+Open data
-Basic information
Entry | Database: PDB / ID: 8pxd | ||||||
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Title | Crystal structure of the C-terminal domain of Hh1412 | ||||||
Components | Disulfide bond oxidoreductase/isomerase - Dsb | ||||||
Keywords | OXIDOREDUCTASE / disulfide bond formation / Dsb | ||||||
Function / homology | Thioredoxin-like superfamily / Uncharacterized protein Function and homology information | ||||||
Biological species | Helicobacter hepaticus ATCC 51449 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å | ||||||
Authors | Wilk, P. / Orlikowska, M. / Roszczenko-Jasinska, P. / Jagusztyn-Krynicka, E.K. | ||||||
Funding support | Poland, 1items
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Citation | Journal: To Be Published Title: Crystal structures of Disulfide oxidoreductase/isomerase from Helicobacter hepaticus. Authors: Roszczenko-Jasinska, P. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8pxd.cif.gz | 69.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8pxd.ent.gz | 49.5 KB | Display | PDB format |
PDBx/mmJSON format | 8pxd.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8pxd_validation.pdf.gz | 421.2 KB | Display | wwPDB validaton report |
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Full document | 8pxd_full_validation.pdf.gz | 421.9 KB | Display | |
Data in XML | 8pxd_validation.xml.gz | 7.7 KB | Display | |
Data in CIF | 8pxd_validation.cif.gz | 10 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/px/8pxd ftp://data.pdbj.org/pub/pdb/validation_reports/px/8pxd | HTTPS FTP |
-Related structure data
Related structure data | 8pxeC 8pxfC C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 24351.004 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: Appears to be proteolytically cleaved in the crystallization drop. Source: (gene. exp.) Helicobacter hepaticus ATCC 51449 (bacteria) Gene: HH_1412 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta / Variant (production host): (DE3) LacIq / References: UniProt: Q7VGB0 |
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#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: Morpheus A4; 0.06 M Divalents, 0.1 M Buffer System 1 6.5, 50 % v/v Precipitant Mix 4 |
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-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P13 (MX1) / Wavelength: 0.976 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 22, 2021 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.976 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.09→35.96 Å / Num. obs: 8910 / % possible obs: 99.6 % / Redundancy: 12.38 % / CC1/2: 0.993 / Rmerge(I) obs: 0.21 / Rrim(I) all: 0.219 / Net I/σ(I): 6.41 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.2→35.954 Å / SU ML: 0.32 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 34.61 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.2→35.954 Å
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Refine LS restraints |
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LS refinement shell |
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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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