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- PDB-6i6g: Dehaloperoxidase B from Amphitrite ornata - complex with 5-bromoindole -
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Open data
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Basic information
Entry | Database: PDB / ID: 6i6g | ||||||
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Title | Dehaloperoxidase B from Amphitrite ornata - complex with 5-bromoindole | ||||||
![]() | Dehaloperoxidase B | ||||||
![]() | OXIDOREDUCTASE / 5-bromoindole / Peroxidase / Globin | ||||||
Function / homology | ![]() oxygen carrier activity / oxygen binding / peroxidase activity / heme binding / metal ion binding Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Moreno-Chicano, T. / Ebrahim, A.E. / Worrall, J.A.R. / Strange, R.W. / Axford, D. / Sherrell, D.A. / Sugimoto, H. / Tono, K. / Owada, S. / Duyvesteyn, H. | ||||||
![]() | ![]() Title: High-throughput structures of protein-ligand complexes at room temperature using serial femtosecond crystallography. Authors: Moreno-Chicano, T. / Ebrahim, A. / Axford, D. / Appleby, M.V. / Beale, J.H. / Chaplin, A.K. / Duyvesteyn, H.M.E. / Ghiladi, R.A. / Owada, S. / Sherrell, D.A. / Strange, R.W. / Sugimoto, H. / ...Authors: Moreno-Chicano, T. / Ebrahim, A. / Axford, D. / Appleby, M.V. / Beale, J.H. / Chaplin, A.K. / Duyvesteyn, H.M.E. / Ghiladi, R.A. / Owada, S. / Sherrell, D.A. / Strange, R.W. / Sugimoto, H. / Tono, K. / Worrall, J.A.R. / Owen, R.L. / Hough, M.A. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 118.3 KB | Display | ![]() |
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PDB format | ![]() | 92.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.1 MB | Display | ![]() |
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Full document | ![]() | 1.1 MB | Display | |
Data in XML | ![]() | 13.9 KB | Display | |
Data in CIF | ![]() | 18.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6i7cC ![]() 6i7fC ![]() 6qwgC ![]() 3ixfS S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 |
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Unit cell |
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Components
#1: Protein | Mass: 15414.462 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #2: Chemical | #3: Chemical | #4: Chemical | #5: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.29 Å3/Da / Density % sol: 46.29 % / Description: Microcrystals |
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Crystal grow | Temperature: 277 K / Method: batch mode / pH: 6 Details: 5.5 mg/ml DHP-B in 20 mM MES pH 6.0 mixed with 35% PEG 4000, 200mM AmSO4 at a ratio of 1:4 in a total volume of 250 microlitres |
-Data collection
Diffraction | Mean temperature: 301 K / Serial crystal experiment: Y |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MPCCD / Detector: CCD / Date: Oct 11, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.24 Å / Relative weight: 1 |
Reflection | Resolution: 1.85→45.631 Å / Num. obs: 24840 / % possible obs: 100 % / Redundancy: 908 % / CC1/2: 1 / R split: 0.055 / Net I/σ(I): 12 |
Reflection shell | Resolution: 1.85→1.9 Å / Mean I/σ(I) obs: 1.56 / CC1/2: 0.65 / R split: 0.66 / % possible all: 100 |
Serial crystallography measurement | Collection time total: 80 hours / Focal spot size: 1.66 µm2 / Pulse duration: 10 fsec. / Pulse energy: 289 µJ / Pulse photon energy: 10.01 keV / XFEL pulse repetition rate: 30 Hz |
Serial crystallography sample delivery | Description: Silicon nitride fixed target / Method: fixed target |
Serial crystallography sample delivery fixed target | Sample dehydration prevention: Mylar film / Sample solvent: Mother liquor |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 3ixf Resolution: 1.85→45.631 Å / SU ML: 0.25 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 18.38
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 114.09 Å2 / Biso mean: 44.1014 Å2 / Biso min: 27.29 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.85→45.631 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 9 / % reflection obs: 100 %
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