[English] 日本語
Yorodumi
- PDB-8b37: Crystal structure of Pyrobaculum aerophilum potassium-independent... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8b37
TitleCrystal structure of Pyrobaculum aerophilum potassium-independent proton pumping membrane integral pyrophosphatase in complex with imidodiphosphate and magnesium, and with bound sulphate
ComponentsK(+)-insensitive pyrophosphate-energized proton pump
KeywordsMEMBRANE PROTEIN / K+-independence / Ion-selectivity / Membrane Proteins / Membrane-bound pyrophosphatases.
Function / homologyH+-exporting diphosphatase / diphosphate hydrolysis-driven proton transmembrane transporter activity / Pyrophosphate-energised proton pump / Inorganic H+ pyrophosphatase / inorganic diphosphate phosphatase activity / magnesium ion binding / plasma membrane / IMIDODIPHOSPHORIC ACID / K(+)-insensitive pyrophosphate-energized proton pump
Function and homology information
Biological speciesPyrobaculum aerophilum (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.84 Å
AuthorsStrauss, J. / Wilkinson, C. / Vidilaseris, K. / Ribeiro, O. / Liu, J. / Hillier, J. / Malinen, A. / Gehl, B. / Jeuken, L.C. / Pearson, A.R. / Goldman, A.
Funding supportEuropean Union, United Kingdom, Finland, Germany, 8items
OrganizationGrant numberCountry
H2020 Marie Curie Actions of the European Commission722687European Union
Other governmentUniversity of Leeds 110th Anniversary Fellowship University of Leeds
Biotechnology and Biological Sciences Research Council (BBSRC)BB/M021610/1 United Kingdom
Academy of Finland1322609 Finland
Academy of Finland308105 Finland
Academy of Finland307775 Finland
German Research Foundation (DFG)EXC1074 Germany
German Research Foundation (DFG)EXC2056 Germany
CitationJournal: Embo Rep. / Year: 2024
Title: Functional and structural asymmetry suggest a unifying principle for catalysis in membrane-bound pyrophosphatases.
Authors: Strauss, J. / Wilkinson, C. / Vidilaseris, K. / de Castro Ribeiro, O.M. / Liu, J. / Hillier, J. / Wichert, M. / Malinen, A.M. / Gehl, B. / Jeuken, L.J. / Pearson, A.R. / Goldman, A.
History
DepositionSep 16, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 17, 2024Provider: repository / Type: Initial release
Revision 1.1Feb 21, 2024Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: K(+)-insensitive pyrophosphate-energized proton pump
B: K(+)-insensitive pyrophosphate-energized proton pump
hetero molecules


Theoretical massNumber of molelcules
Total (without water)153,46615
Polymers152,7732
Non-polymers69313
Water1267
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8500 Å2
ΔGint-190 kcal/mol
Surface area42600 Å2
MethodPISA
Unit cell
Length a, b, c (Å)107.190, 88.020, 116.750
Angle α, β, γ (deg.)90.000, 106.946, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11TYRTYRLEULEU(chain 'A' and (resid 6 through 281 or resid 286 through 715 or resid 800 through 806))AA6 - 2914 - 37
12ASNASNILEILE(chain 'A' and (resid 6 through 281 or resid 286 through 715 or resid 800 through 806))AA35 - 7543 - 83
13GLYGLYLYSLYS(chain 'A' and (resid 6 through 281 or resid 286 through 715 or resid 800 through 806))AA83 - 20291 - 210
14GLUGLULEULEU(chain 'A' and (resid 6 through 281 or resid 286 through 715 or resid 800 through 806))AA209 - 281217 - 289
15GLYGLYVALVAL(chain 'A' and (resid 6 through 281 or resid 286 through 715 or resid 800 through 806))AA286 - 403294 - 411
16PHEPHESERSER(chain 'A' and (resid 6 through 281 or resid 286 through 715 or resid 800 through 806))AA408 - 507416 - 515
17ASPASPGLUGLU(chain 'A' and (resid 6 through 281 or resid 286 through 715 or resid 800 through 806))AA516 - 577524 - 585
18PROPROPROPRO(chain 'A' and (resid 6 through 281 or resid 286 through 715 or resid 800 through 806))AA582 - 715590 - 723
192PN2PN2PN2PN(chain 'A' and (resid 6 through 281 or resid 286 through 715 or resid 800 through 806))AH806
210TYRTYRLEULEU(chain 'B' and (resid 6 through 202 or resid 209 through 715 or resid 800 through 806))BB6 - 2914 - 37
211ASNASNILEILE(chain 'B' and (resid 6 through 202 or resid 209 through 715 or resid 800 through 806))BB35 - 7543 - 83
212GLYGLYLYSLYS(chain 'B' and (resid 6 through 202 or resid 209 through 715 or resid 800 through 806))BB83 - 20291 - 210
213GLUGLULEULEU(chain 'B' and (resid 6 through 202 or resid 209 through 715 or resid 800 through 806))BB209 - 281217 - 289
214GLYGLYVALVAL(chain 'B' and (resid 6 through 202 or resid 209 through 715 or resid 800 through 806))BB286 - 403294 - 411
215PHEPHESERSER(chain 'B' and (resid 6 through 202 or resid 209 through 715 or resid 800 through 806))BB408 - 507416 - 515
216ASPASPGLUGLU(chain 'B' and (resid 6 through 202 or resid 209 through 715 or resid 800 through 806))BB516 - 577524 - 585
217PROPROPROPRO(chain 'B' and (resid 6 through 202 or resid 209 through 715 or resid 800 through 806))BB582 - 715590 - 723
2182PN2PN2PN2PN(chain 'B' and (resid 6 through 202 or resid 209 through 715 or resid 800 through 806))BN806

