+Open data
-Basic information
Entry | Database: PDB / ID: 2jiz | ||||||
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Title | The Structure of F1-ATPase inhibited by resveratrol. | ||||||
Components |
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Keywords | HYDROLASE / MITOCHONDRION / PYRROLIDONE CARBOXYLIC ACID | ||||||
Function / homology | Function and homology information Formation of ATP by chemiosmotic coupling / Cristae formation / : / : / Mitochondrial protein degradation / : / proton motive force-driven ATP synthesis / proton motive force-driven mitochondrial ATP synthesis / proton-transporting ATP synthase complex, catalytic core F(1) / H+-transporting two-sector ATPase ...Formation of ATP by chemiosmotic coupling / Cristae formation / : / : / Mitochondrial protein degradation / : / proton motive force-driven ATP synthesis / proton motive force-driven mitochondrial ATP synthesis / proton-transporting ATP synthase complex, catalytic core F(1) / H+-transporting two-sector ATPase / proton-transporting ATPase activity, rotational mechanism / proton-transporting ATP synthase activity, rotational mechanism / ADP binding / ATP hydrolysis activity / ATP binding / plasma membrane Similarity search - Function | ||||||
Biological species | BOS TAURUS (cattle) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å | ||||||
Authors | Gledhill, J.R. / Montgomery, M.G. / Leslie, A.G.W. / Walker, J.E. | ||||||
Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2007 Title: Mechanism of Inhibition of Bovine F1-ATPase by Resveratrol and Related Polyphenols. Authors: Gledhill, J.R. / Montgomery, M.G. / Leslie, A.G.W. / Walker, J.E. | ||||||
History |
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Remark 700 | SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AA" IN EACH CHAIN ON SHEET RECORDS BELOW ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 13-STRANDED BARREL THIS IS REPRESENTED BY A 14-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "BA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 11-STRANDED BARREL THIS IS REPRESENTED BY A 12-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "CA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 11-STRANDED BARREL THIS IS REPRESENTED BY A 12-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "HA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 11-STRANDED BARREL THIS IS REPRESENTED BY A 12-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "IA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 11-STRANDED BARREL THIS IS REPRESENTED BY A 12-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "JA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 11-STRANDED BARREL THIS IS REPRESENTED BY A 12-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2jiz.cif.gz | 1.2 MB | Display | PDBx/mmCIF format |
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PDB format | pdb2jiz.ent.gz | 1017.3 KB | Display | PDB format |
PDBx/mmJSON format | 2jiz.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ji/2jiz ftp://data.pdbj.org/pub/pdb/validation_reports/ji/2jiz | HTTPS FTP |
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-Related structure data
Related structure data | 2jj1C 2jj2C 1w0jS 2uys 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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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments:
NCS ensembles :
NCS oper: (Code: given Matrix: (1, -2.0E-5, 0.00118), Vector: |
-Components
-ATP SYNTHASE SUBUNIT ... , 2 types, 12 molecules ABCHIJDEFKLM
#1: Protein | Mass: 55332.219 Da / Num. of mol.: 6 / Fragment: RESIDUES 44-553 / Source method: isolated from a natural source / Source: (natural) BOS TAURUS (cattle) / Organ: HEART / References: UniProt: P19483, EC: 3.6.1.34 #2: Protein | Mass: 51757.836 Da / Num. of mol.: 6 / Fragment: RESIDUES 47-528 / Source method: isolated from a natural source / Source: (natural) BOS TAURUS (cattle) / Organ: HEART / References: UniProt: P00829, EC: 3.6.1.34 |
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-Protein , 1 types, 2 molecules GN
#3: Protein | Mass: 30185.674 Da / Num. of mol.: 2 / Fragment: RESIDUES 26-297 / Source method: isolated from a natural source / Source: (natural) BOS TAURUS (cattle) / Organ: HEART / References: UniProt: P05631, EC: 3.6.1.34 |
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-Non-polymers , 8 types, 3917 molecules
#4: Chemical | ChemComp-ANP / #5: Chemical | ChemComp-MG / #6: Chemical | ChemComp-GOL / #7: Chemical | #8: Chemical | #9: Chemical | #10: Chemical | #11: Water | ChemComp-HOH / | |
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-Details
Sequence details | RESIDUE GLN 44 IN UNIPROT SEQUENCE IS MODIFIED TO AN N-TERMINAL PYRROLIDONE CARBOXYLIC ACID RESIDUE ...RESIDUE GLN 44 IN UNIPROT SEQUENCE IS MODIFIED TO AN N-TERMINAL PYRROLIDON |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.87 Å3/Da / Density % sol: 56.79 % / Description: NONE |
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Crystal grow | pH: 8.2 / Details: pH 8.2 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.933 |
Detector | Type: ADSC CCD / Detector: CCD |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.933 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→66.82 Å / Num. obs: 299020 / % possible obs: 84.7 % / Redundancy: 1.4 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 7.8 |
Reflection shell | Resolution: 2.3→2.42 Å / Redundancy: 1.4 % / Rmerge(I) obs: 0.24 / Mean I/σ(I) obs: 2.1 / % possible all: 77.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1W0J Resolution: 2.3→138.68 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.932 / SU B: 10.737 / SU ML: 0.142 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.314 / ESU R Free: 0.227 / 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: 1.4 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 45.17 Å2
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Refinement step | Cycle: LAST / Resolution: 2.3→138.68 Å
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Refine LS restraints |
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