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Yorodumi- PDB-3tgw: Crystal structure of subunit B mutant H156A of the A1AO ATP synthase -
+Open data
-Basic information
Entry | Database: PDB / ID: 3tgw | ||||||
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Title | Crystal structure of subunit B mutant H156A of the A1AO ATP synthase | ||||||
Components | V-type ATP synthase beta chain | ||||||
Keywords | HYDROLASE / ATP synthesis / hydrogen Ion Transport | ||||||
Function / homology | Function and homology information proton-transporting two-sector ATPase complex, catalytic domain / vacuolar acidification / proton motive force-driven plasma membrane ATP synthesis / proton-transporting ATPase activity, rotational mechanism / proton-transporting ATP synthase activity, rotational mechanism / ATP binding Similarity search - Function | ||||||
Biological species | Methanosarcina mazei (archaea) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.75 Å | ||||||
Authors | Tadwal, V.S. / Manimekalai, M.S.S. / Jeyakanthan, J. / Gruber, G. | ||||||
Citation | Journal: To be Published Title: Structure of subunit A mutants H156A, N157A and N157T of the A1AO ATP synthase Authors: Tadwal, V.S. / Manimekalai, M.S.S. / Gruber, G. #1: Journal: Proteins / Year: 2009 Title: Spectroscopic and crystallographic studies of the mutant R416W give insight into the nucleotide binding traits of subunit B of the A1Ao ATP synthase Authors: Kumar, A. / Manimekalai, M.S. / Balakrishna, A.M. / Hunke, C. / Weigelt, S. / Sewald, N. / Gruber, G. #2: Journal: Acta Crystallogr.,Sect.D / Year: 2008 Title: Structure of the nucleotide-binding subunit B of the energy producer A1A0 ATP synthase in complex with adenosine diphosphate Authors: Kumar, A. / Manimekalai, M.S. / Gruber, G. #3: Journal: J.Struct.Biol. / Year: 2009 Title: A second transient position of ATP on its trail to the nucleotide-binding site of subunit B of the motor protein A(1)A(0) ATP synthase Authors: Manimekalai, M.S. / Kumar, A. / Balakrishna, A.M. / Gruber, G. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3tgw.cif.gz | 217.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3tgw.ent.gz | 169 KB | Display | PDB format |
PDBx/mmJSON format | 3tgw.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/tg/3tgw ftp://data.pdbj.org/pub/pdb/validation_reports/tg/3tgw | HTTPS FTP |
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-Related structure data
Related structure data | 3ssaC 3tivC 2c61S 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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-Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 50301.223 Da / Num. of mol.: 2 / Mutation: H156A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Methanosarcina mazei (archaea) / Strain: Go1 / Gene: ahaB, atpB, MM_0779 / Plasmid: pET9d-His6 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) References: UniProt: Q60187, H+-transporting two-sector ATPase |
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-Non-polymers , 7 types, 1142 molecules
#2: Chemical | ChemComp-GOL / #3: Chemical | ChemComp-P33 / | #4: Chemical | #5: Chemical | ChemComp-AES / | #6: Chemical | ChemComp-PG4 / | #7: Chemical | ChemComp-PG0 / | #8: Water | ChemComp-HOH / | |
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-Details
Sequence details | RESIDUE 2 IS A VAL ACCORDING TO REFERENCE 1 (AAC06376) OF DATABASE UNIPROTKB/SWISSPROT Q60187 (VATB_METMA). |
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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: 46.36 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 5 Details: 30% glycerol, PEG 400, 0.1M Sodium Chloride, 0.1M Sodium citrate, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL12B2 / Wavelength: 1 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 16, 2009 / Details: mirrors | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Redundancy: 5.7 % / Av σ(I) over netI: 15.85 / Number: 534901 / Rmerge(I) obs: 0.065 / Χ2: 0.41 / D res high: 1.75 Å / D res low: 30 Å / Num. obs: 93442 / % possible obs: 99.4 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Diffraction reflection shell |
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Reflection | Resolution: 1.75→30 Å / Num. all: 93768 / Num. obs: 93321 / % possible obs: 99.4 % / Observed criterion σ(I): -3 / Redundancy: 5.7 % / Biso Wilson estimate: 18.4 Å2 / Rmerge(I) obs: 0.065 / Χ2: 0.412 / Net I/σ(I): 5.6 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Phasing
Phasing | Method: molecular replacement | |||||||||
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Phasing MR | Rfactor: 36.33 / Model details: Phaser MODE: MR_AUTO
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2C61 Resolution: 1.75→20.1 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.953 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 2.009 / SU ML: 0.066 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / ESU R Free: 0.107 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES: REFINED INDIVIDUALLY
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 84.33 Å2 / Biso mean: 24.9083 Å2 / Biso min: 6.55 Å2
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Refinement step | Cycle: LAST / Resolution: 1.75→20.1 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.749→1.794 Å / Total num. of bins used: 20
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