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- PDB-4a01: Crystal Structure of the H-Translocating Pyrophosphatase -

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Basic information

Entry
Database: PDB / ID: 4a01
TitleCrystal Structure of the H-Translocating Pyrophosphatase
ComponentsPROTON PYROPHOSPHATASE
KeywordsHYDROLASE / MEMBRANE PROTEIN / PROTON PUMPING
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
IMIDODIPHOSPHORIC ACID / : / Pyrophosphate-energized vacuolar membrane proton pump / Pyrophosphate-energized vacuolar membrane proton pump
Similarity search - Component
Biological speciesVIGNA RADIATA (mung bean)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.35 Å
AuthorsLin, S.-M. / Tsai, J.-Y. / Hsiao, C.-D. / Chiu, C.-L. / Pan, R.-L. / Sun, Y.-J.
CitationJournal: Nature / Year: 2012
Title: Crystal Structure of a Membrane Embedded H1-Translocating Pyrophosphatase
Authors: Lin, S.-M. / Tsai, J.-Y. / Hsiao, C.-D. / Chiu, C.-L. / Pan, R.-L. / Sun, Y.-J.
History
DepositionSep 7, 2011Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 28, 2012Provider: repository / Type: Initial release
Revision 1.1Apr 25, 2012Group: Other
Revision 1.2Nov 13, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_entry_details / pdbx_modification_feature / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _pdbx_entry_details.has_protein_modification / _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_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_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_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_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 / _struct_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 700 SHEET DETERMINATION METHOD: AUTHOR PROVIDED.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: PROTON PYROPHOSPHATASE
B: PROTON PYROPHOSPHATASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)165,20425
Polymers160,1862
Non-polymers5,01823
Water10,665592
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area15040 Å2
ΔGint-215.4 kcal/mol
Surface area42400 Å2
MethodPISA
Unit cell
Length a, b, c (Å)218.619, 88.241, 159.105
Angle α, β, γ (deg.)90.00, 125.53, 90.00
Int Tables number5
Space group name H-MC121

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Components

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Protein / Sugars , 2 types, 11 molecules AB

#1: Protein PROTON PYROPHOSPHATASE / H-TRANSLOCATING PYROPHOSPHATASE


Mass: 80092.828 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) VIGNA RADIATA (mung bean) / Plasmid: PYVH6 / Production host: SACCHAROMYCES CEREVISIAE (brewer's yeast) / Strain (production host): BJ2168
References: UniProt: O22124, UniProt: P21616*PLUS, inorganic diphosphatase
#5: Sugar
ChemComp-DMU / DECYL-BETA-D-MALTOPYRANOSIDE / DECYLMALTOSIDE


Type: D-saccharide / Mass: 482.562 Da / Num. of mol.: 9
Source method: isolated from a genetically manipulated source
Formula: C22H42O11 / Comment: detergent*YM

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Non-polymers , 4 types, 606 molecules

#2: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: K
#4: Chemical ChemComp-2PN / IMIDODIPHOSPHORIC ACID


Mass: 176.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: H5NO6P2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 592 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY
Sequence detailsTHE PROTEIN SEQUENCE OF ENTRY 4A01 HAD BEEN PUBLISHED AT PLANT PHYSIOL (1995) V.109, P1125-1127 AND ...THE PROTEIN SEQUENCE OF ENTRY 4A01 HAD BEEN PUBLISHED AT PLANT PHYSIOL (1995) V.109, P1125-1127 AND THE SEQUENCE OF RESIDUE 476 IS PHE. MEANWHILE, FROM THE ELECTRON DENSITY OMIT MAP, WE DETERMINED THAT RESIDUE 476 IS PHE.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 3.97 Å3/Da / Density % sol: 69 % / Description: NONE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: BL13B1 / Wavelength: 0.9
DetectorType: ADSC CCD / Detector: CCD
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 2.35→30 Å / Num. obs: 100220 / % possible obs: 98.7 % / Observed criterion σ(I): 2 / Redundancy: 3.84 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 20.8
Reflection shellResolution: 2.35→2.43 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.5 / Mean I/σ(I) obs: 2.7 / % possible all: 98.5

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Processing

Software
NameVersionClassification
REFMAC5.5.0109refinement
HKL-2000data reduction
SCALEPACKdata scaling
PHENIXphasing
RefinementMethod to determine structure: MAD
Starting model: NONE

Resolution: 2.35→30 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.946 / SU B: 5.074 / SU ML: 0.119 / Cross valid method: THROUGHOUT / ESU R: 0.2 / ESU R Free: 0.172 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20314 5005 5 %RANDOM
Rwork0.16803 ---
obs0.16981 95106 97.43 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 42.995 Å2
Baniso -1Baniso -2Baniso -3
1-0.94 Å20 Å2-3.1 Å2
2---0.86 Å20 Å2
3----3.69 Å2
Refinement stepCycle: LAST / Resolution: 2.35→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10862 0 305 592 11759
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0240.02211374
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.0561.99415447
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.43951476
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.69723.908348
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.068151764
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.5781528
X-RAY DIFFRACTIONr_chiral_restr0.1630.21906
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0218048
X-RAY DIFFRACTIONr_gen_planes_other
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_it0.9481.57290
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.7211672
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.93834084
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it4.5254.53775
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.35→2.411 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.276 306 -
Rwork0.243 5927 -
obs--82.75 %

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