[English] 日本語
Yorodumi- PDB-5vyu: Crystal structure of the WbkC N-formyltransferase from Brucella m... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5vyu | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of the WbkC N-formyltransferase from Brucella melitensis in complex with GDP-perosaminea and N-10-formyltetrahydrofolate | ||||||
Components | Gdp-mannose 4,6-dehydratase / gdp-4-amino-4,6-dideoxy-d-mannose formyltransferase | ||||||
Keywords | TRANSFERASE / deoxysugar / brucellosis | ||||||
Function / homology | Function and homology information GDP-perosamine N-formyltransferase / GDP-mannose 4,6-dehydratase activity / methionyl-tRNA formyltransferase activity / lipopolysaccharide biosynthetic process / cytosol Similarity search - Function | ||||||
Biological species | Brucella melitensis biotype 1 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.2 Å | ||||||
Authors | Riegert, A.S. / Chantigian, D.P. / Thoden, J.B. / Holden, H.M. | ||||||
Funding support | United States, 1items
| ||||||
Citation | Journal: Biochemistry / Year: 2017 Title: Biochemical Characterization of WbkC, an N-Formyltransferase from Brucella melitensis. Authors: Riegert, A.S. / Chantigian, D.P. / Thoden, J.B. / Tipton, P.A. / Holden, H.M. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 5vyu.cif.gz | 117.9 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb5vyu.ent.gz | 88.1 KB | Display | PDB format |
PDBx/mmJSON format | 5vyu.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5vyu_validation.pdf.gz | 1.6 MB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 5vyu_full_validation.pdf.gz | 1.6 MB | Display | |
Data in XML | 5vyu_validation.xml.gz | 21.7 KB | Display | |
Data in CIF | 5vyu_validation.cif.gz | 30.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/vy/5vyu ftp://data.pdbj.org/pub/pdb/validation_reports/vy/5vyu | HTTPS FTP |
-Related structure data
Related structure data | 5vyrSC 5vysC 5vytC S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 29235.553 Da / Num. of mol.: 2 / Mutation: D78A, F142A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Brucella melitensis biotype 1 (strain 16M / ATCC 23456 / NCTC 10094) (bacteria) Strain: 16M / ATCC 23456 / NCTC 10094 / Gene: BMEI1418 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta2(DE3) References: UniProt: F8WJP6, Transferases; Transferring one-carbon groups; Hydroxymethyl-, formyl- and related transferases, GDP-mannose 4,6-dehydratase #2: Chemical | #3: Chemical | ChemComp-JB2 / | #4: Chemical | ChemComp-GDP / | #5: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.25 Å3/Da / Density % sol: 45.41 % |
---|---|
Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6 Details: 13-155 PEG-5000, 2% GLYCEROL, 5 mM GDP-perosamine, 5 mM folinic acid |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å |
Detector | Type: Bruker Platinum 135 / Detector: CCD / Date: Nov 9, 2016 / Details: montel |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→50 Å / Num. obs: 27823 / % possible obs: 98.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 8 % / Rmerge(I) obs: 0.091 / Rsym value: 0.091 / Net I/σ(I): 10 |
Reflection shell | Resolution: 2.2→2.3 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.401 / Mean I/σ(I) obs: 2.6 / Num. unique obs: 3311 / Rsym value: 0.401 / % possible all: 96.3 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5vyr Resolution: 2.2→50 Å / Cor.coef. Fo:Fc: 0.924 / Cor.coef. Fo:Fc free: 0.87 / SU B: 8.226 / SU ML: 0.197 / Cross valid method: THROUGHOUT / ESU R: 0.3 / ESU R Free: 0.235 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 21.689 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: 1 / Resolution: 2.2→50 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
|