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Yorodumi- PDB-7n7b: crystal structure of the N-formyltrasferase HCAN_0200 from Helico... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7n7b | ||||||
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Title | crystal structure of the N-formyltrasferase HCAN_0200 from Helicobacter canadensis on complex with folinic acid and dTDP-3-aminofucose | ||||||
Components | Formyl_trans_N domain-containing protein | ||||||
Keywords | TRANSFERASE / folinic acid / formyltransferase / aminofucose | ||||||
Function / homology | methionyl-tRNA formyltransferase activity / Formyl transferase, N-terminal / Formyl transferase / Formyl transferase, N-terminal domain superfamily / cytosol / Chem-FON / Chem-T3F / Formyl transferase N-terminal domain-containing protein Function and homology information | ||||||
Biological species | Helicobacter canadensis MIT 98-5491 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / FOURIER SYNTHESIS / Resolution: 2 Å | ||||||
Authors | Heisdorf, C.J. / Thoden, J.B. / Holden, H.M. | ||||||
Funding support | United States, 1items
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Citation | Journal: Protein Sci. / Year: 2021 Title: Investigation of the enzymes required for the biosynthesis of an unusual formylated sugar in the emerging human pathogen Helicobacter canadensis. Authors: Heisdorf, C.J. / Griffiths, W.A. / Thoden, J.B. / Holden, H.M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7n7b.cif.gz | 141.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7n7b.ent.gz | 107.4 KB | Display | PDB format |
PDBx/mmJSON format | 7n7b.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/n7/7n7b ftp://data.pdbj.org/pub/pdb/validation_reports/n7/7n7b | HTTPS FTP |
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-Related structure data
Related structure data | 7n63C 7n67C 7n7aSC 7n7cC 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
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 33065.656 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Helicobacter canadensis MIT 98-5491 (bacteria) Gene: HCAN_0200 / Production host: Escherichia coli (E. coli) / References: UniProt: C5ZW02 |
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-Non-polymers , 5 types, 464 molecules
#2: Chemical | #3: Chemical | #4: Chemical | ChemComp-MES / | #5: Chemical | ChemComp-EDO / #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: 2.68 Å3/Da / Density % sol: 54.08 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5 Details: 11-14% PEG-8000, 2% DMSO, 100 mM homopipes (pH 5). Crystals soaked in 26% PEG-8000, 600 mM NaCl, 5 mM folinic acis, 10 mM dTDP-Fuc3N, 100 mM MES (pH 6) |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SEALED TUBE / Type: BRUKER D8 QUEST / Wavelength: 1.5418 Å |
Detector | Type: Bruker PHOTON II / Detector: PIXEL / Date: Oct 18, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2→50 Å / Num. obs: 45715 / % possible obs: 96.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.6 % / Rsym value: 0.074 / Net I/σ(I): 13.5 |
Reflection shell | Resolution: 2→2.1 Å / Redundancy: 3.5 % / Mean I/σ(I) obs: 2.8 / Num. unique obs: 5967 / Rsym value: 0.334 / % possible all: 93 |
-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS Starting model: 7n7a Resolution: 2→29.64 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.906 / SU B: 5.184 / SU ML: 0.141 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.187 / ESU R Free: 0.179 / 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: 86.33 Å2 / Biso mean: 30.505 Å2 / Biso min: 11.44 Å2
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Refinement step | Cycle: final / Resolution: 2→29.64 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2→2.052 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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