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- PDB-3tiv: Crystal structure of subunit B mutant N157A of the A1AO ATP synthase -

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Basic information

Entry
Database: PDB / ID: 3tiv
TitleCrystal structure of subunit B mutant N157A of the A1AO ATP synthase
ComponentsV-type ATP synthase beta chain
KeywordsHYDROLASE / ATP synthesis / hydrogen Ion Transport
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 / plasma membrane
Similarity search - Function
ATPase, A1 complex, beta subunit / Rossmann fold - #12240 / V-type ATP synthase regulatory subunit B/beta / : / C-terminal domain of V and A type ATP synthase / 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 ...ATPase, A1 complex, beta subunit / Rossmann fold - #12240 / V-type ATP synthase regulatory subunit B/beta / : / C-terminal domain of V and A type ATP synthase / 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 / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
4-(2-AMINOETHYL)BENZENESULFONYL FLUORIDE / A-type ATP synthase subunit B
Similarity search - Component
Biological speciesMethanosarcina mazei (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.75 Å
AuthorsTadwal, 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
DepositionAug 22, 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

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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)102,45518
Polymers100,6512
Non-polymers1,80416
Water18,1411007
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4680 Å2
ΔGint-19 kcal/mol
Surface area31120 Å2
MethodPISA
Unit cell
Length a, b, c (Å)73.715, 95.770, 130.158
Angle α, β, γ (deg.)90.00, 90.00, 90.00
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: 50325.270 Da / Num. of mol.: 2 / Mutation: N157A
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, 1023 molecules

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


Mass: 92.094 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-PG0 / 2-(2-METHOXYETHOXY)ETHANOL / PEG 6000


Mass: 120.147 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H12O3 / Comment: precipitant*YM
#4: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#5: Chemical ChemComp-AES / 4-(2-AMINOETHYL)BENZENESULFONYL FLUORIDE / AEBSF


Mass: 203.234 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H10FNO2S
#6: Chemical ChemComp-1PE / PENTAETHYLENE GLYCOL / PEG400


Mass: 238.278 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H22O6 / Comment: precipitant*YM
#7: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1007 / Source method: isolated from a natural source / Formula: H2O

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Details

Sequence detailsRESIDUE 2 IS A VAL ACCORDING TO REFERENCE 1 (AAC06376) OF DATABASE UNIPROTKB/SWISSPROT Q60187 (VATB_METMA).

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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: 2.28 Å3/Da / Density % sol: 46.11 %
Crystal growTemperature: 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

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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: Nov 16, 2009 / Details: mirrors
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionRedundancy: 5.6 % / Number: 522760 / Rmerge(I) obs: 0.079 / Χ2: 0.48 / D res high: 1.75 Å / D res low: 30 Å / Num. obs: 93152 / % possible obs: 99.6
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsChi squaredRedundancy
3.773099.210.0310.385.6
2.993.7710010.0640.8065.8
2.612.9910010.0890.6795.8
2.372.6110010.0940.4325.8
2.22.3710010.1090.4135.8
2.072.210010.1380.3895.8
1.972.0710010.1960.4025.8
1.891.9710010.2720.4095.7
1.811.8999.910.3680.4095.4
1.751.8196.910.4380.4154.4
ReflectionResolution: 1.75→19.5 Å / Num. all: 93152 / Num. obs: 93071 / % possible obs: 99.6 % / Observed criterion σ(I): -3 / Redundancy: 5.6 % / Rmerge(I) obs: 0.079 / Net I/σ(I): 14.3
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsDiffraction-ID% possible all
1.75-1.814.40.4381.9196.9
1.81-1.895.40.3682.94199.9
1.89-1.975.70.2724.271100
1.97-2.075.80.1965.961100
2.07-2.25.80.1388.081100
2.2-2.375.80.10910.461100
2.37-2.615.80.09412.51100
2.61-2.995.80.08915.981100
2.99-3.775.80.06423.381100
3.77-305.60.03128.46199.2

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Phasing

PhasingMethod: molecular replacement
Phasing MRRfactor: 36.81 / Model details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.5 Å19.76 Å
Translation2.5 Å19.76 Å

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Processing

Software
NameVersionClassificationNB
PHASER2.1.4phasing
REFMAC5.5.0072refinement
PDB_EXTRACT3.1data extraction
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2C61

2c61


Resolution: 1.75→19.46 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.949 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 2.036 / SU ML: 0.066 / Isotropic thermal model: ISOTROPIC / Cross valid method: THROUGHOUT / ESU R: 0.111 / ESU R Free: 0.106 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.1991 4664 5 %RANDOM
Rwork0.16659 ---
obs0.16824 88407 99.67 %-
all-93152 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 20.553 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 1.75→19.46 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6676 0 117 1007 7800
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0227089
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.1931.9899616
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8725917
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.71323.951324
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.298151201
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.1731558
X-RAY DIFFRACTIONr_chiral_restr0.0870.21072
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0215382
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.6191.54382
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.17927093
X-RAY DIFFRACTIONr_scbond_it1.85532707
X-RAY DIFFRACTIONr_scangle_it3.1964.52495
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.75→1.795 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.287 355 -
Rwork0.264 6172 -
obs--96.03 %

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