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Yorodumi- PDB-2jdi: Ground state structure of F1-ATPase from bovine heart mitochondri... -
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-Basic information
Entry | Database: PDB / ID: 2jdi | ||||||
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Title | Ground state structure of F1-ATPase from bovine heart mitochondria (Bovine F1-ATPase crystallised in the absence of azide) | ||||||
Components | (ATP SYNTHASE ...) x 5 | ||||||
Keywords | HYDROLASE / ATP PHOSPHORYLASE / ATP SYNTHESIS | ||||||
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 transmembrane transporter activity ...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 transmembrane transporter activity / proton motive force-driven ATP synthesis / proton-transporting ATP synthase complex, catalytic core F(1) / H+-transporting two-sector ATPase / proton-transporting ATPase activity, rotational mechanism / proton transmembrane transport / proton-transporting ATP synthase activity, rotational mechanism / proton motive force-driven mitochondrial ATP synthesis / aerobic respiration / ADP binding / mitochondrial inner membrane / ATP hydrolysis activity / ATP binding / plasma membrane Similarity search - Function | ||||||
Biological species | BOS TAURUS (cattle) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å | ||||||
Authors | Bowler, M.W. / Montgomery, M.G. / Leslie, A.G.W. / Walker, J.E. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2007 Title: Ground State Structure of F1-ATPase from Bovine Heart Mitochondria at 1.9 A Resolution Authors: Bowler, M.W. / 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. 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. 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 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 | 2jdi.cif.gz | 657.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2jdi.ent.gz | 531.2 KB | Display | PDB format |
PDBx/mmJSON format | 2jdi.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2jdi_validation.pdf.gz | 2 MB | Display | wwPDB validaton report |
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Full document | 2jdi_full_validation.pdf.gz | 2 MB | Display | |
Data in XML | 2jdi_validation.xml.gz | 131.9 KB | Display | |
Data in CIF | 2jdi_validation.cif.gz | 191.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/jd/2jdi ftp://data.pdbj.org/pub/pdb/validation_reports/jd/2jdi | HTTPS FTP |
-Related structure data
Related structure data | 2ck3S 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 ... , 5 types, 9 molecules ABCDEFGHI
#1: Protein | Mass: 55301.207 Da / Num. of mol.: 3 / Fragment: RESIDUES 44-553 / Source method: isolated from a natural source / Source: (natural) BOS TAURUS (cattle) / Organ: HEART / Organelle: MITOCHONDRIA / Tissue: MUSCLE References: UniProt: P19483, H+-transporting two-sector ATPase #2: Protein | Mass: 51757.836 Da / Num. of mol.: 3 / Fragment: RESIDUES 47-528 / Source method: isolated from a natural source / Details: MITOCHONDRIA / Source: (natural) BOS TAURUS (cattle) / Organ: HEART / Tissue: MUSCLE References: UniProt: P00829, H+-transporting two-sector ATPase #3: Protein | | Mass: 30300.760 Da / Num. of mol.: 1 / Fragment: RESIDUES 26-298 / Source method: isolated from a natural source / Source: (natural) BOS TAURUS (cattle) / Organ: HEART / Organelle: MITOCHONDRIA / Tissue: MUSCLE / References: UniProt: P05631, EC: 3.6.1.34 #4: Protein | | Mass: 15074.813 Da / Num. of mol.: 1 / Fragment: RESIDUES 23-168 / Source method: isolated from a natural source / Source: (natural) BOS TAURUS (cattle) / Organ: HEART / Organelle: MITOCHONDRIA / Tissue: MUSCLE / References: UniProt: P05630, EC: 3.6.1.34 #5: Protein/peptide | | Mass: 5662.693 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) BOS TAURUS (cattle) / Organ: HEART / Organelle: MITOCHONDRIA / Tissue: MUSCLE / References: UniProt: P05632, EC: 3.6.1.34 |
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-Non-polymers , 3 types, 2332 molecules
#6: Chemical | ChemComp-ANP / #7: Chemical | ChemComp-MG / #8: Water | ChemComp-HOH / | |
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-Details
Sequence details | RESIDUE NUMBERING: BY CONVENTION, THE FIFTH AMINO ACID (SERINE) IN THE BETA SUBUNITS (CHAINS D,E,F) ...RESIDUE NUMBERING: BY CONVENTION |
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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: 2.29 Å3/Da / Density % sol: 46.3 % |
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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, 0.004% (W/V) PHENYLMETHYLSULFONYL FLUORIDE AND 12% (W/V) POLYETHYLENE GLYCOL 6000 |
-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 / Date: Nov 13, 2006 / Details: MIRRORS |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.933 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→20 Å / Num. obs: 194499 / % possible obs: 72.8 % / Redundancy: 3.1 % / Biso Wilson estimate: 23.5 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 15.9 |
Reflection shell | Resolution: 1.9→1.96 Å / Redundancy: 1.5 % / Rmerge(I) obs: 0.26 / Mean I/σ(I) obs: 1.7 / % possible all: 18.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2CK3 Resolution: 1.9→20 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.926 / SU B: 7.257 / SU ML: 0.098 / TLS residual ADP flag: UNVERIFIED / Cross valid method: THROUGHOUT / ESU R: 0.217 / ESU R Free: 0.179 / 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: 20.58 Å2
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Refinement step | Cycle: LAST / Resolution: 1.9→20 Å
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Refine LS restraints |
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