- PDB-1yq4: Avian respiratory complex ii with 3-nitropropionate and ubiquinone -
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Open data
ID or keywords:
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Basic information
Entry
Database: PDB / ID: 1yq4
Title
Avian respiratory complex ii with 3-nitropropionate and ubiquinone
Components
(SUCCINATE DEHYDROGENASE CYTOCHROME B, ...) x 2
Succinate dehydrogenase flavoprotein subunit
succinate dehydrogenase Ip subunit
Keywords
OXIDOREDUCTASE / COMPLEX II / MEMBRANE PROTEIN / HEME PROTEIN / IRON SULFUR PROTEIN / CYTOCHROME B / REDOX ENZYME / RESPIRATORY CHAIN / OXALOACETATE NITROPROPIONATE UBIQUINONE
Function / homology
Function and homology information
The tricarboxylic acid cycle / succinate metabolic process / TIM22 mitochondrial import inner membrane insertion complex / : / mitochondrial electron transport, succinate to ubiquinone / succinate dehydrogenase / succinate dehydrogenase (quinone) activity / protein insertion into mitochondrial inner membrane / oxidoreductase activity, acting on the CH-CH group of donors / anaerobic respiration ...The tricarboxylic acid cycle / succinate metabolic process / TIM22 mitochondrial import inner membrane insertion complex / : / mitochondrial electron transport, succinate to ubiquinone / succinate dehydrogenase / succinate dehydrogenase (quinone) activity / protein insertion into mitochondrial inner membrane / oxidoreductase activity, acting on the CH-CH group of donors / anaerobic respiration / 3 iron, 4 sulfur cluster binding / protein transmembrane transporter activity / ubiquinone binding / tricarboxylic acid cycle / aerobic respiration / respiratory electron transport chain / mitochondrial membrane / 2 iron, 2 sulfur cluster binding / flavin adenine dinucleotide binding / 4 iron, 4 sulfur cluster binding / mitochondrial inner membrane / electron transfer activity / heme binding / metal ion binding / plasma membrane Similarity search - Function
HETEROGEN 3NP LIGAND HAS REACTED WITH ARG AND LOST TWO OXYGENS.
Remark 999
SEQUENCE SEQUENCE 1-71 OF SUCCINATE DEHYDROGENASE FP SUBUNIT DO NOT MATCH TO ANY OF THE DATABASE ...SEQUENCE SEQUENCE 1-71 OF SUCCINATE DEHYDROGENASE FP SUBUNIT DO NOT MATCH TO ANY OF THE DATABASE SEQUENCE. THE SEQUENCE OF SUCCINATE DEHYDROGENASE CYTOCHROME B, LARGE SUBUNIT IS NOT AVAILABLE IN ANY OF THE DATABASE SEQUENCE AT THE TIME OF PROCESSING.
Mass: 18.015 Da / Num. of mol.: 575 / Source method: isolated from a natural source / Formula: H2O
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Experimental details
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Experiment
Experiment
Method: X-RAY DIFFRACTION / Number of used crystals: 1
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Sample preparation
Crystal
Density Matthews: 3.49 Å3/Da / Density % sol: 63.8 % Description: LOW COMPLETENESS IN OUTER SHELLS IS DUE TO DETECTOR GEOMETRY WHICH WAS A COMPROMISE BETWEEN RESOLVING SPOTS AND COLLECTING HIGH RESOLUTION DATA. NO REFLECTION WHICH FELL ON DETECTOR SURFACE WAS EXCLUDED.
Crystal grow
Temperature: 278 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 50 G/L PEG-3350, 25 ML/L ISOPROPANOL,15 ML/L PEG-400 0.05 M NA-HEPES, 0.01 M TRIS-HCL, 0.0016 M MNCL2, 0.0013 M MGCL2, 0.0015 M NA-AZIDE, 0.00025 M NA-EDTA, 3-NITROPROPIONATE, pH 7.50, VAPOR ...Details: 50 G/L PEG-3350, 25 ML/L ISOPROPANOL,15 ML/L PEG-400 0.05 M NA-HEPES, 0.01 M TRIS-HCL, 0.0016 M MNCL2, 0.0013 M MGCL2, 0.0015 M NA-AZIDE, 0.00025 M NA-EDTA, 3-NITROPROPIONATE, pH 7.50, VAPOR DIFFUSION, SITTING DROP, temperature 278K
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Data collection
Diffraction
Mean temperature: 100 K
Diffraction source
Source: SYNCHROTRON / Site: ALS / Beamline: 5.0.3 / Wavelength: 1 / Wavelength: 1 Å
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