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- PDB-6afx: Proton pyrophosphatase - E225A -

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Basic information

Entry
Database: PDB / ID: 6afx
TitleProton pyrophosphatase - E225A
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: 2.301 Å
AuthorsTsai, J.-Y. / Tang, K.-Z. / 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
Revision 1.3Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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)162,53725
Polymers160,0702
Non-polymers2,46723
Water8,791488
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12010 Å2
ΔGint-190 kcal/mol
Surface area42940 Å2
MethodPISA
Unit cell
Length a, b, c (Å)217.197, 88.321, 158.843
Angle α, β, γ (deg.)90.000, 125.140, 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: 80034.797 Da / Num. of mol.: 2 / Mutation: E225A
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, 511 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.: 488 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY

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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: TPS 05A / Wavelength: 1 Å
DetectorType: RAYONIX MX300-HS / Detector: CCD / Date: Mar 8, 2018
RadiationMonochromator: LN2-Cooled Fixed-Exit Double Crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.3→30 Å / Num. obs: 141563 / % possible obs: 99 % / Redundancy: 7.5 % / Biso Wilson estimate: 27.58 Å2 / Rmerge(I) obs: 0.071 / Rpim(I) all: 0.028 / Rrim(I) all: 0.076 / Χ2: 0.952 / Net I/σ(I): 10.7
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.3-2.386.40.70799520.8850.2880.7650.83692
2.38-2.486.90.607106660.9220.2430.6550.83799
2.48-2.597.50.474108150.9560.1840.5080.857100
2.59-2.737.70.32108130.9810.1230.3430.872100
2.73-2.97.70.227107860.990.0870.2430.892100
2.9-3.127.70.15108750.9940.0580.1610.928100
3.12-3.437.70.101108460.9960.0390.1081.025100
3.43-3.937.70.063108750.9980.0240.0681.206100
3.93-4.957.60.041109220.9990.0160.0451.23999.9
4.95-307.40.029110010.9990.0120.0320.7899.1

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Processing

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

4a01


Resolution: 2.301→29.801 Å / SU ML: 0.17 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 22.06
RfactorNum. reflection% reflection
Rfree0.1989 3004 2.12 %
Rwork0.1648 --
obs0.1656 141563 66.16 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 82.72 Å2 / Biso mean: 24.33 Å2 / Biso min: 5.28 Å2
Refinement stepCycle: final / Resolution: 2.301→29.801 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10854 0 147 488 11489
Biso mean--37.49 27.67 -
Num. residues----1480
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00811192
X-RAY DIFFRACTIONf_angle_d1.06515163
X-RAY DIFFRACTIONf_chiral_restr0.0681826
X-RAY DIFFRACTIONf_plane_restr0.0041870
X-RAY DIFFRACTIONf_dihedral_angle_d12.783888
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 21

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.3013-2.33910.2469490.21452239228822
2.3391-2.37940.2569580.20652668272627
2.3794-2.42260.234660.20542998306430
2.4226-2.46920.2509690.20363319338833
2.4692-2.51960.2603780.19823704378237
2.5196-2.57430.2414810.19574006408741
2.5743-2.63420.2365980.19214585468346
2.6342-2.70.21791110.18955145525651
2.7-2.7730.20141220.1865655577757
2.773-2.85450.22591350.18156288642363
2.8545-2.94660.19651560.17166734689067
2.9466-3.05180.22641440.1687141728572
3.0518-3.17380.21691620.17347699786177
3.1738-3.31810.20081870.16858271845884
3.3181-3.49280.18411980.16619006920490
3.4928-3.71120.20092140.1669644985896
3.7112-3.99720.18152180.156298871010599
3.9972-4.39830.1982160.1498998110197100
4.3983-5.03210.18222210.1368993510156100
5.0321-6.32990.19382120.1696995910171100
6.3299-29.80330.18482090.16299695990497

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