+Open data
-Basic information
Entry | Database: PDB / ID: 6ku6 | ||||||
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Title | OSM1 mutant - R326A | ||||||
Components | Fumarate reductase 2 | ||||||
Keywords | OXIDOREDUCTASE / Fumarase reductase mutant R326A | ||||||
Function / homology | Function and homology information fumarate reductase (NADH) / fumarate reductase (NADH) activity / FAD metabolic process / protein folding in endoplasmic reticulum / FMN binding / endoplasmic reticulum / mitochondrion Similarity search - Function | ||||||
Biological species | Saccharomyces cerevisiae (brewer's yeast) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.007 Å | ||||||
Authors | Park, H.H. / Kim, C.M. | ||||||
Funding support | Korea, Republic Of, 1items
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Citation | Journal: Crystals / Year: 2019 Title: Crystal Structure of the Active Site Mutant Form of Soluble Fumarate Reductase, Osm1 Authors: Kim, C.M. / Kwon, S. / Jung, K.H. / Park, H.H. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6ku6.cif.gz | 203.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6ku6.ent.gz | 166.7 KB | Display | PDB format |
PDBx/mmJSON format | 6ku6.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6ku6_validation.pdf.gz | 970.2 KB | Display | wwPDB validaton report |
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Full document | 6ku6_full_validation.pdf.gz | 985.1 KB | Display | |
Data in XML | 6ku6_validation.xml.gz | 42.4 KB | Display | |
Data in CIF | 6ku6_validation.cif.gz | 61.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ku/6ku6 ftp://data.pdbj.org/pub/pdb/validation_reports/ku/6ku6 | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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2 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments:
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-Components
#1: Protein | Mass: 51509.559 Da / Num. of mol.: 2 / Mutation: R326A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) Strain: ATCC 204508 / S288c / Gene: OSM1, YJR051W, J1659 / Production host: Escherichia coli (E. coli) / References: UniProt: P21375, fumarate reductase (NADH) #2: Chemical | #3: Chemical | #4: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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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: 2.11 Å3/Da / Density % sol: 41.8 % |
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Crystal grow | Temperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 5.5 / Details: PEG 3350, BIS TRIS pH 5.5 |
-Data collection
Diffraction | Mean temperature: 104.15 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: PAL/PLS / Beamline: 5C (4A) / Wavelength: 0.9795 Å |
Detector | Type: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Jun 13, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 |
Reflection | Resolution: 2.007→38.145 Å / Num. obs: 56568 / % possible obs: 99.9 % / Redundancy: 6.5 % / Rsym value: 0.156 / Net I/σ(I): 15.0625 |
Reflection shell | Resolution: 2.007→2.03 Å / Num. unique obs: 639 / Rsym value: 0.491 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.007→38.145 Å / SU ML: 0.24 / Cross valid method: THROUGHOUT / σ(F): 1.38 / Phase error: 30.53
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 58.83 Å2 / Biso mean: 24.3615 Å2 / Biso min: 9.89 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.007→38.145 Å
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Refine LS restraints NCS |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0
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