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Yorodumi- PDB-2dtn: Crystal structure of Helicobacter pylori undecaprenyl pyrophospha... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2dtn | ||||||
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Title | Crystal structure of Helicobacter pylori undecaprenyl pyrophosphate synthase complexed with pyrophosphate | ||||||
Components | undecaprenyl pyrophosphate synthase | ||||||
Keywords | TRANSFERASE / Helicobacter pylori / cis prenyltransferase | ||||||
Function / homology | Function and homology information di-trans,poly-cis-undecaprenyl-diphosphate synthase activity / polyprenol biosynthetic process / Transferases; Transferring alkyl or aryl groups, other than methyl groups / magnesium ion binding / cytosol Similarity search - Function | ||||||
Biological species | Helicobacter pylori (bacteria) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.5 Å | ||||||
Authors | Guo, R.T. / Kuo, C.J. / Chen, C.L. / Ko, T.P. / Liang, P.H. / Wang, A.H.-J. | ||||||
Citation | Journal: To be Published Title: Biochemical characterization, crystal structure, and inhibitors of Helicobacter pylori undecaprenyl pyrophosphate synthase Authors: Kuo, C.J. / Guo, R.T. / Lu, I.L. / Liu, H.G. / Wu, S.Y. / Ko, T.P. / Wang, A.H.-J. / Liang, P.H. | ||||||
History |
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Remark 999 | SEQUENCE A sequence database reference for this protein does not currently exist. This protein is ...SEQUENCE A sequence database reference for this protein does not currently exist. This protein is C234A mutant. 11 amino acids in the N-terminal are the cloning artifacts (MLSATQPLSEK). |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2dtn.cif.gz | 99.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2dtn.ent.gz | 76.6 KB | Display | PDB format |
PDBx/mmJSON format | 2dtn.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2dtn_validation.pdf.gz | 451.8 KB | Display | wwPDB validaton report |
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Full document | 2dtn_full_validation.pdf.gz | 461.7 KB | Display | |
Data in XML | 2dtn_validation.xml.gz | 19.2 KB | Display | |
Data in CIF | 2dtn_validation.cif.gz | 26.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/dt/2dtn ftp://data.pdbj.org/pub/pdb/validation_reports/dt/2dtn | HTTPS FTP |
-Related structure data
Related structure data | 2d2rS 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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Unit cell |
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Details | The biological assembly is a dimer as solved structure |
-Components
#1: Protein | Mass: 28575.924 Da / Num. of mol.: 2 / Mutation: C234A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Helicobacter pylori (bacteria) / Plasmid: pET32 Xa/LIC / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) References: UniProt: P55984, ditrans,polycis-undecaprenyl-diphosphate synthase [(2E,6E)-farnesyl-diphosphate specific] #2: Chemical | ChemComp-DPO / | #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: 1.96 Å3/Da / Density % sol: 37.2 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion / pH: 8 Details: 0.15M KSCN, 15% PEG600, 2% PEG5KMME, pH 8.0, VAPOR DIFFUSION, temperature 298.0K |
-Data collection
Diffraction | Mean temperature: 113 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å |
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Mar 5, 2006 / Details: mirrors |
Radiation | Monochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→50 Å / Num. all: 16203 / Num. obs: 15618 / % possible obs: 96 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 8.83 % / Rmerge(I) obs: 0.059 / Net I/σ(I): 42.3 |
Reflection shell | Resolution: 2.5→2.59 Å / Redundancy: 9 % / Rmerge(I) obs: 0.159 / Mean I/σ(I) obs: 5.2 / Num. unique all: 14131 / % possible all: 91.2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2D2R Resolution: 2.5→50 Å / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Displacement parameters | Biso mean: 49.49 Å2 | |||||||||||||||||||||||||
Refine analyze | Luzzati coordinate error obs: 0.3 Å / Luzzati d res low obs: 5 Å / Luzzati sigma a obs: 0.28 Å | |||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.5→50 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.5→2.59 Å
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