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Yorodumi- PDB-4pwp: Crystal structure of DsbA from the Gram positive bacterium Coryne... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4pwp | ||||||
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Title | Crystal structure of DsbA from the Gram positive bacterium Corynebacterium diphtheriae | ||||||
Components | DsbA | ||||||
Keywords | STRUCTURAL GENOMICS / thioredoxin domain / disulfide bond isomerase | ||||||
Function / homology | DsbA, N-terminal domain / Thioredoxin / Thioredoxin-like fold / Thioredoxin domain profile. / Thioredoxin domain / Thioredoxin-like superfamily / membrane / Secreted protein Function and homology information | ||||||
Biological species | Corynebacterium diphtheriae (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.803 Å | ||||||
Authors | Um, S.H. / Kim, J.S. / Jiao, L. / Yoon, B.Y. / Jo, I. / Ha, N.C. | ||||||
Citation | Journal: To be Published Title: Crystal structure and biochemical characterization of DsbA from the Gram positive bacterium Corynebacterium diphtheriae Authors: Um, S.H. / Kim, J.S. / Jiao, L. / Yoon, B.Y. / Jo, I. / Ha, N.C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4pwp.cif.gz | 63.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4pwp.ent.gz | 50.4 KB | Display | PDB format |
PDBx/mmJSON format | 4pwp.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4pwp_validation.pdf.gz | 431.7 KB | Display | wwPDB validaton report |
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Full document | 4pwp_full_validation.pdf.gz | 433.1 KB | Display | |
Data in XML | 4pwp_validation.xml.gz | 13.8 KB | Display | |
Data in CIF | 4pwp_validation.cif.gz | 20.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/pw/4pwp ftp://data.pdbj.org/pub/pdb/validation_reports/pw/4pwp | HTTPS FTP |
-Related 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: 27047.551 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Corynebacterium diphtheriae (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: Q6NJK4*PLUS |
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#2: Chemical | ChemComp-GOL / |
#3: Water | ChemComp-HOH / |
Sequence details | THE SEQUENCE OF THIS PROTEIN WAS NOT AVAILABLE AT THE UNIPROT KNOWLEDGEBASE DATABASE (UNIPROTKB) AT ...THE SEQUENCE OF THIS PROTEIN WAS NOT AVAILABLE AT THE UNIPROT KNOWLEDGEB |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.14 Å3/Da / Density % sol: 42.39 % |
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Crystal grow | Temperature: 287 K / Method: vapor diffusion, hanging drop / pH: 8 Details: 30% PEG 2K, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 287K |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: PAL/PLS / Beamline: 5C (4A) / Wavelength: 1 Å | |||||||||||||||||||||
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 26, 2013 | |||||||||||||||||||||
Radiation | Monochromator: double mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 | |||||||||||||||||||||
Reflection | Resolution: 1.48→50 Å / Num. all: 41100 / Num. obs: 40982 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 | |||||||||||||||||||||
Reflection shell |
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-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 1.803→30.856 Å / SU ML: 0.16 / σ(F): 0.93 / Phase error: 17.98 / Stereochemistry target values: MLHL
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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: 1.803→30.856 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: 14
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