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- PDB-3b2q: Intermediate position of ATP on its trail to the binding pocket i... -

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Basic information

Entry
Database: PDB / ID: 3b2q
TitleIntermediate position of ATP on its trail to the binding pocket inside the subunit B mutant R416W of the energy converter 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 / 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 ...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 / ADENOSINE-5'-TRIPHOSPHATE / CITRIC ACID / V-type ATP synthase beta chain
Similarity search - Component
Biological speciesMethanosarcina mazei (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.1 Å
AuthorsKumar, A. / Manimekalai, M.S.S. / Balakrishna, A.M. / Hunke, C. / Gruber, G.
Citation
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.S. / Balakrishna, A.M. / Hunke, C. / Weigelt, S. / Sewald, N. / Gruber, G.
#1: 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
DepositionOct 19, 2007Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Sep 9, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: 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 / pdbx_initial_refinement_model
Remark 999SEQUENCE The sequence is based on reference 1 in the database, VATB_METMA. A2VAL, B2VAL are ...SEQUENCE The sequence is based on reference 1 in the database, VATB_METMA. A2VAL, B2VAL are conflicts of VATB_METMA.

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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)104,0705
Polymers103,1672
Non-polymers9033
Water14,916828
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6150 Å2
ΔGint-15 kcal/mol
Surface area30730 Å2
MethodPISA
Unit cell
Length a, b, c (Å)73.473, 96.094, 130.275
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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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: atpB / 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


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


Mass: 203.234 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H10FNO2S / Comment: protease inhibitor*YM
#4: Chemical ChemComp-CIT / CITRIC ACID


Mass: 192.124 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H8O7
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 828 / 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: 2.23 Å3/Da / Density % sol: 44.81 %
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), pH 5.00, VAPOR DIFFUSION, SITTING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: BL13C1 / Wavelength: 0.97315
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Aug 28, 2007 / Details: MIRRORS
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97315 Å / Relative weight: 1
ReflectionResolution: 2→30 Å / Num. obs: 62523 / % possible obs: 99.4 % / Redundancy: 3.3 % / Biso Wilson estimate: 11.7 Å2 / Rmerge(I) obs: 0.088 / Net I/σ(I): 13.8084
Reflection shellResolution: 2→2.07 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.594 / Mean I/σ(I) obs: 2.264 / % possible all: 98.7

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation2.08 Å26.96 Å
Translation2.08 Å26.96 Å

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
CNS1.1refinement
PDB_EXTRACT3data extraction
ADSCQuantumdata collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2C61

2c61


Resolution: 2.1→26.96 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 508828.96 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: ENGH & HUBER
RfactorNum. reflection% reflectionSelection details
Rfree0.237 5244 10.2 %RANDOM
Rwork0.189 ---
obs0.189 51314 94.1 %-
all-73949 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 78.2139 Å2 / ksol: 0.383038 e/Å3
Displacement parametersBiso mean: 31 Å2
Baniso -1Baniso -2Baniso -3
1-11.66 Å20 Å20 Å2
2---4.41 Å20 Å2
3----7.26 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.28 Å0.21 Å
Luzzati d res low-5 Å
Luzzati sigma a0.26 Å0.21 Å
Refinement stepCycle: LAST / Resolution: 2.1→26.96 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6692 0 57 828 7577
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.009
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.8
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d24.1
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d2.17
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.4241.5
X-RAY DIFFRACTIONc_mcangle_it2.2462
X-RAY DIFFRACTIONc_scbond_it2.1922
X-RAY DIFFRACTIONc_scangle_it3.3352.5
LS refinement shellResolution: 2.1→2.23 Å / Rfactor Rfree error: 0.01 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.28 859 11 %
Rwork0.237 6961 -
obs--87.2 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater.top
X-RAY DIFFRACTION3atp_xplor_par.paramatp_xplor_top.top
X-RAY DIFFRACTION4aes-cit_xplor_par.paramaes-cit_xplor_top-c.top

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