+Open data
-Basic information
Entry | Database: PDB / ID: 2cly | ||||||
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Title | Subcomplex of the stator of bovine mitochondrial ATP synthase | ||||||
Components |
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Keywords | HYDROLASE / MITOCHONDRIA / MITOCHONDRION / ION TRANSPORT / CF(0) / STATOR / TRANSPORT / ACETYLATION / ATP SYNTHASE / HYDROGEN ION TRANSPORT / TRANSIT PEPTIDE / PERIPHERAL STALK | ||||||
Function / homology | Function and homology information Formation of ATP by chemiosmotic coupling / Cristae formation / mitochondrial proton-transporting ATP synthase, stator stalk / mitochondrial proton-transporting ATP synthase complex, coupling factor F(o) / mitochondrial proton-transporting ATP synthase complex / proton motive force-driven mitochondrial ATP synthesis / proton motive force-driven ATP synthesis / proton transmembrane transporter activity / proton-transporting ATP synthase activity, rotational mechanism Similarity search - Function | ||||||
Biological species | BOS TAURUS (cattle) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.8 Å | ||||||
Authors | Kane Dickson, V. / Silvester, J.A. / Fearnley, I.M. / Leslie, A.G.W. / Walker, J.E. | ||||||
Citation | Journal: Embo J. / Year: 2006 Title: On the Structure of the Stator of the Mitochondrial ATP Synthase. Authors: Kane Dickson, V. / Silvester, J.A. / Fearnley, I.M. / Leslie, A.G.W. / Walker, J.E. #1: Journal: Acta Crystallogr.,Sect.F / Year: 2006 Title: The Expression, Purification, Crystallization and Preliminary X-Ray Analysis of a Subcomplex of the Peripheral Stalk of ATP Synthase from Bovine Mitochondria Authors: Silvester, J.A. / Kane Dickson, V. / Runswick, M.J. / Leslie, A.G.W. / Walker, J.E. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2cly.cif.gz | 133.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2cly.ent.gz | 109.2 KB | Display | PDB format |
PDBx/mmJSON format | 2cly.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/cl/2cly ftp://data.pdbj.org/pub/pdb/validation_reports/cl/2cly | HTTPS FTP |
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-Related structure data
Related structure data | |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments:
NCS ensembles :
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-Components
#1: Protein | Mass: 24702.709 Da / Num. of mol.: 2 / Fragment: STATOR SUBCOMPLEX Source method: isolated from a genetically manipulated source Source: (gene. exp.) BOS TAURUS (cattle) / Organ: HEART / Plasmid: PET / Production host: ESCHERICHIA COLI BL21(DE3) (bacteria) / Variant (production host): C41 References: UniProt: P13619, H+-transporting two-sector ATPase #2: Protein | Mass: 18588.256 Da / Num. of mol.: 2 / Fragment: STATOR SUBCOMPLEX Source method: isolated from a genetically manipulated source Source: (gene. exp.) BOS TAURUS (cattle) / Organ: HEART / Plasmid: PET / Production host: ESCHERICHIA COLI BL21(DE3) (bacteria) / Variant (production host): C41 References: UniProt: P13620, H+-transporting two-sector ATPase #3: Protein | Mass: 9118.253 Da / Num. of mol.: 2 / Fragment: STATOR SUBCOMPLEX Source method: isolated from a genetically manipulated source Source: (gene. exp.) BOS TAURUS (cattle) / Organ: HEART / Plasmid: PET / Production host: ESCHERICHIA COLI BL21(DE3) (bacteria) / Variant (production host): C41 References: UniProt: P02721, H+-transporting two-sector ATPase #4: Water | ChemComp-HOH / | Sequence details | RESIDUES 79-183 ONLY NO PRESEQUENC | |
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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: 3.2 Å3/Da / Density % sol: 61.5 % Description: SE MET STRUCTURE SOLVED USING SHARP. NATIVE STRUCTURE WHICH HAD A DIFFERENT UNIT CELL WAS SOLVED USING PHASER AND PARTIAL SEMET MODEL. |
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Crystal grow | pH: 8 Details: 100 MM TRIS, 150 MM NACL, 17% PEG 5K MME, 7.5% GLYCEROL, 1% PICOLINE, pH 8.00 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 1.771 |
Detector | Type: ADSC CCD / Detector: CCD / Date: May 5, 2005 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.771 Å / Relative weight: 1 |
Reflection | Resolution: 2.8→65 Å / Num. obs: 21257 / % possible obs: 94.1 % / Observed criterion σ(I): 2 / Redundancy: 11 % / Biso Wilson estimate: 94.95 Å2 / Rmerge(I) obs: 0.1 / Net I/σ(I): 19.7 |
Reflection shell | Resolution: 2.8→2.95 Å / Redundancy: 9.6 % / Rmerge(I) obs: 0.94 / Mean I/σ(I) obs: 2.4 / % possible all: 77.4 |
-Processing
Software |
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Refinement | Method to determine structure: MAD / Resolution: 2.8→115.47 Å / Cor.coef. Fo:Fc: 0.942 / Cor.coef. Fo:Fc free: 0.91 / SU B: 38.096 / SU ML: 0.347 / Cross valid method: THROUGHOUT / ESU R: 1.817 / ESU R Free: 0.423 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.1 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 66.83 Å2
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Refinement step | Cycle: LAST / Resolution: 2.8→115.47 Å
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Refine LS restraints |
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