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- PDB-6afs: Proton pyrophosphatase - two phosphates-bound -

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Basic information

Entry
Database: PDB / ID: 6afs
TitleProton pyrophosphatase - two phosphates-bound
ComponentsPyrophosphate-energized vacuolar membrane proton pump
KeywordsMEMBRANE PROTEIN / Hydrolase / Proton pumping / Vigna radiata
Function / homology
Function and homology information


H+-exporting diphosphatase / diphosphate hydrolysis-driven proton transmembrane transporter activity / inorganic diphosphate phosphatase activity / vacuolar membrane / metal ion binding
Similarity search - Function
Pyrophosphate-energised proton pump / Inorganic H+ pyrophosphatase
Similarity search - Domain/homology
Chem-1PG / : / PHOSPHATE ION / Pyrophosphate-energized vacuolar membrane proton pump
Similarity search - Component
Biological speciesVigna radiata var. radiata (mung bean)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.299 Å
AuthorsTsai, J.-Y. / Li, K.-M. / Sun, Y.-J.
Funding support Taiwan, 1items
OrganizationGrant numberCountry
Taiwan
CitationJournal: J. Mol. Biol. / Year: 2019
Title: Roles of the Hydrophobic Gate and Exit Channel in Vigna radiata Pyrophosphatase Ion Translocation.
Authors: Tsai, J.Y. / Tang, K.Z. / Li, K.M. / Hsu, B.L. / Chiang, Y.W. / Goldman, A. / Sun, Y.J.
History
DepositionAug 8, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 10, 2019Provider: repository / Type: Initial release
Revision 1.1Apr 24, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.name
Revision 1.2Nov 22, 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 / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Pyrophosphate-energized vacuolar membrane proton pump
B: Pyrophosphate-energized vacuolar membrane proton pump
hetero molecules


Theoretical massNumber of molelcules
Total (without water)162,65325
Polymers160,1862
Non-polymers2,46723
Water7,206400
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13000 Å2
ΔGint-186 kcal/mol
Surface area41650 Å2
MethodPISA
Unit cell
Length a, b, c (Å)217.641, 88.433, 159.050
Angle α, β, γ (deg.)90.000, 125.470, 90.000
Int Tables number5
Space group name H-MC121

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Pyrophosphate-energized vacuolar membrane proton pump / Pyrophosphate-energized inorganic pyrophosphatase / H(+)-PPase / Vacuolar H(+)-pyrophosphatase


Mass: 80092.828 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vigna radiata var. radiata (mung bean) / Plasmid: pYVH6 / Production host: Saccharomyces cerevisiae (brewer's yeast) / Strain (production host): BJ2168 / References: UniProt: P21616, inorganic diphosphatase

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Non-polymers , 5 types, 423 molecules

#2: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: PO4
#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: K
#5: Chemical
ChemComp-1PG / 2-(2-{2-[2-(2-METHOXY-ETHOXY)-ETHOXY]-ETHOXY}-ETHOXY)-ETHANOL


Mass: 252.305 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C11H24O6
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 400 / 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: 3.89 Å3/Da / Density % sol: 68.39 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 100 mM MES (pH 6.5), 250 mM MgCl2, 23% (w/v) PEG2KMME and 10% glycerol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: BL15A1 / Wavelength: 1 Å
DetectorType: RAYONIX MX300HE / Detector: CCD / Date: Dec 19, 2015
RadiationMonochromator: LN2-Cooled, Fixed-Exit Double Crystal Monochromator
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.299→30 Å / Num. obs: 105163 / % possible obs: 96.2 % / Redundancy: 3.9 % / Biso Wilson estimate: 45.23 Å2 / Rmerge(I) obs: 0.083 / Rpim(I) all: 0.048 / Rrim(I) all: 0.097 / Χ2: 1.036 / Net I/σ(I): 11.2
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.3-2.383.71.468102040.6960.8461.71.08694
2.38-2.483.81.048103080.8040.6011.2131.08395
2.48-2.593.80.731104140.8670.4190.8461.10595.8
2.59-2.733.80.468105470.940.2710.5431.12496.7
2.73-2.93.80.324106170.9660.1870.3751.0697.3
2.9-3.123.90.208107210.9810.1190.241.0698.4
3.12-3.434.10.128108710.9890.0720.1470.97799.5
3.43-3.933.60.07796620.990.0480.0911.05588.4
3.93-4.9540.041108540.9980.0230.0470.92698.7
4.95-3040.029109650.9990.0160.0340.9398.2

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Processing

Software
NameVersionClassification
PHENIX1.8.2_1309refinement
SCALEPACKdata scaling
PDB_EXTRACT3.24data extraction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4A01

4a01


Resolution: 2.299→24.488 Å / SU ML: 0.26 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 30.2
RfactorNum. reflection% reflection
Rfree0.2402 1993 1.9 %
Rwork0.2076 --
obs0.2082 104814 95.8 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 92.06 Å2 / Biso mean: 42.91 Å2 / Biso min: 21.77 Å2
Refinement stepCycle: final / Resolution: 2.299→24.488 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10855 0 151 400 11406
Biso mean--54.17 44.47 -
Num. residues----1479
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00811197
X-RAY DIFFRACTIONf_angle_d1.12115167
X-RAY DIFFRACTIONf_chiral_restr0.0741824
X-RAY DIFFRACTIONf_plane_restr0.0051871
X-RAY DIFFRACTIONf_dihedral_angle_d14.5873896
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.2988-2.35620.38181360.3376988712492
2.3562-2.41990.35761400.30047220736094
2.4199-2.4910.32141410.27467245738695
2.491-2.57140.28911400.24417283742396
2.5714-2.66320.27271430.21797374751796
2.6632-2.76960.24891440.20587393753797
2.7696-2.89550.27541440.20117432757697
2.8955-3.04790.2611460.19617508765498
3.0479-3.23850.26331450.2037559770499
3.2385-3.48790.22581480.195276227770100
3.4879-3.83770.26971270.24566575670285
3.8377-4.39020.22811400.19087232737294
4.3902-5.52070.21781500.17997705785599
5.5207-24.48970.17921490.19277685783498

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