+Open data
-Basic information
Entry | Database: PDB / ID: 2ck3 | ||||||
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Title | Azide inhibited bovine F1-ATPase | ||||||
Components | (ATP SYNTHASE SUBUNIT ...) x 5 | ||||||
Keywords | HYDROLASE | ||||||
Function / homology | Function and homology information Formation of ATP by chemiosmotic coupling / Cristae formation / mitochondrial proton-transporting ATP synthase complex assembly / mitochondrial envelope / : / proton-transporting ATP synthase complex / : / : / Mitochondrial protein degradation / proton motive force-driven ATP synthesis ...Formation of ATP by chemiosmotic coupling / Cristae formation / mitochondrial proton-transporting ATP synthase complex assembly / mitochondrial envelope / : / proton-transporting ATP synthase complex / : / : / Mitochondrial protein degradation / proton motive force-driven ATP synthesis / proton motive force-driven mitochondrial ATP synthesis / proton transmembrane transporter activity / 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 / aerobic respiration / proton transmembrane transport / ADP binding / mitochondrial inner membrane / ATP hydrolysis activity / mitochondrion / ATP binding / plasma membrane Similarity search - Function | ||||||
Biological species | BOS TAURUS (cattle) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å | ||||||
Authors | Bowler, M.W. / Montgomery, M.G. / Leslie, A.G.W. / Walker, J.E. | ||||||
Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2006 Title: How Azide Inhibits ATP Hydrolysis by the F-Atpases. Authors: Bowler, M.W. / Montgomery, M.G. / Leslie, A.G. / Walker, J.E. #1: Journal: Acta Crystallogr.,Sect.D / Year: 2006 Title: Reproducible Improvements in Order and Diffraction Limit of Crystals of Bovine Mitochondrial F(1)- ATPase by Controlled Dehydration. Authors: Bowler, M.W. / Montgomery, M.G. / Leslie, A.G. / Walker, J.E. #2: Journal: Embo J. / Year: 2004 Title: The Structure of Bovine F1-ATPase Inhibited by Adp and Beryllium Fluoride Authors: Kagawa, R. / Montgomery, M.G. / Braig, K. / Leslie, A.G.W. / Walker, J.E. #3: Journal: Cell(Cambridge,Mass.) / Year: 2001 Title: Tructure of Bovine Mitochondrial F1-ATPase with Nucleotide Bound to All Three Catalytic Sites Implications for the Mechanism of Rotary Catalysis Authors: Menz, R.I. / Walker, J.E. / Leslie, A.G.W. #4: Journal: Nat.Struct.Biol. / Year: 2000 Title: The Structure of the Central Stalk in Bovine F1- ATPase at 2.4A Resolution Authors: Gibbons, C. / Montgomery, M.G. / Leslie, A.G.W. / Walker, J.E. #5: Journal: Science / Year: 1999 Title: Molecular Architecture of the Rotary Motor in ATP Synthase Authors: Stock, D. / Leslie, A.G.W. / Walker, J.E. #6: Journal: Angew.Chem.Int.Ed.Engl. / Year: 1998 Title: ATP Synthesis by Rotary Catalysis (Nobel Lecture) Authors: Walker, J.E. #7: Journal: Nature / Year: 1994 Title: Structure at 2.8 A Resolution of F1-ATPase from Bovine Heart Mitochondria Authors: Abrahams, J.P. / Leslie, A.G.W. / Lutter, R. / Walker, J.E. #8: Journal: J.Mol.Biol. / Year: 1993 Title: Crystallization of F1-ATPase from Bovine Heart Mitochondria Authors: Lutter, R. / Abrahams, J.P. / Van Raaij, M.J. / Todd, R.J. / Lundqvist, T. / Buchanan, S.K. / Leslie, A.G. / 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. THE SHEETS PRESENTED AS "BA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 6-STRANDED BARREL THIS IS REPRESENTED BY A 7-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. 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. THE SHEETS PRESENTED AS "FA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 5-STRANDED BARREL THIS IS REPRESENTED BY A 6-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 | 2ck3.cif.gz | 658.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2ck3.ent.gz | 532.6 KB | Display | PDB format |
PDBx/mmJSON format | 2ck3.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2ck3_validation.pdf.gz | 2 MB | Display | wwPDB validaton report |
