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Yorodumi- PDB-5map: X-ray generated oxyferrous complex of DtpA from Streptomyces lividans -
+Open data
-Basic information
Entry | Database: PDB / ID: 5map | ||||||
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Title | X-ray generated oxyferrous complex of DtpA from Streptomyces lividans | ||||||
Components | DtpA | ||||||
Keywords | OXIDOREDUCTASE / peroxidase radiolysis oxygen dye-type | ||||||
Function / homology | Function and homology information iron import into cell / Oxidoreductases; Acting on a peroxide as acceptor; Peroxidases / peroxidase activity / heme binding / metal ion binding Similarity search - Function | ||||||
Biological species | Streptomyces lividans TK24 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.49 Å | ||||||
Authors | Moreno Chicano, T. / Chaplin, A.K. / Worrall, J.A.R. / Strange, R.W. / Hough, M.A. | ||||||
Funding support | United Kingdom, 1items
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Citation | Journal: IUCrJ / Year: 2017 Title: Photoreduction and validation of haem-ligand intermediate states in protein crystals by in situ single-crystal spectroscopy and diffraction. Authors: Kekilli, D. / Moreno-Chicano, T. / Chaplin, A.K. / Horrell, S. / Dworkowski, F.S.N. / Worrall, J.A.R. / Strange, R.W. / Hough, M.A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5map.cif.gz | 167.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5map.ent.gz | 130.4 KB | Display | PDB format |
PDBx/mmJSON format | 5map.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5map_validation.pdf.gz | 1.1 MB | Display | wwPDB validaton report |
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Full document | 5map_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | 5map_validation.xml.gz | 34.4 KB | Display | |
Data in CIF | 5map_validation.cif.gz | 51.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ma/5map ftp://data.pdbj.org/pub/pdb/validation_reports/ma/5map | HTTPS FTP |
-Related structure data
Related structure data | 5mjhC 4grcS S: Starting model for refinement C: citing same article (ref.) |
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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: 40524.270 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Streptomyces lividans TK24 (bacteria) / Gene: SLIV_18505 / Plasmid: pET28a / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A076MAJ9 #2: Chemical | #3: Chemical | #4: 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: 2.05 Å3/Da / Density % sol: 40.01 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 5.5 Details: Crystals were grown by the vapour diffusion hanging drop method using a ferric protein solution at 13 mg/ml equilibrated against a reservoir consisting of 17-24% PEG 3000 and 50-100 mM sodium citrate, pH 5.5. |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: BM30A / Wavelength: 0.98 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 2, 2015 / Details: mirrors |
Radiation | Monochromator: Si (111) Double Crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 |
Reflection | Resolution: 1.49→40 Å / Num. obs: 103431 / % possible obs: 98.3 % / Redundancy: 2.9 % / CC1/2: 0.993 / Rmerge(I) obs: 0.11 / Net I/σ(I): 8 |
Reflection shell | Resolution: 1.49→1.52 Å / Redundancy: 3 % / Rmerge(I) obs: 0.912 / Num. measured obs: 7839 / CC1/2: 0.509 / % possible all: 99.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4GRC Resolution: 1.49→40 Å / SU B: 2.326 / SU ML: 0.086 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.098 / ESU R Free: 0.098 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING
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Displacement parameters | Biso mean: 13.21 Å2
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Refinement step | Cycle: 1 / Resolution: 1.49→40 Å
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LS refinement shell | Highest resolution: 1.49 Å / Rfactor Rfree: 0.293 / Rfactor Rwork: 0.279 |