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- PDB-6afz: Proton pyrophosphatase-E225H mutant -

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Basic information

Entry
Database: PDB / ID: 6afz
TitleProton pyrophosphatase-E225H mutant
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: 2.483 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_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_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 1.3Nov 6, 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)162,67125
Polymers160,2042
Non-polymers2,46723
Water3,783210
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12490 Å2
ΔGint-185 kcal/mol
Surface area42010 Å2
MethodPISA
Unit cell
Length a, b, c (Å)215.605, 88.023, 158.194
Angle α, β, γ (deg.)90.000, 124.990, 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: 80101.859 Da / Num. of mol.: 2 / Mutation: E225H
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, 233 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.: 210 / 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: 3.84 Å3/Da / Density % sol: 67.95 %
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: 2.48→30 Å / Num. obs: 83058 / % possible obs: 97.4 % / Redundancy: 4.1 % / Biso Wilson estimate: 54.47 Å2 / Rmerge(I) obs: 0.094 / Rpim(I) all: 0.052 / Rrim(I) all: 0.108 / Χ2: 1.018 / Net I/σ(I): 8.3
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.48-2.573.50.97370840.6160.5651.1290.88983.4
2.57-2.673.80.78879670.770.4420.9070.92594.4
2.67-2.794.10.64284060.880.3560.7360.98599.4
2.79-2.944.30.48985240.9180.2680.5591.008100
2.94-3.124.30.34985110.9470.1920.3991.078100
3.12-3.364.30.22985100.9680.1260.2621.099100
3.36-3.74.30.14184940.9870.0770.1611.05199.9
3.7-4.244.20.07484760.9970.0410.0851.03999.5
4.24-5.334.10.05385160.9980.030.0610.95499.2
5.33-304.10.0385700.9990.0170.0351.08998.2

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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: 2.483→25.7 Å / SU ML: 0.32 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 29.6
RfactorNum. reflection% reflection
Rfree0.2348 1999 2.41 %
Rwork0.2013 --
obs0.2021 82958 96.67 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 104.97 Å2 / Biso mean: 50.58 Å2 / Biso min: 23.96 Å2
Refinement stepCycle: final / Resolution: 2.483→25.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10864 0 144 210 11218
Biso mean--62.91 46.71 -
Num. residues----1480
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00811201
X-RAY DIFFRACTIONf_angle_d1.14415176
X-RAY DIFFRACTIONf_chiral_restr0.0761826
X-RAY DIFFRACTIONf_plane_restr0.0051872
X-RAY DIFFRACTIONf_dihedral_angle_d14.7773889
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 (%)
2.4832-2.54520.39081090.34934400450974
2.5452-2.6140.3321300.3265255538589
2.614-2.69080.36131420.30155736587896
2.6908-2.77750.33971460.27965907605399
2.7775-2.87670.2941460.244959336079100
2.8767-2.99170.24351470.218759836130100
2.9917-3.12760.26331460.207559216067100
3.1276-3.29220.2341470.196159606107100
3.2922-3.4980.20991470.18759586105100
3.498-3.76730.25561480.179459926140100
3.7673-4.1450.19981470.16895966611399
4.145-4.74160.17461470.16085941608899
4.7416-5.96160.21391480.19815990613899
5.9616-25.70180.23881490.20076017616698

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