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Yorodumi- PDB-3hd5: Crystal structure of a thiol:disulfide interchange protein dsbA f... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3hd5 | ||||||
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Title | Crystal structure of a thiol:disulfide interchange protein dsbA from Bordetella parapertussis | ||||||
Components | Thiol:disulfide interchange protein dsbA | ||||||
Keywords | OXIDOREDUCTASE / dsbA / Protein Structure Initiative II(PSI II) / NYSGXRC / 11213n / Structural Genomics / New York SGX Research Center for Structural Genomics / Disulfide bond / Periplasm / Redox-active center | ||||||
Function / homology | Function and homology information protein-disulfide reductase activity / cell redox homeostasis / periplasmic space Similarity search - Function | ||||||
Biological species | Bordetella parapertussis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.35 Å | ||||||
Authors | Palani, K. / Burley, S.K. / Swaminathan, S. / New York SGX Research Center for Structural Genomics (NYSGXRC) | ||||||
Citation | Journal: To be Published Title: Crystal structure of a thiol:disulfide interchange protein dsbA from Bordetella parapertussis Authors: Palani, K. / Burley, S.K. / Swaminathan, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3hd5.cif.gz | 115.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3hd5.ent.gz | 95.2 KB | Display | PDB format |
PDBx/mmJSON format | 3hd5.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3hd5_validation.pdf.gz | 441.9 KB | Display | wwPDB validaton report |
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Full document | 3hd5_full_validation.pdf.gz | 448.8 KB | Display | |
Data in XML | 3hd5_validation.xml.gz | 22.6 KB | Display | |
Data in CIF | 3hd5_validation.cif.gz | 31.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/hd/3hd5 ftp://data.pdbj.org/pub/pdb/validation_reports/hd/3hd5 | HTTPS FTP |
-Related structure data
Similar structure data | |
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Other databases |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 21916.898 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bordetella parapertussis (bacteria) / Gene: BPP4354, dsbA / Plasmid: BC-pSGX3 (BC) / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q7W2Q0 #2: 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: 298 K / Method: vapor diffusion, sitting drop / pH: 5.5 Details: 0.2M Lithium sulfate monohydrate, 0.1M Bis-Tris, 25% Polyethylene glycol 3,350., pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 298.0K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 0.979 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 29, 2009 / Details: MIRRORS |
Radiation | Monochromator: Si(III) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 2.35→36.71 Å / Num. all: 53663 / Num. obs: 53663 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 13.5 % / Biso Wilson estimate: 24.1 Å2 / Rmerge(I) obs: 0.123 / Net I/σ(I): 8 |
Reflection shell | Resolution: 2.35→2.43 Å / Redundancy: 13.8 % / Rmerge(I) obs: 0.524 / Mean I/σ(I) obs: 3 / Num. unique all: 5342 / % possible all: 99.9 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 2.35→36.71 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 56725.4 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 26.5054 Å2 / ksol: 0.342284 e/Å3 | |||||||||||||||||||||||||
Displacement parameters | Biso mean: 32.1 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.35→36.71 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.35→2.5 Å / Rfactor Rfree error: 0.019 / Total num. of bins used: 6
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Xplor file |
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