+Open data
-Basic information
Entry | Database: PDB / ID: 1lj1 | |||||||||
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Title | Crystal structure of Q363F/R402A mutant flavocytochrome c3 | |||||||||
Components | flavocytochrome c3 | |||||||||
Keywords | OXIDOREDUCTASE / flavocytochrome / fumarate reductase | |||||||||
Function / homology | Function and homology information fumarate reductase (cytochrome) / fumarate reductase (quinol) / : / anaerobic electron transport chain / succinate dehydrogenase (quinone) activity / anaerobic respiration / steroid metabolic process / FMN binding / outer membrane-bounded periplasmic space / periplasmic space ...fumarate reductase (cytochrome) / fumarate reductase (quinol) / : / anaerobic electron transport chain / succinate dehydrogenase (quinone) activity / anaerobic respiration / steroid metabolic process / FMN binding / outer membrane-bounded periplasmic space / periplasmic space / electron transfer activity / metal ion binding Similarity search - Function | |||||||||
Biological species | Shewanella frigidimarina (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å | |||||||||
Authors | Mowat, C.G. / Pankhurst, K.L. / Miles, C.S. / Leys, D. / Walkinshaw, M.D. / Reid, G.A. / Chapman, S.K. | |||||||||
Citation | Journal: Biochemistry / Year: 2002 Title: Engineering Water to act as the active site acid catalyst in a soluble fumarate reductase Authors: Mowat, C.G. / Pankhurst, K.L. / Miles, C.S. / Leys, D. / Walkinshaw, M.D. / Reid, G.A. / Chapman, S.K. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1lj1.cif.gz | 276.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1lj1.ent.gz | 216.3 KB | Display | PDB format |
PDBx/mmJSON format | 1lj1.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1lj1_validation.pdf.gz | 1.1 MB | Display | wwPDB validaton report |
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Full document | 1lj1_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | 1lj1_validation.xml.gz | 29.3 KB | Display | |
Data in CIF | 1lj1_validation.cif.gz | 50.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/lj/1lj1 ftp://data.pdbj.org/pub/pdb/validation_reports/lj/1lj1 | HTTPS FTP |
-Related structure data
Related structure data | 1m64C 1qjdS 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
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 60560.164 Da / Num. of mol.: 2 / Mutation: Q363F, R402A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Shewanella frigidimarina (bacteria) / Gene: fcc / Plasmid: pMMB503EH / Production host: Shewanella frigidimarina (bacteria) / Strain (production host): EG301 References: UniProt: Q02469, UniProt: P0C278*PLUS, succinate dehydrogenase |
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-Non-polymers , 5 types, 1644 molecules
#2: Chemical | #3: Chemical | ChemComp-HEM / #4: Chemical | #5: Chemical | #6: 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: 2.36 Å3/Da / Density % sol: 47.45 % | |||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: TrisHCl, PEG8000, sodium chloride, sodium fumarate, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K | |||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 4 ℃ / pH: 8.5 | |||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: BW7B / Wavelength: 0.8459 Å |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Sep 7, 2001 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.8459 Å / Relative weight: 1 |
Reflection | Resolution: 2→20 Å / Num. all: 75611 / Num. obs: 75611 / % possible obs: 94.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 18 Å2 / Rmerge(I) obs: 0.072 / Net I/σ(I): 9.2 |
Reflection shell | Resolution: 2→2.07 Å / Rmerge(I) obs: 0.226 / Mean I/σ(I) obs: 2.49 / Num. unique all: 7365 / % possible all: 92.8 |
Reflection | *PLUS Lowest resolution: 15 Å / Num. measured all: 412535 / Rmerge(I) obs: 0.072 |
Reflection shell | *PLUS Rmerge(I) obs: 0.226 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1QJD Resolution: 2→15 Å / SU B: 4.33382 / SU ML: 0.12065 / Cross valid method: R Free / σ(F): 0 / σ(I): 0 / ESU R: 0.19419 / ESU R Free: 0.1826 / Stereochemistry target values: Engh & Huber
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Displacement parameters | Biso mean: 18 Å2 | ||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2→15 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2→2.07 Å
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Refinement | *PLUS Highest resolution: 2 Å / Lowest resolution: 15 Å / % reflection Rfree: 5 % / Rfactor Rfree: 0.2347 / Rfactor Rwork: 0.1608 | ||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor Rfree: 0.263 / Rfactor Rwork: 0.184 |