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Yorodumi- PDB-5bjy: x-ray structure of the PglF 4,5-dehydratase from campylobacter je... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5bjy | ||||||
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Title | x-ray structure of the PglF 4,5-dehydratase from campylobacter jejuni, variant M405Y, in complex with UDP | ||||||
Components | WlaL protein | ||||||
Keywords | MEMBRANE PROTEIN / short chain dehydrogenase / 4 / 6-dehydratase / deoxysugar | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Campylobacter jejuni (Campylobacter) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å | ||||||
Authors | Riegert, A.S. / Thoden, J.B. / Holden, H.M. | ||||||
Funding support | United States, 1items
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Citation | Journal: Biochemistry / Year: 2017 Title: Structural and Biochemical Investigation of PglF from Campylobacter jejuni Reveals a New Mechanism for a Member of the Short Chain Dehydrogenase/Reductase Superfamily. Authors: Riegert, A.S. / Thoden, J.B. / Schoenhofen, I.C. / Watson, D.C. / Young, N.M. / 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 | 5bjy.cif.gz | 173.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5bjy.ent.gz | 132.1 KB | Display | PDB format |
PDBx/mmJSON format | 5bjy.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5bjy_validation.pdf.gz | 1.7 MB | Display | wwPDB validaton report |
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Full document | 5bjy_full_validation.pdf.gz | 1.7 MB | Display | |
Data in XML | 5bjy_validation.xml.gz | 35 KB | Display | |
Data in CIF | 5bjy_validation.cif.gz | 52.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bj/5bjy ftp://data.pdbj.org/pub/pdb/validation_reports/bj/5bjy | HTTPS FTP |
-Related structure data
Related structure data | 5bjuSC 5bjvC 5bjwC 5bjxC 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: 40881.402 Da / Num. of mol.: 2 / Fragment: UNP residues 244-590 / Mutation: M405Y Source method: isolated from a genetically manipulated source Source: (gene. exp.) Campylobacter jejuni (Campylobacter) / Gene: wlaL / Production host: Escherichia coli (E. coli) / References: UniProt: O86159 |
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-Non-polymers , 5 types, 741 molecules
#2: Chemical | #3: Chemical | #4: Chemical | ChemComp-EDO / #5: Chemical | ChemComp-NA / #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: 2.52 Å3/Da / Density % sol: 51.26 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6 / Details: 20% PEG-5000, 2% MPD, 10 MM UDP, 100 MM MES |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.9794 Å |
Detector | Type: ADSC QUANTUM 210r / Detector: CCD / Date: Jun 10, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9794 Å / Relative weight: 1 |
Reflection | Resolution: 1.6→50 Å / Num. obs: 103648 / % possible obs: 94.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.6 % / Rmerge(I) obs: 0.066 / Rsym value: 0.066 / Net I/σ(I): 58.3 |
Reflection shell | Resolution: 1.6→1.66 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.126 / Mean I/σ(I) obs: 10.9 / Num. unique obs: 9614 / Rsym value: 0.126 / % possible all: 88.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5BJU Resolution: 1.6→31 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.959 / SU B: 1.498 / SU ML: 0.052 / Cross valid method: THROUGHOUT / ESU R: 0.082 / ESU R Free: 0.082 / 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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 21.747 Å2
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Refinement step | Cycle: 1 / Resolution: 1.6→31 Å
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Refine LS restraints |
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