodumi- PDB-7vq9: Structure of MA1831 from Methanosarcina acetivorans in complex wi... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7vq9 | ||||||
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Title | Structure of MA1831 from Methanosarcina acetivorans in complex with farnesyl thiopyrophosphate and isopentyl S-thiolodiphosphate | ||||||
Components | Di-trans-poly-cis-decaprenylcistransferase | ||||||
Keywords | 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 / Chem-FPS / Chem-ISY / Di-trans-poly-cis-decaprenylcistransferase Function and homology information | ||||||
Biological species | Methanosarcina acetivorans (archaea) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.89 Å | ||||||
Authors | 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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Citation | Journal: Int.J.Biol.Macromol. / Year: 2022 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7vq9.cif.gz | 110.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7vq9.ent.gz | 82.3 KB | Display | PDB format |
PDBx/mmJSON format | 7vq9.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7vq9_validation.pdf.gz | 2.3 MB | Display | wwPDB validaton report |
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Full document | 7vq9_full_validation.pdf.gz | 2.3 MB | Display | |
Data in XML | 7vq9_validation.xml.gz | 22.6 KB | Display | |
Data in CIF | 7vq9_validation.cif.gz | 32.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/vq/7vq9 ftp://data.pdbj.org/pub/pdb/validation_reports/vq/7vq9 | HTTPS FTP |
-Related structure data
Related structure data | 7vqaC 7vqbC 7vqcC 7vqdC 7caqS S: Starting model for refinement 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
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 25824.670 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Methanosarcina acetivorans (strain ATCC 35395 / DSM 2834 / JCM 12185 / C2A) (archaea) Gene: uppS, MA_1831 / Plasmid: pET32a / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q8TPS4 |
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-Non-polymers , 5 types, 411 molecules
#2: Chemical | #3: Chemical | #4: Chemical | #5: Chemical | ChemComp-SO4 / #6: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | Y |
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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: 2.57 Å3/Da / Density % sol: 52.15 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 8 Details: 1.5M 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: Jun 18, 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: 1.87→35.88 Å / Num. obs: 41757 / % possible obs: 98.7 % / Redundancy: 7.4 % / CC1/2: 0.999 / Rmerge(I) obs: 0.055 / Rpim(I) all: 0.02 / Rrim(I) all: 0.059 / Net I/σ(I): 20.8 | ||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 7CAQ Resolution: 1.89→35.88 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.947 / SU B: 2.404 / SU ML: 0.071 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.116 / ESU R Free: 0.116 / 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: 95.27 Å2 / Biso mean: 23.398 Å2 / Biso min: 10.15 Å2
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Refinement step | Cycle: final / Resolution: 1.89→35.88 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.89→1.939 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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