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Yorodumi- PDB-2ji2: X-ray structure of E114A mutant of superoxide reductase from Desu... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2ji2 | ||||||
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Title | X-ray structure of E114A mutant of superoxide reductase from Desulfoarculus baarsii in the native, reduced form | ||||||
Components | Desulfoferrodoxin | ||||||
Keywords | OXIDOREDUCTASE / RAMAN SPECTROSCOPY / SUPEROXIDE REDUCTASE / INTERMEDIATE TRAPPING / MICROSPECTROPHOTOMETRY / DETOXIFICATION / ELECTRON TRANSPORT / IRON / TRANSPORT / REDOX STATES / METAL-BINDING | ||||||
Function / homology | Function and homology information superoxide reductase / superoxide reductase activity / removal of superoxide radicals / iron ion binding Similarity search - Function | ||||||
Biological species | Desulfarculus baarsii (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å | ||||||
Authors | Katona, G. / Carpentier, P. / Niviere, V. / Amara, P. / Adam, V. / Ohana, J. / Tsanov, N. / Bourgeois, D. | ||||||
Citation | Journal: Science / Year: 2007 Title: Raman-assisted crystallography reveals end-on peroxide intermediates in a nonheme iron enzyme. Authors: Katona, G. / Carpentier, P. / Niviere, V. / Amara, P. / Adam, V. / Ohana, J. / Tsanov, N. / Bourgeois, D. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2ji2.cif.gz | 127 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2ji2.ent.gz | 98.2 KB | Display | PDB format |
PDBx/mmJSON format | 2ji2.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ji/2ji2 ftp://data.pdbj.org/pub/pdb/validation_reports/ji/2ji2 | HTTPS FTP |
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-Related structure data
Related structure data | 2ji1C 2ji3C 1vziS 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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2 |
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Unit cell |
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Components on special symmetry positions |
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Noncrystallographic symmetry (NCS) | NCS oper:
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-Components
-Protein , 1 types, 4 molecules ABCD
#1: Protein | Mass: 14118.362 Da / Num. of mol.: 4 / Mutation: E114A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Desulfarculus baarsii (bacteria) / Gene: dfx, rbo, Deba_2050 / Plasmid: PMLE47A / Production host: Escherichia coli DH5[alpha] (bacteria) / References: UniProt: Q46495, superoxide reductase |
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-Non-polymers , 5 types, 584 molecules
#2: Chemical | ChemComp-FE / #3: Chemical | ChemComp-NO3 / #4: Chemical | ChemComp-FE2 / #5: Chemical | ChemComp-CA / #6: Water | ChemComp-HOH / | |
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-Details
Compound details | ENGINEERED RESIDUE IN CHAIN A, GLU 113 TO ALA ENGINEERED RESIDUE IN CHAIN B, GLU 113 TO ALA ...ENGINEERED |
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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: 2.6 Å3/Da / Density % sol: 52.9 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 9 Details: 16% PEG 4000, 100 MM TRIS/HNO3 PH9.0, 0.2 M CA(NO3)2 AND 25MG/ML PROTEIN MIXED 1:1 HANGING DROP VAPOUR DIFFUSION, 20 C, pH 9.00 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.979 |
Detector | Type: ADSC CCD / Detector: CCD / Date: May 12, 2005 / Details: MIRRORS |
Radiation | Monochromator: SI(311) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 1.7→47.4 Å / Num. obs: 62357 / % possible obs: 95.4 % / Observed criterion σ(I): -3 / Redundancy: 4.2 % / Biso Wilson estimate: 21.3 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 10.1 |
Reflection shell | Resolution: 1.7→1.8 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.34 / Mean I/σ(I) obs: 4 / % possible all: 82.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1VZI Resolution: 1.7→47.4 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 3796608.16 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: MAXIMUM LIKELIHOOD AMPLITUDE
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 54.5748 Å2 / ksol: 0.367168 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 24.8 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.7→47.4 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.7→1.81 Å / Rfactor Rfree error: 0.013 / Total num. of bins used: 6
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Xplor file |
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