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Yorodumi- PDB-5bn5: Structural basis for a unique ATP synthase core complex from Nano... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5bn5 | ||||||
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Title | Structural basis for a unique ATP synthase core complex from Nanoarcheaum equitans | ||||||
Components |
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Keywords | HYDROLASE / ATP Synthase / Nanoarcheaum equitans / Catalytic core | ||||||
Function / homology | Function and homology information proton motive force-driven plasma membrane ATP synthesis / H+-transporting two-sector ATPase / proton-transporting ATPase activity, rotational mechanism / proton-transporting ATP synthase activity, rotational mechanism / ATP binding Similarity search - Function | ||||||
Biological species | Nanoarchaeum equitans Kin4-M (archaea) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.997 Å | ||||||
Authors | Mohanty, S. / Jobichen, C. / Chichili, V.P.R. / Sivaraman, J. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2015 Title: Structural Basis for a Unique ATP Synthase Core Complex from Nanoarcheaum equitans Authors: Mohanty, S. / Jobichen, C. / Chichili, V.P.R. / Velazquez-Campoy, A. / Low, B.C. / Hogue, C.W.V. / Sivaraman, J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5bn5.cif.gz | 199.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5bn5.ent.gz | 157.6 KB | Display | PDB format |
PDBx/mmJSON format | 5bn5.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bn/5bn5 ftp://data.pdbj.org/pub/pdb/validation_reports/bn/5bn5 | HTTPS FTP |
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-Related structure data
Related structure data | 5bn3C 5bn4C 5bo5C 3gqbS C: citing same article (ref.) 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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Details | The biological assembly is hetero-hexameric |
-Components
#1: Protein | Mass: 64768.305 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Nanoarchaeum equitans Kin4-M (archaea) / Strain: Kin4-M / Gene: atpA, NEQ103 Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria) Strain (production host): BL21-Gold(DE3)pLysS AG References: UniProt: Q74MJ7, H+-transporting two-sector ATPase |
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#2: Protein | Mass: 46674.777 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Nanoarchaeum equitans Kin4-M (archaea) / Strain: Kin4-M / Gene: NEQ263 Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria) Strain (production host): BL21-Gold(DE3)pLysS AG / References: UniProt: Q74MS5 |
#3: Chemical | ChemComp-SO4 / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 3.49 Å3/Da / Density % sol: 64.75 % |
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Crystal grow | Temperature: 280 K / Method: vapor diffusion, hanging drop / pH: 6.5 / Details: 0.1M MES, 1.6M Ammonium sulphate |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å |
Detector | Type: RIGAKU SATURN 944+ / Detector: CCD / Date: Oct 9, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection twin | Operator: h,-h-k,-l / Fraction: 0.157 |
Reflection | Resolution: 3→33 Å / Num. obs: 29083 / % possible obs: 96.9 % / Redundancy: 4 % / Net I/σ(I): 5.3 |
Reflection shell | Resolution: 3→3.05 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.39 / Mean I/σ(I) obs: 3.1 / % possible all: 87 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3GQB Resolution: 2.997→32.108 Å / Cross valid method: FREE R-VALUE / σ(F): 2.09 / Phase error: 33.87 / Stereochemistry target values: TWIN_LSQ_F
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Solvent computation | Shrinkage radii: 0.73 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 7.97 Å2 / ksol: 0.322 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 2.997→32.108 Å
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Refine LS restraints |
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LS refinement shell |
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