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Yorodumi- PDB-6v2t: X-ray structure of a sugar N-formyltransferase from Shewanella sp... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6v2t | ||||||
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Title | X-ray structure of a sugar N-formyltransferase from Shewanella sp FDAARGOS_354 | ||||||
Components | dTDP-4-amino-4,6- ... | ||||||
Keywords | TRANSFERASE / N-formyltransferase / lipopolysaccharide / o-antigen | ||||||
Function / homology | Function and homology information hydroxymethyl-, formyl- and related transferase activity / biosynthetic process Similarity search - Function | ||||||
Biological species | Shewanella sp. FDAARGOS_354 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å | ||||||
Authors | Girardi, N.M. / Thoden, J.B. / Holden, H.M. | ||||||
Funding support | United States, 1items
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Citation | Journal: Protein Sci. / Year: 2020 Title: Misannotations of the genes encoding sugar N-formyltransferases. Authors: Girardi, N.M. / 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 | 6v2t.cif.gz | 127.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6v2t.ent.gz | 95.9 KB | Display | PDB format |
PDBx/mmJSON format | 6v2t.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6v2t_validation.pdf.gz | 537.2 KB | Display | wwPDB validaton report |
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Full document | 6v2t_full_validation.pdf.gz | 542.8 KB | Display | |
Data in XML | 6v2t_validation.xml.gz | 2.9 KB | Display | |
Data in CIF | 6v2t_validation.cif.gz | 9.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/v2/6v2t ftp://data.pdbj.org/pub/pdb/validation_reports/v2/6v2t | HTTPS FTP |
-Related structure data
Related structure data | 6v33C 4yfyS 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
-DTDP-4-amino-4,6- ... , 1 types, 2 molecules AB
#1: Protein | Mass: 30460.605 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Shewanella sp. FDAARGOS_354 (bacteria) / Gene: CEQ32_00475 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta2 / References: UniProt: A0A1Z4A6S6 |
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-Non-polymers , 6 types, 299 molecules
#2: Chemical | #3: Chemical | #4: Chemical | #5: Chemical | ChemComp-PO4 / | #6: Chemical | ChemComp-NA / | #7: 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: 2.62 Å3/Da / Density % sol: 53.14 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 9-14% PEG-5000, 200 mM N(C2H5)4Cl, 5 mM TDP-Qui4N, 5 mM folinic acid |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.9876 Å |
Detector | Type: ADSC QUANTUM 210r / Detector: CCD / Date: Mar 9, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9876 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→50 Å / Num. obs: 45110 / % possible obs: 94.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.4 % / Rsym value: 0.031 / Net I/σ(I): 56.8 |
Reflection shell | Resolution: 1.9→1.97 Å / Redundancy: 3.2 % / Mean I/σ(I) obs: 5.6 / Num. unique obs: 4036 / Rsym value: 0.155 / % possible all: 86.1 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4yfy Resolution: 1.9→27.1 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.938 / SU B: 3.862 / SU ML: 0.112 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.152 / ESU R Free: 0.155 / 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: 115.36 Å2 / Biso mean: 37.676 Å2 / Biso min: 22.26 Å2
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Refinement step | Cycle: final / Resolution: 1.9→27.1 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.9→1.946 Å / Rfactor Rfree error: 0
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