NCS oper: (Code: givenMatrix: (-0.682792931713, -0.00748929439109, -0.730573557468), (-0.00250242749683, -0.999917621891, 0.0125891734653), (-0.730607658226, 0.0104240060169, 0.682717943107)Vector: ...NCS oper: (Code: given
Matrix: (-0.682792931713, -0.00748929439109, -0.730573557468), (-0.00250242749683, -0.999917621891, 0.0125891734653), (-0.730607658226, 0.0104240060169, 0.682717943107)
Vector: 11.7395838615, -8.30170682806, 5.3366665906)

-
Components

#1: Protein K(+)-insensitive pyrophosphate-energized proton pump / Membrane-bound proton-translocating pyrophosphatase / Pyrophosphate-energized inorganic ...Membrane-bound proton-translocating pyrophosphatase / Pyrophosphate-energized inorganic pyrophosphatase / H(+)-PPase


Mass: 76386.641 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pyrobaculum aerophilum (archaea)
Strain: ATCC 51768 / DSM 7523 / JCM 9630 / CIP 104966 / NBRC 100827 / IM2
Gene: hppA, PAE1771 / Production host: Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: Q8ZWI8, H+-exporting diphosphatase
#2: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-2PN / IMIDODIPHOSPHORIC ACID


Mass: 176.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: H5NO6P2 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4 / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 7 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 3.45 Å3/Da / Density % sol: 64.33 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 30-33% PEG 400, 0.1 M MES pH 6.5, 0.05 M LiSO4, and 0.05 M NaCl

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.966 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Nov 1, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.966 Å / Relative weight: 1
ReflectionResolution: 3.84→19.97 Å / Num. obs: 13069 / % possible obs: 87.6 % / Redundancy: 5 % / Biso Wilson estimate: 112.15 Å2 / CC1/2: 0.979 / Net I/σ(I): 3.9
Reflection shellResolution: 3.84→3.98 Å / Num. unique obs: 653 / CC1/2: 0.404

-
Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
XDSdata reduction
XSCALEdata scaling
STARANISOdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5LZQ

5lzq


Resolution: 3.84→19.97 Å / SU ML: 0.6561 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 42.611
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.3107 667 5.11 %
Rwork0.289 12386 -
obs0.2901 13053 65.32 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 106.95 Å2
Refinement stepCycle: LAST / Resolution: 3.84→19.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9689 0 33 7 9729
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00199863
X-RAY DIFFRACTIONf_angle_d0.491213483
X-RAY DIFFRACTIONf_chiral_restr0.03351722
X-RAY DIFFRACTIONf_plane_restr0.00311656
X-RAY DIFFRACTIONf_dihedral_angle_d13.23413281
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.84-4.130.3411570.3413994X-RAY DIFFRACTION26.7
4.13-4.540.3811880.30741851X-RAY DIFFRACTION49.04
4.54-5.190.31191060.29462375X-RAY DIFFRACTION62.1
5.19-6.50.34312070.36163319X-RAY DIFFRACTION88.11
6.5-19.970.28042090.24973847X-RAY DIFFRACTION99.17
Refinement TLS params.Method: refined / Origin x: -7.38371920412 Å / Origin y: -3.98945958326 Å / Origin z: 33.3006907892 Å
111213212223313233
T0.761539973867 Å2-0.0443121007259 Å20.0856904431395 Å2-0.485042398234 Å2-0.0408970480169 Å2--0.578482349707 Å2
L1.57531257473 °2-0.20008318612 °20.120460501252 °2-1.73165329471 °2-0.103233609114 °2--1.56649792312 °2
S-0.0413822888853 Å °0.000113887547153 Å °-0.0476334435518 Å °0.15923339801 Å °0.0271103109303 Å °0.0627784628792 Å °0.161130850969 Å °0.148182330549 Å °0.00703187072351 Å °
Refinement TLS groupSelection details: all

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more