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- PDB-5gpj: Crystal Structure of Proton-Pumping Pyrophosphatase -

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Basic information

Entry
Database: PDB / ID: 5gpj
TitleCrystal Structure of Proton-Pumping Pyrophosphatase
ComponentsPyrophosphate-energized vacuolar membrane proton pump
KeywordsHYDROLASE / Vigna radiata / Proton-Pumping / Phosphate-bound
Function / homologyH+-exporting diphosphatase / diphosphate hydrolysis-driven proton transmembrane transporter activity / Pyrophosphate-energised proton pump / Inorganic H+ pyrophosphatase / inorganic diphosphate phosphatase activity / vacuolar membrane / metal ion binding / PHOSPHATE ION / Pyrophosphate-energized vacuolar membrane proton pump
Function and homology information
Biological speciesVigna radiata var. radiata (mung bean)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.5 Å
AuthorsLi, K.M. / Tsai, J.Y. / Sun, Y.J.
Funding support Taiwan, 2items
OrganizationGrant numberCountry
Ministry of Science and Technolgy101-2311-B-007-009-MY3 and 103-2627-M-007-008 Taiwan
Academia SinicaAS-103-TP-B11 Taiwan
CitationJournal: Nat Commun / Year: 2016
Title: Membrane pyrophosphatases from Thermotoga maritima and Vigna radiata suggest a conserved coupling mechanism
Authors: Li, K.M. / Wilkinson, C. / Kellosalo, J. / Tsai, J.Y. / Kajander, T. / Jeuken, L.J. / Sun, Y.J. / Goldman, A.
History
DepositionAug 3, 2016Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 28, 2016Provider: repository / Type: Initial release
Revision 1.1Nov 8, 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 / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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_seq_id / _struct_conn.ptnr2_label_asym_id
Revision 1.2Oct 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
C: Pyrophosphate-energized vacuolar membrane proton pump
D: Pyrophosphate-energized vacuolar membrane proton pump
hetero molecules


Theoretical massNumber of molelcules
Total (without water)324,95816
Polymers324,3844
Non-polymers57412
Water00
1
A: Pyrophosphate-energized vacuolar membrane proton pump
B: Pyrophosphate-energized vacuolar membrane proton pump
hetero molecules


Theoretical massNumber of molelcules
Total (without water)162,4798
Polymers162,1922
Non-polymers2876
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6950 Å2
ΔGint-127 kcal/mol
Surface area43510 Å2
MethodPISA
2
C: Pyrophosphate-energized vacuolar membrane proton pump
D: Pyrophosphate-energized vacuolar membrane proton pump
hetero molecules


Theoretical massNumber of molelcules
Total (without water)162,4798
Polymers162,1922
Non-polymers2876
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6770 Å2
ΔGint-123 kcal/mol
Surface area43810 Å2
MethodPISA
Unit cell
Length a, b, c (Å)225.703, 81.637, 264.845
Angle α, β, γ (deg.)90.00, 92.87, 90.00
Int Tables number5
Space group name H-MC121

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Components

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


Mass: 81095.875 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Details: Phosphate-bound / 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
#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.: 8 / Source method: obtained synthetically / Formula: Mg
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: 3.99 Å3/Da / Density % sol: 69.15 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.2
Details: 100mM sodium/potassium phosphate (pH 6.2), 200mM NaCl, and 37%(w/v) PEG600

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: BL15A1 / Wavelength: 1 Å
DetectorType: RAYONIX MX300HE / Detector: CCD / Date: Mar 15, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.5→30 Å / Num. obs: 54540 / % possible obs: 92.2 % / Redundancy: 3.5 % / Rmerge(I) obs: 0.168 / Net I/σ(I): 7.5
Reflection shellResolution: 3.5→3.62 Å / Redundancy: 3.5 % / Rmerge(I) obs: 1.175 / Mean I/σ(I) obs: 1.11 / % possible all: 85.1

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Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
PDB_EXTRACT3.2data extraction
HKL-2000data processing
HKL-2000data scaling
MOLREPphasing
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4A01

4a01


Resolution: 3.5→30 Å / Cor.coef. Fo:Fc: 0.92 / Cor.coef. Fo:Fc free: 0.871 / SU B: 45.007 / SU ML: 0.636 / Cross valid method: THROUGHOUT / ESU R Free: 0.693
RfactorNum. reflection% reflectionSelection details
Rfree0.30378 3027 5.3 %RANDOM
Rwork0.2256 ---
obs0.22979 54540 91.11 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 119.6 Å2
Baniso -1Baniso -2Baniso -3
1-9.45 Å2-0 Å23.38 Å2
2--0.43 Å20 Å2
3----10.17 Å2
Refinement stepCycle: LAST / Resolution: 3.5→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms21385 0 28 0 21413
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.01921818
X-RAY DIFFRACTIONr_bond_other_d0.0060.0221465
X-RAY DIFFRACTIONr_angle_refined_deg1.4761.96929643
X-RAY DIFFRACTIONr_angle_other_deg1.055349283
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.97652899
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.43523.909683
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.433153465
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.271552
X-RAY DIFFRACTIONr_chiral_restr0.0790.23598
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0224455
X-RAY DIFFRACTIONr_gen_planes_other0.0020.024717
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it6.00211.66111641
X-RAY DIFFRACTIONr_mcbond_other6.00111.66111640
X-RAY DIFFRACTIONr_mcangle_it9.73317.48214525
X-RAY DIFFRACTIONr_mcangle_other9.73317.48214526
X-RAY DIFFRACTIONr_scbond_it5.49812.20710177
X-RAY DIFFRACTIONr_scbond_other5.49112.20510174
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other9.30718.09315113
X-RAY DIFFRACTIONr_long_range_B_refined14.15594.55626079
X-RAY DIFFRACTIONr_long_range_B_other14.15494.55526079
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 3.5→3.558 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.447 203 -
Rwork0.4 3198 -
obs--72.83 %

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