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Yorodumi- PDB-5vys: Crystal structure of the WbkC N-formyltransferase (C47S variant) ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5vys | ||||||
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Title | Crystal structure of the WbkC N-formyltransferase (C47S variant) from Brucella melitensis | ||||||
Components | Gdp-mannose 4,6-dehydratase / gdp-4-amino-4,6-dideoxy-d-mannose formyltransferase | ||||||
Keywords | TRANSFERASE / brucellosis / deoxysugar | ||||||
Function / homology | Function and homology information GDP-perosamine N-formyltransferase / GDP-mannose 4,6-dehydratase activity / lipopolysaccharide biosynthetic process / transferase activity 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
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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 |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5vys.cif.gz | 121.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5vys.ent.gz | 91.1 KB | Display | PDB format |
PDBx/mmJSON format | 5vys.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/vy/5vys ftp://data.pdbj.org/pub/pdb/validation_reports/vy/5vys | HTTPS FTP |
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-Related structure data
Related structure data | 5vyrSC 5vytC 5vyuC 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: 29295.584 Da / Num. of mol.: 2 / Mutation: C47S, D78A 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 |
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-Non-polymers , 5 types, 256 molecules
#2: Chemical | #3: Chemical | ChemComp-EDO / | #4: Chemical | #5: Chemical | ChemComp-GMP / | #6: 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: 2.18 Å3/Da / Density % sol: 43.48 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 19-25%PEG-5000, 5 mM GDP-perosamine, 5 mM folinic acid, 100 mM MOPS |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å |
Detector | Type: Bruker Platinum 135 / Detector: CCD / Date: Aug 25, 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: 27237 / % possible obs: 99.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 14.1 % / Rmerge(I) obs: 0.096 / Rsym value: 0.096 / Net I/σ(I): 12.3 |
Reflection shell | Resolution: 2.2→2.3 Å / Redundancy: 8.1 % / Rmerge(I) obs: 0.405 / Mean I/σ(I) obs: 4 / Num. unique obs: 3263 / Rsym value: 0.405 / % possible all: 98.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5vyr Resolution: 2.2→29.965 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.893 / SU B: 7.214 / SU ML: 0.176 / Cross valid method: THROUGHOUT / ESU R: 0.29 / ESU R Free: 0.235 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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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 mean: 28.643 Å2
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Refinement step | Cycle: 1 / Resolution: 2.2→29.965 Å
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Refine LS restraints |
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