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- PDB-6afv: Proton pyrophosphatase-L555K mutant -

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Basic information

Entry
Database: PDB / ID: 6afv
TitleProton pyrophosphatase-L555K 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: 2.701 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
Revision 1.3Oct 23, 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)162,43324
Polymers160,2182
Non-polymers2,21522
Water3,909217
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12470 Å2
ΔGint-189 kcal/mol
Surface area42360 Å2
MethodPISA
Unit cell
Length a, b, c (Å)221.347, 88.619, 160.955
Angle α, β, γ (deg.)90.000, 126.050, 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: 80108.852 Da / Num. of mol.: 2 / Mutation: L555K
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, 239 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.: 6 / Source method: obtained synthetically / Formula: C11H24O6
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 217 / 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: 3.98 Å3/Da / Density % sol: 69.12 %
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: 2.7→30 Å / Num. obs: 68580 / % possible obs: 99.6 % / Redundancy: 4.1 % / Biso Wilson estimate: 63.28 Å2 / Rmerge(I) obs: 0.111 / Rpim(I) all: 0.063 / Rrim(I) all: 0.128 / Χ2: 1.081 / Net I/σ(I): 8.7
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.7-2.83.81.10966140.6810.6391.2831.07397.5
2.8-2.9140.95368310.7450.5421.0981.199.7
2.91-3.044.10.69168610.8480.3890.7951.106100
3.04-3.24.20.55468480.8450.310.6361.105100
3.2-3.44.20.35368750.9210.1970.4041.094100
3.4-3.664.20.21968510.9660.1220.2511.094100
3.66-4.034.20.12168920.990.0670.1381.075100
4.03-4.614.10.07168770.9960.040.0821.03199.8
4.61-5.84.10.0669190.9970.0330.0691.03199.9
5.8-3040.03570120.9980.020.0411.199.2

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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: 2.701→28.059 Å / SU ML: 0.38 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 29.32
RfactorNum. reflection% reflection
Rfree0.2385 1997 2.92 %
Rwork0.1967 --
obs0.1979 68484 98.82 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 124.53 Å2 / Biso mean: 53.6 Å2 / Biso min: 24 Å2
Refinement stepCycle: final / Resolution: 2.701→28.059 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10864 0 134 217 11215
Biso mean--66.37 53.09 -
Num. residues----1480
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00811190
X-RAY DIFFRACTIONf_angle_d1.13915162
X-RAY DIFFRACTIONf_chiral_restr0.0751824
X-RAY DIFFRACTIONf_plane_restr0.0041872
X-RAY DIFFRACTIONf_dihedral_angle_d14.2683888
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 (%)
2.7009-2.76840.38961260.34034197432388
2.7684-2.84320.37031400.31154670481099
2.8432-2.92680.37031440.291647624906100
2.9268-3.02110.29821430.257247574900100
3.0211-3.1290.2681440.250947814925100
3.129-3.25410.29641430.231647794922100
3.2541-3.40190.29521450.209448094954100
3.4019-3.58090.2481430.199547834926100
3.5809-3.80480.23311440.184347884932100
3.8048-4.09770.21321440.16747984942100
4.0977-4.50860.19261440.157748034947100
4.5086-5.15750.20441450.151948224967100
5.1575-6.48460.24151460.201948404986100
6.4846-28.06050.19991460.18814898504499

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