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- PDB-3ssa: Crystal structure of subunit B mutant N157T of the A1AO ATP synthase -

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Basic information

Entry
Database: PDB / ID: 3ssa
TitleCrystal structure of subunit B mutant N157T of the A1AO ATP synthase
ComponentsV-type ATP synthase beta chain
KeywordsHYDROLASE / ATP binding
Function / homology
Function and homology information


proton-transporting two-sector ATPase complex, catalytic domain / proton motive force-driven plasma membrane ATP synthesis / proton-transporting ATP synthase activity, rotational mechanism / ATP binding
Similarity search - Function
ATPase, A1 complex, beta subunit / Rossmann fold - #12240 / V-type ATP synthase regulatory subunit B/beta / ATPase, F1/V1/A1 complex, alpha/beta subunit, N-terminal domain / ATP synthase alpha/beta family, beta-barrel domain / ATPase, alpha/beta subunit, nucleotide-binding domain, active site / ATP synthase alpha and beta subunits signature. / ATPase, F1/V1/A1 complex, alpha/beta subunit, nucleotide-binding domain / ATP synthase alpha/beta family, nucleotide-binding domain / P-loop containing nucleoside triphosphate hydrolase ...ATPase, A1 complex, beta subunit / Rossmann fold - #12240 / V-type ATP synthase regulatory subunit B/beta / ATPase, F1/V1/A1 complex, alpha/beta subunit, N-terminal domain / ATP synthase alpha/beta family, beta-barrel domain / ATPase, alpha/beta subunit, nucleotide-binding domain, active site / ATP synthase alpha and beta subunits signature. / ATPase, F1/V1/A1 complex, alpha/beta subunit, nucleotide-binding domain / ATP synthase alpha/beta family, nucleotide-binding domain / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
4-(2-AMINOETHYL)BENZENESULFONYL FLUORIDE / DI(HYDROXYETHYL)ETHER / TRIETHYLENE GLYCOL / V-type ATP synthase beta chain
Similarity search - Component
Biological speciesMethanosarcina mazei (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.7 Å
AuthorsSundararaman, L. / 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: Sundararaman, L. / 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
DepositionJul 8, 2011Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Sep 5, 2012Provider: repository / Type: Initial release
Revision 1.1Nov 1, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: V-type ATP synthase beta chain
B: V-type ATP synthase beta chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)103,12025
Polymers100,6542
Non-polymers2,46623
Water19,9251106
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10370 Å2
ΔGint-47 kcal/mol
Surface area30930 Å2
MethodPISA
Unit cell
Length a, b, c (Å)73.335, 95.803, 130.367
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein V-type ATP synthase beta chain / V-ATPase subunit B


Mass: 50327.242 Da / Num. of mol.: 2 / Mutation: N157T
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, 1129 molecules

#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-1PE / PENTAETHYLENE GLYCOL / PEG400 / Polyethylene glycol


Mass: 238.278 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H22O6 / Comment: precipitant*YM
#5: Chemical ChemComp-AES / 4-(2-AMINOETHYL)BENZENESULFONYL FLUORIDE / AEBSF / AEBSF


Mass: 203.234 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H10FNO2S / Comment: protease inhibitor*YM
#6: Chemical
ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C4H10O3
#7: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL / Polyethylene glycol


Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O4
#8: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1106 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.27 Å3/Da / Density % sol: 45.93 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 5
Details: 30% glycerol, PEG 400, 0.1M Sodium Chloride and 0.1M Sodium citrate (pH 5.0), vapor diffusion, hanging drop, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL12B2 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 7, 2010 / Details: mirrors
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionRedundancy: 5.4 % / Av σ(I) over netI: 20.8 / Number: 552277 / Rmerge(I) obs: 0.044 / Χ2: 0.44 / D res high: 1.7 Å / D res low: 30 Å / Num. obs: 101545 / % possible obs: 99.5
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsChi squaredRedundancy
3.663097.310.0180.1745.4
2.913.6699.910.0260.2425.6
2.542.9110010.0450.3475.7
2.312.5410010.0750.5295.7
2.142.3110010.1020.7135.6
2.022.1410010.1250.6525.5
1.912.0210010.1510.5295.4
1.831.9110010.1870.4335.3
1.761.8399.910.2390.3955.2
1.71.7698.110.2840.3824.9
ReflectionResolution: 1.7→30 Å / Num. all: 102059 / Num. obs: 101545 / % possible obs: 99.5 % / Observed criterion σ(I): -3 / Redundancy: 5.4 % / Biso Wilson estimate: 18.934 Å2 / Rmerge(I) obs: 0.044 / Χ2: 0.44 / Net I/σ(I): 7.8
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
1.7-1.764.90.28498920.382198.1
1.76-1.835.20.239100710.395199.9
1.83-1.915.30.187100890.4331100
1.91-2.025.40.151101070.5291100
2.02-2.145.50.125101380.6521100
2.14-2.315.60.102101670.7131100
2.31-2.545.70.075101930.5291100
2.54-2.915.70.045101990.3471100
2.91-3.665.60.026103170.242199.9
3.66-305.40.018103720.174197.3

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACT3.1data extraction
Blu-Icedata collection
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2C61

2c61


Resolution: 1.7→13.45 Å / Cor.coef. Fo:Fc: 0.976 / Cor.coef. Fo:Fc free: 0.959 / WRfactor Rfree: 0.1916 / WRfactor Rwork: 0.1429 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.8739 / SU B: 1.877 / SU ML: 0.062 / SU R Cruickshank DPI: 0.0898 / SU Rfree: 0.0969 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.097 / Stereochemistry target values: Engh & Huber
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES
RfactorNum. reflection% reflectionSelection details
Rfree0.1931 5072 5 %RANDOM
Rwork0.1458 ---
all0.158 101813 --
obs0.1482 101467 99.66 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 78.41 Å2 / Biso mean: 25.3045 Å2 / Biso min: 7.48 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 1.7→13.45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6648 0 155 1106 7909
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.030.0227162
X-RAY DIFFRACTIONr_angle_refined_deg2.3791.9939717
X-RAY DIFFRACTIONr_dihedral_angle_1_deg12.8085932
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.97323.963328
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.394151217
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.6651559
X-RAY DIFFRACTIONr_chiral_restr0.2620.21082
X-RAY DIFFRACTIONr_gen_planes_refined0.0150.0215427
X-RAY DIFFRACTIONr_mcbond_it1.5131.54394
X-RAY DIFFRACTIONr_mcangle_it2.47427130
X-RAY DIFFRACTIONr_scbond_it3.87332768
X-RAY DIFFRACTIONr_scangle_it6.2234.52549
LS refinement shellResolution: 1.697→1.74 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.249 359 -
Rwork0.217 6741 -
all-7100 -
obs--96.69 %

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