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Open data
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Basic information
Entry | Database: PDB / ID: 2h89 | |||||||||
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Title | Avian Respiratory Complex II with Malonate Bound | |||||||||
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![]() | OXIDOREDUCTASE / COMPLEX II / MEMBRANE PROTEIN / HEME PROTEIN / IRON SULFUR PROTEIN / CYTOCHROME B / REDOX ENZYME / RESPIRATORY CHAIN / MALONATE / UBIQUINONE | |||||||||
Function / homology | ![]() 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 | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | ![]() ![]() | |||||||||
![]() | Huang, L.S. / Shen, J.T. / Wang, A.C. / Berry, E.A. | |||||||||
![]() | ![]() Title: Crystallographic studies of the binding of ligands to the dicarboxylate site of Complex II, and the identity of the ligand in the Authors: Huang, L.S. / Shen, J.T. / Wang, A.C. / Berry, E.A. #1: ![]() Title: 3-nitropropionic acid is a suicide inhibitor of mitochondrial respiration that, upon oxidation by complex II, forms a covalent adduct with a catalytic base arginine in the active site of the enzyme. Authors: Huang, L.S. / Sun, G. / Cobessi, D. / Wang, A.C. / Shen, J.T. / Tung, E.Y. / Anderson, V.E. / Berry, E.A. #2: ![]() Title: Crystallization of mitochondrial respiratory complex II from chicken heart: a membrane-protein complex diffracting to 2.0 A Authors: Huang, L.S. / Borders, T.M. / Shen, J.T. / Wang, C.J. / Berry, E.A. #3: ![]() Title: Crystal structure of mitochondrial respiratory membrane protein complex II. Authors: Sun, F. / Huo, X. / Zhai, Y. / Wang, A. / Xu, J. / Su, D. / Bartlam, M. / Rao, Z. | |||||||||
History |
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Remark 999 | SEQUENCE SEQUENCE 1-71 OF SUCCINATE DEHYDROGENASE FP SUBUNIT DOES NOT MATCH TO ANY SEQUENCE IN THE ...SEQUENCE SEQUENCE 1-71 OF SUCCINATE DEHYDROGENASE FP SUBUNIT DOES NOT MATCH TO ANY SEQUENCE IN THE DATABASE. THE SEQUENCE OF SUCCINATE DEHYDROGENASE CYTOCHROME B, LARGE SUBUNIT IS NOT AVAILABLE IN ANY OF THE DATABASE SEQUENCES AT THE TIME OF PROCESSING. |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 255.2 KB | Display | ![]() |
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PDB format | ![]() | 196.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.6 MB | Display | ![]() |
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Full document | ![]() | 1.7 MB | Display | |
Data in XML | ![]() | 53.1 KB | Display | |
Data in CIF | ![]() | 74.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2h88C ![]() 1yq3S S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
-Protein , 2 types, 2 molecules AB
#1: Protein | Mass: 68256.922 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
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#2: Protein | Mass: 28685.221 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
-SUCCINATE DEHYDROGENASE CYTOCHROME B, ... , 2 types, 2 molecules CD
#3: Protein | Mass: 15392.052 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
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#4: Protein | Mass: 10971.604 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
-Sugars , 1 types, 1 molecules ![](data/chem/img/BHG.gif)
#12: Sugar | ChemComp-BHG / |
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-Non-polymers , 10 types, 630 molecules ![](data/chem/img/K.gif)
![](data/chem/img/FAD.gif)
![](data/chem/img/MLI.gif)
![](data/chem/img/FES.gif)
![](data/chem/img/SF4.gif)
![](data/chem/img/F3S.gif)
![](data/chem/img/HEM.gif)
![](data/chem/img/PEE.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/FAD.gif)
![](data/chem/img/MLI.gif)
![](data/chem/img/FES.gif)
![](data/chem/img/SF4.gif)
![](data/chem/img/F3S.gif)
![](data/chem/img/HEM.gif)
![](data/chem/img/PEE.gif)
![](data/chem/img/HOH.gif)
#5: Chemical | #6: Chemical | ChemComp-FAD / | #7: Chemical | ChemComp-MLI / | #8: Chemical | ChemComp-UNL / Num. of mol.: 40 / Source method: obtained synthetically #9: Chemical | ChemComp-FES / | #10: Chemical | ChemComp-SF4 / | #11: Chemical | ChemComp-F3S / | #13: Chemical | ChemComp-HEM / | #14: Chemical | #15: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.51 Å3/Da / Density % sol: 64.99 % |
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Crystal grow | Temperature: 277 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, 0.0005 M MALONATE, 0.0005 M MNCL2, 0.0013 M MGCL2, 0.0015 M NA-AZIDE, 0.00025 M NA-EDTA., 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, 0.0005 M MALONATE, 0.0005 M MNCL2, 0.0013 M MGCL2, 0.0015 M NA-AZIDE, 0.00025 M NA-EDTA., pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 25, 2004 |
Radiation | Monochromator: Double-crystal, Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.1 Å / Relative weight: 1 |
Reflection | Resolution: 2.29→60 Å / Num. all: 63148 / Num. obs: 63148 / % possible obs: 78.6 % / Observed criterion σ(F): -999 / Observed criterion σ(I): -3 / Redundancy: 2.4 % / Biso Wilson estimate: 52.7 Å2 / Rsym value: 0.158 / Net I/σ(I): 7 |
Reflection shell | Resolution: 2.29→2.33 Å / Redundancy: 1.5 % / Mean I/σ(I) obs: 1.2 / Num. unique all: 724 / Rsym value: 0.545 / % possible all: 18.5 |
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Processing
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Refinement | Method to determine structure: rigid body refinement of previous Starting model: 1YQ3 Resolution: 2.4→50.74 Å / Rfactor Rfree error: 0.005 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 60.4229 Å2 / ksol: 0.257581 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 59.8 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.4→50.74 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.4→2.46 Å / Rfactor Rfree error: 0.037 / Total num. of bins used: 15
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