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Yorodumi- PDB-5bn4: Structure of a unique ATP synthase NeqA-NeqB in complex with ANP ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5bn4 | ||||||
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Title | Structure of a unique ATP synthase NeqA-NeqB in complex with ANP 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 / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.699 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 | 5bn4.cif.gz | 215.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5bn4.ent.gz | 166.8 KB | Display | PDB format |
PDBx/mmJSON format | 5bn4.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bn/5bn4 ftp://data.pdbj.org/pub/pdb/validation_reports/bn/5bn4 | HTTPS FTP |
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-Related structure data
Related structure data | 5bn3C 5bn5C 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-ANP / |
#4: Chemical | ChemComp-MG / |
#5: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 3.52 Å3/Da / Density % sol: 65.04 % |
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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: SYNCHROTRON / Site: NSRRC / Beamline: BL13B1 / Wavelength: 0.9798 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Feb 20, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9798 Å / Relative weight: 1 |
Reflection | Resolution: 2.63→50 Å / Num. obs: 39977 / % possible obs: 99.8 % / Redundancy: 5.7 % / Net I/σ(I): 5.7 |
Reflection shell | Resolution: 2.63→2.68 Å / Redundancy: 4.3 % / Rmerge(I) obs: 0.51 / Mean I/σ(I) obs: 2.8 / % possible all: 97.3 |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3GQB Resolution: 2.699→27.37 Å / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 31.05 / Stereochemistry target values: TWIN_LSQ_F
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Solvent computation | Shrinkage radii: 0.98 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 41.204 Å2 / ksol: 0.35 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 2.699→27.37 Å
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Refine LS restraints |
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LS refinement shell |
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