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- PDB-3eiu: A second transient position of ATP on its trail to the nucleotide... -

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Basic information

Entry
Database: PDB / ID: 3eiu
TitleA second transient position of ATP on its trail to the nucleotide-binding site of subunit B of the motor protein A1Ao ATP synthase
ComponentsV-type ATP synthase beta chain
KeywordsHYDROLASE / ATP synthesis / Hydrogen ion transport / Ion transport / 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
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 / ADENOSINE-5'-TRIPHOSPHATE / V-type ATP synthase beta chain
Similarity search - Component
Biological speciesMethanosarcina mazei (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 3.43 Å
AuthorsManimekalai, S.M.S. / Kumar, A. / Balakrishna, A.M. / Gruber, G.
Citation
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(O) ATP synthase
Authors: Manimekalai, M.S.S. / Kumar, A. / Balakrishna, A.M. / Gruber, G.
#1: Journal: Proteins / Year: 2008
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, S.M.S. / Balakrishna, A.M. / Hunke, C. / Weigelt, S. / Sewald, N. / Gruber, G.
#2: Journal: J.Mol.Biol. / Year: 2006
Title: Crystal structure of the archaeal A1Ao ATP synthase subunit B from Methanosarcina mazei Go1: Implications of nucleotide-binding differences in the major A1Ao subunits A and B
Authors: Schafer, I.B. / Bailer, S.M. / Duser, M.G. / Borsch, M. / Bernal, R.A. / Stock, D. / Gruber, G.
History
DepositionSep 17, 2008Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Feb 10, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Oct 25, 2017Group: Refinement description / Category: software
Revision 1.3Nov 10, 2021Group: Database references / Derived calculations / Category: database_2 / 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
Revision 1.4Nov 1, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_comp_id ..._struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_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)103,8784
Polymers103,1672
Non-polymers7102
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5620 Å2
ΔGint-17 kcal/mol
Surface area31030 Å2
MethodPISA
Unit cell
Length a, b, c (Å)75.693, 96.867, 129.631
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11B
21A

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: LEU / Beg label comp-ID: LEU / End auth comp-ID: GLN / End label comp-ID: GLN / Refine code: 4 / Auth seq-ID: 15 - 440 / Label seq-ID: 24 - 449

Dom-IDAuth asym-IDLabel asym-ID
1BB
2AA
DetailsThe biological unit is a monomer

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Components

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


Mass: 51583.688 Da / Num. of mol.: 2 / Mutation: R416W
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methanosarcina mazei (archaea) / Strain: Go1 / Gene: ATP Synthase / Plasmid: pET9D-HIS6 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: Q60187, H+-transporting two-sector ATPase
#2: Chemical ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE / Adenosine triphosphate


Mass: 507.181 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Comment: ATP, energy-carrying molecule*YM
#3: 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
Sequence detailsTHE SEQUENCE IS BASED ON REFERENCE 1 IN THE DATABASE, VATB_METMA. A2VAL, B2VAL ARE CONFLICTS OF 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: 2.3 Å3/Da / Density % sol: 46.6 % / Mosaicity: 0.721 °
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 5
Details: 15% glycerol, 20% PEG 400, 2mM Mg2+ ATP, 0.1M Sodium Chloride, 0.1M Sodium citrate (pH 5.0), vapor diffusion,sitting drop, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: BL13B1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 7, 2007 / Details: mirrors
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.4→30 Å / Num. all: 13292 / Num. obs: 12055 / % possible obs: 91 % / Redundancy: 3.5 % / Biso Wilson estimate: 78.55 Å2 / Rmerge(I) obs: 0.167 / Χ2: 1.049 / Net I/σ(I): 8.493
Reflection shellResolution: 3.4→3.52 Å / Redundancy: 2.4 % / Rmerge(I) obs: 0.473 / Mean I/σ(I) obs: 1.94 / Num. unique all: 1094 / Χ2: 0.899 / % possible all: 85.7

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation3.64 Å25.38 Å
Translation3.64 Å25.38 Å

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
REFMACrefinement
PDB_EXTRACT3.006data extraction
ADSCQuantumdata collection
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2C61

2c61


Resolution: 3.43→24.62 Å / Cor.coef. Fo:Fc: 0.891 / Cor.coef. Fo:Fc free: 0.782 / WRfactor Rfree: 0.282 / WRfactor Rwork: 0.213 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.754 / SU B: 46.784 / SU ML: 0.698 / SU R Cruickshank DPI: 0.673 / SU Rfree: 0.868 / TLS residual ADP flag: LIKELY RESIDUAL / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.86 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.315 595 4.9 %RANDOM
Rwork0.246 ---
all0.308 11433 --
obs0.249 12032 90.52 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 104.44 Å2 / Biso mean: 72.12 Å2 / Biso min: 20 Å2
Baniso -1Baniso -2Baniso -3
1-0.18 Å20 Å20 Å2
2---0.01 Å20 Å2
3----0.17 Å2
Refinement stepCycle: LAST / Resolution: 3.43→24.62 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6506 0 44 0 6550
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0226678
X-RAY DIFFRACTIONr_angle_refined_deg0.9971.9829065
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.1995838
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.39124.102295
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.034151113
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.041547
X-RAY DIFFRACTIONr_chiral_restr0.0670.21023
X-RAY DIFFRACTIONr_gen_planes_refined0.0020.025052
X-RAY DIFFRACTIONr_nbd_refined0.1870.23287
X-RAY DIFFRACTIONr_nbtor_refined0.2990.24512
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1260.2273
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1790.237
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0970.25
X-RAY DIFFRACTIONr_mcbond_it0.2331.54274
X-RAY DIFFRACTIONr_mcangle_it0.42126741
X-RAY DIFFRACTIONr_scbond_it0.24432669
X-RAY DIFFRACTIONr_scangle_it0.4174.52324
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: B / Ens-ID: 1 / Number: 3082 / Refine-ID: X-RAY DIFFRACTION

TypeRms dev position (Å)Weight position
MEDIUM POSITIONAL0.550.5
MEDIUM THERMAL0.122
LS refinement shellResolution: 3.426→3.513 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.403 40 -
Rwork0.309 679 -
all-719 -
obs--75.84 %
Refinement TLS params.Method: refined / Origin x: -25.6518 Å / Origin y: -9.1795 Å / Origin z: 22.8981 Å
111213212223313233
T-0.5142 Å2-0.0249 Å20.0847 Å2--0.3446 Å2-0.0099 Å2---0.1515 Å2
L0.7275 °2-0.1558 °20.356 °2-0.8541 °20.3585 °2--1.8073 °2
S-0.0186 Å °-0.1101 Å °0.0311 Å °0.0596 Å °-0.0259 Å °0.172 Å °0.1313 Å °0.0802 Å °0.0445 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A15 - 440
2X-RAY DIFFRACTION1B15 - 440

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