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- PDB-6aft: Proton pyrophosphatase - E301Q -

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Basic information

Entry
Database: PDB / ID: 6aft
TitleProton pyrophosphatase - E301Q
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: 2.492 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 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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)162,65125
Polymers160,1842
Non-polymers2,46723
Water9,044502
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10270 Å2
ΔGint-91 kcal/mol
Surface area43070 Å2
MethodPISA
Unit cell
Length a, b, c (Å)217.126, 88.268, 158.660
Angle α, β, γ (deg.)90.000, 125.250, 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: 80091.844 Da / Num. of mol.: 2 / Mutation: E301Q
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, 525 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.: 502 / 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: 3.88 Å3/Da / Density % sol: 68.26 %
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: Oct 6, 2017
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: 2.4917→30 Å / Num. obs: 81653 / % possible obs: 96.1 % / Redundancy: 3.6 % / Biso Wilson estimate: 39.26 Å2 / Rmerge(I) obs: 0.075 / Rpim(I) all: 0.028 / Rrim(I) all: 0.076 / Χ2: 0.952 / Net I/σ(I): 16.3
Reflection shellResolution: 2.5→2.59 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.267 / Num. unique obs: 9952 / CC1/2: 0.885 / Rpim(I) all: 0.288 / Rrim(I) all: 0.765 / Χ2: 0.836 / % possible all: 81.6

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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: 2.492→29.789 Å / SU ML: 0.23 / Cross valid method: THROUGHOUT / σ(F): 1.37 / Phase error: 24.58
RfactorNum. reflection% reflection
Rfree0.2082 1997 2.45 %
Rwork0.176 --
obs0.1768 81592 95.1 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 79.86 Å2 / Biso mean: 20.44 Å2 / Biso min: 3.86 Å2
Refinement stepCycle: final / Resolution: 2.492→29.789 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10862 0 151 502 11515
Biso mean--34.1 23.24 -
Num. residues----1480
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00711204
X-RAY DIFFRACTIONf_angle_d1.04315177
X-RAY DIFFRACTIONf_chiral_restr0.071826
X-RAY DIFFRACTIONf_plane_restr0.0041872
X-RAY DIFFRACTIONf_dihedral_angle_d13.5113898
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 (%)
2.4917-2.5540.25621000.23184063416368
2.554-2.6230.26261260.21144995512185
2.623-2.70010.24181350.20065380551590
2.7001-2.78720.23191410.19325640578194
2.7872-2.88670.22991470.18265829597699
2.8867-3.00220.22591490.177559806129100
3.0022-3.13870.23341500.178859216071100
3.1387-3.3040.23761490.171659516100100
3.304-3.51070.23591500.166759736123100
3.5107-3.78130.18281500.165559796129100
3.7813-4.16090.20561490.163559526101100
4.1609-4.76090.16791490.15715940608999
4.7609-5.99020.21241510.17935983613499
5.9902-29.79150.18341510.18366009616098

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