+Open data
-Basic information
Entry | Database: PDB / ID: 4d7l | ||||||
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Title | Methionine sulfoxide reductase A of Corynebacterium diphtheriae | ||||||
Components | PEPTIDE METHIONINE SULFOXIDE REDUCTASE MSRA | ||||||
Keywords | OXIDOREDUCTASE / THIOL DISULFIDE EXCHANGE | ||||||
Function / homology | Function and homology information peptide-methionine (S)-S-oxide reductase / peptide-methionine (S)-S-oxide reductase activity / protein modification process => GO:0036211 Similarity search - Function | ||||||
Biological species | CORYNEBACTERIUM DIPHTHERIAE NCTC 13129 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.895 Å | ||||||
Authors | Van Molle, I. / Tossounian, M.A. / Pedre, B. / Wahni, K. / Vertommen, D. / Messens, J. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2015 Title: Corynebacterium Diphtheriae Methionine Sulfoxide Reductase a Exploits a Unique Mycothiol Redox Relay Mechanism. Authors: Tossounian, M. / Pedre, B. / Wahni, K. / Erdogan, H. / Vertommen, D. / Van Molle, I. / Messens, J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4d7l.cif.gz | 276.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4d7l.ent.gz | 222.9 KB | Display | PDB format |
PDBx/mmJSON format | 4d7l.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/d7/4d7l ftp://data.pdbj.org/pub/pdb/validation_reports/d7/4d7l | HTTPS FTP |
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-Related structure data
Related structure data | 1ff3S S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 26145.139 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) CORYNEBACTERIUM DIPHTHERIAE NCTC 13129 (bacteria) Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): ROSETTA / References: UniProt: Q6NEL2 #2: Chemical | #3: Chemical | ChemComp-SO4 / #4: Chemical | ChemComp-PGE / #5: Water | ChemComp-HOH / | Sequence details | THE MSRA GENE WAS CLONED IN THE PET28A VECTOR, WITH A N- TERMINAL HIS-TAG AND A THROMBIN CLEAVAGE ...THE MSRA GENE WAS CLONED IN THE PET28A VECTOR, WITH A N- TERMINAL HIS-TAG AND A THROMBIN CLEAVAGE SITE, RESULTING IN THE FOLLOWING ADDITIONAL | |
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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: 2.73 Å3/Da / Density % sol: 54.94 % / Description: NONE |
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Crystal grow | pH: 7 Details: 0.1 M NA CACODYLATE PH 7.0, 0.35 M AMMONIUM SULFATE, 16% PEG8000 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.97857 |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 18, 2014 Details: KIRKPATRICK-BAEZ PAIR OF BI-MORPH MIRRORS PLUS CHANNEL CUT CRYOGENICALLY COOLED MONOCHROMATOR CRYSTAL |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97857 Å / Relative weight: 1 |
Reflection | Resolution: 1.89→50 Å / Num. obs: 67677 / % possible obs: 99.7 % / Observed criterion σ(I): 3 / Redundancy: 8.85 % / Rmerge(I) obs: 0.15 / Net I/σ(I): 11.79 |
Reflection shell | Resolution: 1.89→2.01 Å / Redundancy: 8.5 % / Rmerge(I) obs: 0.9 / Mean I/σ(I) obs: 2.27 / % possible all: 98.1 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1FF3 Resolution: 1.895→41.291 Å / SU ML: 0.19 / σ(F): 1.35 / Phase error: 18.49 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.895→41.291 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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