+Open data
-Basic information
Entry | Database: PDB / ID: 7pq8 | |||||||||
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Title | Crystal structure of Campylobacter jejuni DsbA1 | |||||||||
Components | Thiol:disulfide interchange protein DsbA | |||||||||
Keywords | OXIDOREDUCTASE / disulfide bond / thioredoxin fold / periplasmic / posttranslational modification | |||||||||
Function / homology | Thiol:disulphide interchange protein DsbA/DsbL / DSBA-like thioredoxin domain / DSBA-like thioredoxin domain / isomerase activity / Thioredoxin-like superfamily / oxidoreductase activity / Thiol:disulfide interchange protein DsbA Function and homology information | |||||||||
Biological species | Campylobacter jejuni (Campylobacter) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.329 Å | |||||||||
Authors | Orlikowska, M. / Bocian-Ostrzycka, K.M. / Banas, A.M. / Jagusztyn-Krynicka, E.K. | |||||||||
Funding support | Poland, 2items
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Citation | Journal: Int J Mol Sci / Year: 2021 Title: Interplay between DsbA1, DsbA2 and C8J_1298 Periplasmic Oxidoreductases of Campylobacter jejuni and Their Impact on Bacterial Physiology and Pathogenesis. Authors: Banas, A.M. / Bocian-Ostrzycka, K.M. / Dunin-Horkawicz, S. / Ludwiczak, J. / Wilk, P. / Orlikowska, M. / Wyszynska, A. / Dabrowska, M. / Plichta, M. / Spodzieja, M. / Polanska, M.A. / ...Authors: Banas, A.M. / Bocian-Ostrzycka, K.M. / Dunin-Horkawicz, S. / Ludwiczak, J. / Wilk, P. / Orlikowska, M. / Wyszynska, A. / Dabrowska, M. / Plichta, M. / Spodzieja, M. / Polanska, M.A. / Malinowska, A. / Jagusztyn-Krynicka, E.K. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7pq8.cif.gz | 98.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7pq8.ent.gz | 71.5 KB | Display | PDB format |
PDBx/mmJSON format | 7pq8.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7pq8_validation.pdf.gz | 707.4 KB | Display | wwPDB validaton report |
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Full document | 7pq8_full_validation.pdf.gz | 708.2 KB | Display | |
Data in XML | 7pq8_validation.xml.gz | 12.8 KB | Display | |
Data in CIF | 7pq8_validation.cif.gz | 19.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/pq/7pq8 ftp://data.pdbj.org/pub/pdb/validation_reports/pq/7pq8 | HTTPS FTP |
-Related structure data
Related structure data | 7pq7SC 7pqfC 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
#1: Protein | Mass: 23396.359 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Campylobacter jejuni (Campylobacter) Gene: B5Y32_04750, B7Q70_04295, BCB47_05875, D4Q41_05880, DPG08_09245, DUY05_07510, DYE84_06245, EAX31_06480, F0166_06130, F0J04_04905, F6982_05945, F7521_05270, F7J47_05180, F8803_06690, F9778_ ...Gene: B5Y32_04750, B7Q70_04295, BCB47_05875, D4Q41_05880, DPG08_09245, DUY05_07510, DYE84_06245, EAX31_06480, F0166_06130, F0J04_04905, F6982_05945, F7521_05270, F7J47_05180, F8803_06690, F9778_05085, FVY60_01390, FW488_04080, FZ445_05615, FZ732_06740, G3M94_001567, GFF90_03350, GMG47_05310, GNO00_06010, GXA88_04885, GXS76_000973, GZ489_001237, GZ502_000952 Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Rosetta pLysS / References: UniProt: A0A1J6PBD5 |
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#2: Chemical | ChemComp-PG4 / |
#3: Water | ChemComp-HOH / |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.12 Å3/Da / Density % sol: 41.99 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: 0.12 M Ethylene glycols, 0.1M Tris/BICINE pH 8.5, 50 % v/v Precipitant Mix 1 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.9184 Å |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jun 24, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9184 Å / Relative weight: 1 |
Reflection | Resolution: 1.329→48.86 Å / Num. obs: 51341 / % possible obs: 97.8 % / Redundancy: 3.78 % / CC1/2: 0.99 / Net I/σ(I): 8.94 |
Reflection shell | Resolution: 1.33→1.41 Å / Num. unique obs: 12965 / CC1/2: 0.65 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 7PQ7 Resolution: 1.329→46.889 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.947 / SU B: 2.402 / SU ML: 0.045 / Cross valid method: FREE R-VALUE / ESU R: 0.056 / ESU R Free: 0.063 Details: Hydrogens have been added in their 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 BULK SOLVENT | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 14.025 Å2
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Refinement step | Cycle: LAST / Resolution: 1.329→46.889 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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