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Full document | 2ck3_full_validation.pdf.gz | 2 MB | Display | |
Data in XML | 2ck3_validation.xml.gz | 105.3 KB | Display | |
Data in CIF | 2ck3_validation.cif.gz | 169.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ck/2ck3 ftp://data.pdbj.org/pub/pdb/validation_reports/ck/2ck3 | HTTPS FTP |
-Related structure data
Related structure data | 1w0jS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
-ATP SYNTHASE SUBUNIT ... , 5 types, 9 molecules ABCDEFGHI
#1: Protein | Mass: 55301.207 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Details: MITOCHONDRION / Source: (natural) BOS TAURUS (cattle) / Organ: HEART / Tissue: MUSCLE References: UniProt: P19483, H+-transporting two-sector ATPase #2: Protein | Mass: 51757.836 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Details: MITOCHONDRION / Source: (natural) BOS TAURUS (cattle) / Organ: HEART / Tissue: MUSCLE References: UniProt: P00829, EC: 3.6.1.34, H+-transporting two-sector ATPase #3: Protein | | Mass: 30185.674 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: MITOCHONDRION / Source: (natural) BOS TAURUS (cattle) / Organ: HEART / Tissue: MUSCLE / References: UniProt: P05631, EC: 3.6.1.34 #4: Protein | | Mass: 15074.813 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: MITOCHONDRION / Source: (natural) BOS TAURUS (cattle) / Organ: HEART / Tissue: MUSCLE References: UniProt: P05630, EC: 3.6.1.34, H+-transporting two-sector ATPase #5: Protein/peptide | | Mass: 5662.693 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: MITOCHONDRION / Source: (natural) BOS TAURUS (cattle) / Organ: HEART / Tissue: MUSCLE References: UniProt: P05632, EC: 3.6.1.34, H+-transporting two-sector ATPase |
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-Non-polymers , 6 types, 2420 molecules
#6: Chemical | ChemComp-ANP / #7: Chemical | ChemComp-MG / #8: Chemical | ChemComp-ADP / | #9: Chemical | ChemComp-AZI / | #10: Chemical | ChemComp-PO4 / | #11: Water | ChemComp-HOH / | |
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-Details
Sequence details | REFERENCE FOR THE ALPHA SUBUNIT J.E.WALKER, S.J.POWELL,O.VINAS, AND M.J.RUNSWICK, BIOCHEMISTRY,VOL ...REFERENCE FOR THE ALPHA SUBUNIT J.E.WALKER, S.J.POWELL,O.VINAS, AND M.J.RUNSWICK, BIOCHEMIST |
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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: 2.7 Å3/Da / Density % sol: 47 % / Description: NONE |
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Crystal grow | pH: 8.2 Details: 50 MM TRIS-HCL PH 8.2, 200 MM NACL, 20 MM MGSO4, 250 UM AMP-PNP, 5 UM ADP, 3 MM NAN3, 0.004% (W/V) PHENYLMETHYLSULFONYL FLUORIDE AND 9% (W/V) POLYETHYLENE GLYCOL 6000. |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.98 |
Detector | Type: ADSC CCD / Detector: CCD / Date: Sep 18, 2005 / Details: MIRRORS |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→20 Å / Num. obs: 244566 / % possible obs: 98.8 % / Redundancy: 3.5 % / Biso Wilson estimate: 27.3 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 9.2 |
Reflection shell | Resolution: 1.95→2 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.53 / Mean I/σ(I) obs: 2 / % possible all: 99.1 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1W0J Resolution: 1.95→20 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.941 / SU B: 9.961 / SU ML: 0.125 / TLS residual ADP flag: UNVERIFIED / Cross valid method: THROUGHOUT / ESU R: 0.181 / ESU R Free: 0.153 / 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: 1.2 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 26.49 Å2
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Refinement step | Cycle: LAST / Resolution: 1.95→20 Å
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Refine LS restraints |
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