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Yorodumi- PDB-7n7a: crystal structure of the dTDP-Qui3N N-formyltransferase from Heli... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7n7a | ||||||
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Title | crystal structure of the dTDP-Qui3N N-formyltransferase from Helicobacter canadensis, apo form | ||||||
Components | Formyl_trans_N domain-containing protein | ||||||
Keywords | TRANSFERASE / folate / formyltransferase | ||||||
Function / homology | methionyl-tRNA formyltransferase activity / Formyl transferase, N-terminal / Formyl transferase / Formyl transferase, N-terminal domain superfamily / cytosol / Formyl transferase N-terminal domain-containing protein Function and homology information | ||||||
Biological species | Helicobacter canadensis MIT 98-5491 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.8 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 | 7n7a.cif.gz | 140.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7n7a.ent.gz | 108.1 KB | Display | PDB format |
PDBx/mmJSON format | 7n7a.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7n7a_validation.pdf.gz | 447.3 KB | Display | wwPDB validaton report |
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Full document | 7n7a_full_validation.pdf.gz | 450.6 KB | Display | |
Data in XML | 7n7a_validation.xml.gz | 28.1 KB | Display | |
Data in CIF | 7n7a_validation.cif.gz | 43.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/n7/7n7a ftp://data.pdbj.org/pub/pdb/validation_reports/n7/7n7a | HTTPS FTP |
-Related structure data
Related structure data | 7n63C 7n67C 7n7bC 7n7cC 4lxqS 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
#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 #2: Chemical | ChemComp-EDO / #3: 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: 2.8 Å3/Da / Density % sol: 56.1 % |
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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) |
-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 4, 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: 1.8→50 Å / Num. obs: 65901 / % possible obs: 99.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.6 % / Rsym value: 0.059 / Net I/σ(I): 18.7 |
Reflection shell | Resolution: 1.8→1.87 Å / Redundancy: 4.4 % / Mean I/σ(I) obs: 3.9 / Num. unique obs: 7018 / Rsym value: 0.267 / % possible all: 99.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4lxq Resolution: 1.8→29.67 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.939 / SU B: 2.674 / SU ML: 0.079 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.109 / ESU R Free: 0.108 / 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: 87.51 Å2 / Biso mean: 20.084 Å2 / Biso min: 6.45 Å2
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Refinement step | Cycle: final / Resolution: 1.8→29.67 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.8→1.847 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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