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Yorodumi- PDB-2w6j: Low resolution structures of bovine mitochondrial F1-ATPase durin... -
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-Basic information
Entry | Database: PDB / ID: 2w6j | ||||||
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Title | Low resolution structures of bovine mitochondrial F1-ATPase during controlled dehydration: Hydration State 5. | ||||||
Components |
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Keywords | HYDROLASE / ATP PHOSPHORYLASE (H+ TRANSPORTING) / TRANSIT PEPTIDE / F1FO ATP SYNTHASE / ATP PHOSPHORYLASE / ATP SYNTHASE / ION TRANSPORT / MITOCHONDRION / ATP SYNTHESIS / UBL CONJUGATION / CF(1) / P-LOOP / NUCLEOTIDE-BINDING / HYDROGEN ION TRANSPORT / PYRROLIDONE CARBOXYLIC ACID / ATP-BINDING | ||||||
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: 3.84 Å | ||||||
Authors | Sanchez-Weatherby, J. / Felisaz, F. / Gobbo, A. / Huet, J. / Ravelli, R.B.G. / Bowler, M.W. / Cipriani, F. | ||||||
Citation | Journal: Acta Crystallogr. D Biol. Crystallogr. / Year: 2009 Title: Improving diffraction by humidity control: a novel device compatible with X-ray beamlines. Authors: Sanchez-Weatherby, J. / Bowler, M.W. / Huet, J. / Gobbo, A. / Felisaz, F. / Lavault, B. / Moya, R. / Kadlec, J. / Ravelli, R.B. / Cipriani, F. | ||||||
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 | 2w6j.cif.gz | 520.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2w6j.ent.gz | 409.3 KB | Display | PDB format |
PDBx/mmJSON format | 2w6j.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2w6j_validation.pdf.gz | 502.9 KB | Display | wwPDB validaton report |
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Full document | 2w6j_full_validation.pdf.gz | 532.7 KB | Display | |
Data in XML | 2w6j_validation.xml.gz | 88.5 KB | Display | |
Data in CIF | 2w6j_validation.cif.gz | 125.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/w6/2w6j ftp://data.pdbj.org/pub/pdb/validation_reports/w6/2w6j | HTTPS FTP |
-Related structure data
Related structure data | 2w6eC 2w6fC 2w6gC 2w6hC 2w6iC 1bmfS 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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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 59795.492 Da / Num. of mol.: 3 / 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: 56340.199 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) BOS TAURUS (cattle) / Organ: HEART / Organelle: MITOCHONRIA / Tissue: MUSCLE References: UniProt: P00829, H+-transporting two-sector ATPase #3: Protein | | Mass: 33119.035 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) BOS TAURUS (cattle) / Organ: HEART / Organelle: MITOCHONRIA / Tissue: MUSCLE References: UniProt: P05631, H+-transporting two-sector ATPase #4: Protein | | Mass: 17626.992 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) BOS TAURUS (cattle) / Organ: HEART / Organelle: MITOCHONRIA / Tissue: MUSCLE References: UniProt: P05630, H+-transporting two-sector ATPase #5: Protein | | Mass: 5793.889 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) BOS TAURUS (cattle) / Organ: HEART / Organelle: MITOCHONRIA / Tissue: MUSCLE References: UniProt: P05632, H+-transporting two-sector ATPase |
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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: 2.62 Å3/Da / Density % sol: 52.76 % Description: THE DATA WERE COLLECTED AT ROOM TEMPERATURE, DURING CONTROLLED DEHYDRATION OF CRYSTALS,TO EVALUATE THE CHANGES THAT OCCUR IN CRYSTAL PACKING DURING DEHYDRATION. NO BIOLOGICAL ...Description: THE DATA WERE COLLECTED AT ROOM TEMPERATURE, DURING CONTROLLED DEHYDRATION OF CRYSTALS,TO EVALUATE THE CHANGES THAT OCCUR IN CRYSTAL PACKING DURING DEHYDRATION. NO BIOLOGICAL SIGNIFICANCE SHOULD BE ATTACHED TO THE COORDINATES. |
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Crystal grow | pH: 8.5 Details: 50 MM TRIS-HCL PH 8.2, 200 MM NACL, 20 MM MGSO4, 1 MM ADP, 1 MM ALCL3, 6 MM NAF 0.004% (W/V)PHENYLMETHYLSULFONYL FLUORIDE AND 12% (W/V) POLYETHYLENE GLYCOL 6000 |
-Data collection
Diffraction | Mean temperature: 294 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.933 |
Detector | Type: ADSC CCD / Detector: CCD / Date: Sep 17, 2008 / Details: GE211 |
Radiation | Monochromator: DIAMOND111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.933 Å / Relative weight: 1 |
Reflection | Resolution: 3.84→71.8 Å / Num. obs: 32818 / % possible obs: 96.1 % / Observed criterion σ(I): 3 / Redundancy: 2.5 % / Rmerge(I) obs: 0.15 / Net I/σ(I): 11.5 |
Reflection shell | Resolution: 3.84→4.05 Å / Redundancy: 2.3 % / Rmerge(I) obs: 0.26 / Mean I/σ(I) obs: 2.7 / % possible all: 92.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1BMF Resolution: 3.84→132.45 Å / Cor.coef. Fo:Fc: 0.788 / SU B: 0.002 / SU ML: 0 / ESU R: 1.017 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. THE DATA WERE COLLECTED AT ROOM TEMPERATURE, DURING CONTROLLED DEHYDRATION OF CRYSTALS,TO EVALUATE THE CHANGES THAT OCCUR IN CRYSTAL ...Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. THE DATA WERE COLLECTED AT ROOM TEMPERATURE, DURING CONTROLLED DEHYDRATION OF CRYSTALS,TO EVALUATE THE CHANGES THAT OCCUR IN CRYSTAL PACKING DURING DEHYDRATION. NO BIOLOGICAL SIGNIFICANCE SHOULD BE ATTACHED TO THE COORDINATES.
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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: MASK | ||||||||||||||||
Displacement parameters | Biso mean: 20 Å2
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Refinement step | Cycle: LAST / Resolution: 3.84→132.45 Å
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LS refinement shell | Resolution: 3.84→3.94 Å / Total num. of bins used: 20 /
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