+Open data
-Basic information
Entry | Database: PDB / ID: 6drr | ||||||
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Title | Crystal structure of Cj0485 dehydrogenase | ||||||
Components | Short-chain dehydrogenase | ||||||
Keywords | OXIDOREDUCTASE | ||||||
Function / homology | Enoyl-(Acyl carrier protein) reductase / Short-chain dehydrogenase/reductase SDR / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta / : / Putative oxidoreductase Function and homology information | ||||||
Biological species | Campylobacter jejuni (Campylobacter) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.599 Å | ||||||
Authors | Pluvinage, B. / Boraston, A.B. | ||||||
Citation | Journal: Commun Biol / Year: 2020 Title: The gastrointestinal pathogen Campylobacter jejuni metabolizes sugars with potential help from commensal Bacteroides vulgatus. Authors: Garber, J.M. / Nothaft, H. / Pluvinage, B. / Stahl, M. / Bian, X. / Porfirio, S. / Enriquez, A. / Butcher, J. / Huang, H. / Glushka, J. / Line, E. / Gerlt, J.A. / Azadi, P. / Stintzi, A. / ...Authors: Garber, J.M. / Nothaft, H. / Pluvinage, B. / Stahl, M. / Bian, X. / Porfirio, S. / Enriquez, A. / Butcher, J. / Huang, H. / Glushka, J. / Line, E. / Gerlt, J.A. / Azadi, P. / Stintzi, A. / Boraston, A.B. / Szymanski, C.M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6drr.cif.gz | 128.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6drr.ent.gz | 98.7 KB | Display | PDB format |
PDBx/mmJSON format | 6drr.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6drr_validation.pdf.gz | 449.9 KB | Display | wwPDB validaton report |
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Full document | 6drr_full_validation.pdf.gz | 451.7 KB | Display | |
Data in XML | 6drr_validation.xml.gz | 24.8 KB | Display | |
Data in CIF | 6drr_validation.cif.gz | 37 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/dr/6drr ftp://data.pdbj.org/pub/pdb/validation_reports/dr/6drr | HTTPS FTP |
-Related structure data
Related structure data | 6ds1C 4gvxS 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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2 |
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3 |
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Unit cell |
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-Components
#1: Protein | Mass: 30521.822 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Campylobacter jejuni (Campylobacter) / Gene: A0L11_03550, BKM79_02435, CRM98_01005 / Plasmid: pET30a / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: A0A1E7PQA4, UniProt: Q0PB28*PLUS #2: Chemical | ChemComp-EDO / #3: 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: 2.48 Å3/Da / Density % sol: 50.43 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: 3.4 M 1,6-hexanediol, 0.1 M Tris and 0.2 M MgCl2 (H2O)6 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU MICROMAX-002 / Wavelength: 1.54187 Å |
Detector | Type: DECTRIS PILATUS 200K / Detector: PIXEL / Date: Feb 20, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54187 Å / Relative weight: 1 |
Reflection | Resolution: 1.599→73.88 Å / Num. obs: 76135 / % possible obs: 99.7 % / Redundancy: 4.7 % / Biso Wilson estimate: 15.57 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.071 / Rpim(I) all: 0.028 / Net I/σ(I): 22.9 |
Reflection shell | Resolution: 1.6→1.63 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.328 / Mean I/σ(I) obs: 2.6 / CC1/2: 0.943 / Rpim(I) all: 0.225 / % possible all: 99.1 |
-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4GVX Resolution: 1.599→24.868 Å / SU ML: 0.16 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 21.75
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 64.74 Å2 / Biso mean: 19.174 Å2 / Biso min: 7.94 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.599→24.868 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 26
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