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- PDB-2rkw: Intermediate position of ATP on its trail to the binding pocket i... -

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Basic information

Entry
Database: PDB / ID: 2rkw
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 / 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
V-type ATP synthase beta chain
Similarity search - Component
Biological speciesMethanosarcina mazei (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.81 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 18, 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 / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.4Oct 25, 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

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)103,1672
Polymers103,1672
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4890 Å2
ΔGint-18 kcal/mol
Surface area32260 Å2
MethodPISA
Unit cell
Length a, b, c (Å)73.052, 96.094, 129.941
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

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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: 2.21 Å3/Da / Density % sol: 44.35 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 5
Details: 15% glycerol, 20% PEG 400, 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: Jan 9, 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: 2.8→50 Å / Num. obs: 20054 / % possible obs: 87 % / Redundancy: 5.9 % / Rmerge(I) obs: 0.13 / Net I/σ(I): 8.4
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obs% possible all
2.8-2.94.80.39560.6
2.9-3.0250.38767.9
3.02-3.155.30.37374.9
3.15-3.325.60.31881.9
3.32-3.535.80.25390.2
3.53-3.86.20.19898
3.8-4.186.60.15699.8
4.18-4.796.50.10899.4
4.79-6.036.50.10699.5
6.03-505.80.06995.8

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
PDB_EXTRACT3data extraction
REFMAC5.2.0019refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2C61

2c61


Resolution: 2.81→34.73 Å / Cor.coef. Fo:Fc: 0.909 / Cor.coef. Fo:Fc free: 0.858 / SU B: 29.593 / SU ML: 0.558 / Isotropic thermal model: RESTRAINED / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflection
Rfree0.33 1033 5.2 %
Rwork0.271 --
obs0.274 19988 86.9 %
Solvent computationSolvent model: MASK
Displacement parametersBiso mean: 79.45 Å2
Baniso -1Baniso -2Baniso -3
1-0.14 Å20 Å20 Å2
2--0.11 Å20 Å2
3----0.24 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.67 Å0.49 Å
Luzzati d res low-5 Å
Luzzati sigma a0.95 Å1.16 Å
Refinement stepCycle: LAST / Resolution: 2.81→34.73 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6512 0 0 0 6512
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0226638
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.361.9749005
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.2955838
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.65624.108297
X-RAY DIFFRACTIONr_dihedral_angle_3_deg21.035151118
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.0951548
X-RAY DIFFRACTIONr_chiral_restr0.1030.21021
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.025045
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2350.23690
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.310.24527
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1840.2290
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2020.278
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0280.23
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.3351.54285
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.60926749
X-RAY DIFFRACTIONr_scbond_it0.53732607
X-RAY DIFFRACTIONr_scangle_it0.8944.52256
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.81→2.88 Å
RfactorNum. reflection% reflection
Rfree0.45 42 -
Rwork0.37 923 -
obs--58.7 %
Xplor fileSerial no: 1 / Param file: protein_rep.param

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