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- PDB-2w6e: Low resolution structures of bovine mitochondrial F1-ATPase durin... -
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Basic information
Entry | Database: PDB / ID: 2w6e | ||||||
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Title | Low resolution structures of bovine mitochondrial F1-ATPase during controlled dehydration:hydration state 1. | ||||||
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![]() | HYDROLASE / ATP PHOSPHORYLASE (H+ TRANSPORTING) / TRANSIT PEPTIDE / F1FO ATP PHOSPHORYLASE / ION TRANSPORT / ATP SYNTHESIS / UBL CONJUGATION / CF(1) / P-LOOP / HYDROGEN ION TRANSPORT / PYRROLIDONE CARBOXYLIC ACID | ||||||
Function / homology | ![]() 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 | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Sanchez-Weatherby, J. / Felisaz, F. / Gobbo, A. / Huet, J. / Ravelli, R.B.G. / Bowler, M.W. / Cipriani, F. | ||||||
![]() | ![]() Title: Improving Diffraction by Humidity Control: A Novel Device Compatible with X-Ray Beamlines. Authors: Sanchez-Weatherby, J. / Felisaz, F. / Gobbo, A. / Huet, J. / Ravelli, R.B.G. / Bowler, M.W. / 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 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 SHEETS PRESENTED AS "DA" 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. |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 496.8 KB | Display | ![]() |
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PDB format | ![]() | 389.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
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-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 2w6fC ![]() 2w6gC ![]() 2w6hC ![]() 2w6iC ![]() 2w6jC ![]() 1bmfS S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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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) ![]() ![]() 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) ![]() ![]() 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) ![]() ![]() References: UniProt: P05631, H+-transporting two-sector ATPase #4: Chemical | ChemComp-ADP / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.44 Å3/Da / Density % sol: 63.94 % Description: DATA WERE COLLECTED AT ROOM TEMPERATURE DURING CONTROLLED DEHYDRATION OF THE CRYSTALS IN ORDER TO EVALUATE CHANGES IN CRYSTAL PACKING |
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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: ![]() ![]() ![]() |
Detector | Type: ADSC CCD / Detector: CCD / Date: Oct 29, 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: 6.5→60 Å / Num. obs: 8205 / % possible obs: 91.6 % / Observed criterion σ(I): 3 / Redundancy: 2.4 % / Rmerge(I) obs: 0.23 / Net I/σ(I): 10.5 |
Reflection shell | Resolution: 6.5→6.85 Å / Redundancy: 2.2 % / Rmerge(I) obs: 0.92 / Mean I/σ(I) obs: 1.1 / % possible all: 92.1 |
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Processing
Software |
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1BMF Resolution: 6.5→30 Å / Cor.coef. Fo:Fc: 0.816 / Cor.coef. Fo:Fc free: 0.8 / SU B: 0.009 / SU ML: 0 / Cross valid method: THROUGHOUT / ESU R: 3.5 / ESU R Free: 3.439 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. THIS STRUCTURE WAS DETERMINED TO EVALUATE CHANGING CRYSTAL CONTACTS DURING CONTROLLED DEHYDRATION OF CRYSTALS. NO BIOLOGICAL RELEVANCE ...Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. THIS STRUCTURE WAS DETERMINED TO EVALUATE CHANGING CRYSTAL CONTACTS DURING CONTROLLED DEHYDRATION OF CRYSTALS. NO BIOLOGICAL RELEVANCE SHOULD BE GIVEN TO THESE 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: 6.5→30 Å
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LS refinement shell | Resolution: 6.5→6.66 Å / Total num. of bins used: 20 /
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