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Yorodumi- PDB-4wfw: The crystal structure of Dickeya dadantii GspB from the type 2 se... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4wfw | |||||||||
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Title | The crystal structure of Dickeya dadantii GspB from the type 2 secretion system | |||||||||
Components | General secretion pathway protein B | |||||||||
Keywords | STRUCTURAL PROTEIN / Type 2 Secretion System / GspB | |||||||||
Function / homology | Type II secretion system protein GspB / Type II secretion system protein B / type II protein secretion system complex / protein processing / plasma membrane / General secretion pathway protein B Function and homology information | |||||||||
Biological species | Dickeya dadantii (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.05 Å | |||||||||
Authors | Rycroft, P.B. / Pickersgill, R.W. / Shevchik, V.E. | |||||||||
Funding support | United Kingdom, 1items
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Citation | Journal: To Be Published Title: The crystal structure of Dickeya dadantii GspB from the type 2 secretion system Authors: Rycroft, P.B. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4wfw.cif.gz | 47.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4wfw.ent.gz | 33.7 KB | Display | PDB format |
PDBx/mmJSON format | 4wfw.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4wfw_validation.pdf.gz | 424.6 KB | Display | wwPDB validaton report |
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Full document | 4wfw_full_validation.pdf.gz | 424.7 KB | Display | |
Data in XML | 4wfw_validation.xml.gz | 5.4 KB | Display | |
Data in CIF | 4wfw_validation.cif.gz | 6.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wf/4wfw ftp://data.pdbj.org/pub/pdb/validation_reports/wf/4wfw | HTTPS FTP |
-Related structure data
Related structure data | 3ossS S: Starting model for refinement |
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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: 9921.942 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Dickeya dadantii (strain 3937) (bacteria) Strain: 3937 / Gene: outB, Dda3937_02412 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q01563 |
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#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.17 Å3/Da / Density % sol: 43.28 % |
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Crystal grow | Temperature: 291.15 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: initial hit from nano drop. Scaled up using whisker streak seeding. 0.2M MgCl, 0.1M Tris, 30% w/v PEG4000, pH8.5 PH range: 8.4-8.6 / Temp details: Air Conditioned room |
-Data collection
Diffraction | Mean temperature: 100 K / Ambient temp details: Cryostream |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 1 Å |
Detector | Type: PSI PILATUS 6M / Detector: PIXEL / Date: Aug 9, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.02→36.03 Å / Num. obs: 6380 / % possible obs: 99.2 % / Redundancy: 8.9 % / Net I/σ(I): 30.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3oss Resolution: 2.05→34.91 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.948 / SU B: 11.881 / SU ML: 0.154 / Cross valid method: THROUGHOUT / ESU R: 0.231 / ESU R Free: 0.196 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.9 Å / Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 55.749 Å2
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Refinement step | Cycle: LAST / Resolution: 2.05→34.91 Å
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Refine LS restraints |
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