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Yorodumi- PDB-6yrc: Spectroscopically-validated structure of DtpB from Streptomyces l... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6yrc | ||||||
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Title | Spectroscopically-validated structure of DtpB from Streptomyces lividans in the ferric state | ||||||
Components | Putative iron-dependent peroxidase | ||||||
Keywords | OXIDOREDUCTASE / peroxidase / dye-decolourising / spectroscopically-validated / ferric | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Streptomyces lividans 1326 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.99 Å | ||||||
Authors | Lucic, M. / Dworkowski, F.S.N. / Worrall, J.A.R. / Hough, M.A. | ||||||
Funding support | United Kingdom, 1items
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Citation | Journal: Angew.Chem.Int.Ed.Engl. / Year: 2020 Title: Serial Femtosecond Zero Dose Crystallography Captures a Water-Free Distal Heme Site in a Dye-Decolorising Peroxidase to Reveal a Catalytic Role for an Arginine in Fe IV =O Formation. Authors: Lucic, M. / Svistunenko, D.A. / Wilson, M.T. / Chaplin, A.K. / Davy, B. / Ebrahim, A. / Axford, D. / Tosha, T. / Sugimoto, H. / Owada, S. / Dworkowski, F.S.N. / Tews, I. / Owen, R.L. / ...Authors: Lucic, M. / Svistunenko, D.A. / Wilson, M.T. / Chaplin, A.K. / Davy, B. / Ebrahim, A. / Axford, D. / Tosha, T. / Sugimoto, H. / Owada, S. / Dworkowski, F.S.N. / Tews, I. / Owen, R.L. / Hough, M.A. / Worrall, J.A.R. #1: Journal: Angew.Chem.Int.Ed.Engl. / Year: 2020 Title: Serial Femtosecond Zero Dose Crystallography Captures a Water-Free Distal Heme Site in a Dye-Decolorising Peroxidase to Reveal a Catalytic Role for an Arginine in FeIV=O Formation Authors: Lucic, M. / Svistunenko, D.A. / Wilson, M.T. / Chaplin, A.K. / Davy, B. / Ebrahim, A. / Axford, D. / Tosha, T. / Sugimoto, H. / Owada, S. / Dworkowski, F.S.N. / Tews, I. / Owen, R.L. / ...Authors: Lucic, M. / Svistunenko, D.A. / Wilson, M.T. / Chaplin, A.K. / Davy, B. / Ebrahim, A. / Axford, D. / Tosha, T. / Sugimoto, H. / Owada, S. / Dworkowski, F.S.N. / Tews, I. / Owen, R.L. / Hough, M.A. / Worrall, J.A.R. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6yrc.cif.gz | 384.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6yrc.ent.gz | 323 KB | Display | PDB format |
PDBx/mmJSON format | 6yrc.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/yr/6yrc ftp://data.pdbj.org/pub/pdb/validation_reports/yr/6yrc | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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3 |
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4 |
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5 |
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6 |
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Unit cell |
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-Components
-Protein , 1 types, 6 molecules ABCDEF
#1: Protein | Mass: 34172.223 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Streptomyces lividans 1326 (bacteria) / Gene: SAMN05428941_7146 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A1H2DDB9 |
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-Non-polymers , 5 types, 1172 molecules
#2: Chemical | ChemComp-HEM / #3: Chemical | ChemComp-7PE / #4: Chemical | ChemComp-MG / #5: Chemical | ChemComp-GOL / #6: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | N |
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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: 2.47 Å3/Da / Density % sol: 50.12 % / Description: microcrystals |
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Crystal grow | Temperature: 291 K / Method: batch mode / pH: 7.5 Details: 6-10 mg/mL of protein in 50mM Sodium acteate, 150mM NaCl pH 5 mixed with 100 mM MgCl2, 100 mM HEPES pH 7.5, 16% PEG 4000 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.8 Å |
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Aug 22, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.8 Å / Relative weight: 1 |
Reflection | Resolution: 1.99→49.05 Å / Num. obs: 138089 / % possible obs: 99.2 % / Redundancy: 6.9 % / Biso Wilson estimate: 28.2 Å2 / CC1/2: 0.971 / Rmerge(I) obs: 0.227 / Net I/σ(I): 7.5 |
Reflection shell | Resolution: 1.99→2.02 Å / Redundancy: 5 % / Rmerge(I) obs: 1.02 / Mean I/σ(I) obs: 2.1 / Num. unique obs: 32880 / CC1/2: 0.498 / % possible all: 97.1 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: SFX structure of ferric DtpB Resolution: 1.99→49.05 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.937 / SU B: 4.198 / SU ML: 0.116 / SU R Cruickshank DPI: 0.1699 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.17 / ESU R Free: 0.152 Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 95.89 Å2 / Biso mean: 30.279 Å2 / Biso min: 14.54 Å2
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Refinement step | Cycle: final / Resolution: 1.99→49.05 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.99→2.042 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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