[English] 日本語
Yorodumi
- PDB-7agy: Structure of the N-domain of the K+/H+ antiporter subunit KhtT at... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7agy
TitleStructure of the N-domain of the K+/H+ antiporter subunit KhtT at pH 8.5
ComponentsK(+)/H(+) antiporter subunit KhtT
KeywordsTRANSPORT PROTEIN / Regulatory protein of K+/H+ antiporter
Function / homologyPotassium/proton antiporter subunit KhtT / Regulator of K+ conductance, C-terminal / Regulator of K+ conductance, C-terminal domain superfamily / TrkA-C domain / RCK C-terminal domain profile. / monoatomic cation transmembrane transporter activity / potassium ion transport / plasma membrane / K(+)/H(+) antiporter subunit KhtT
Function and homology information
Biological speciesBacillus subtilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.54 Å
AuthorsCereija, T.B. / Morais-Cabral, J.H.
Funding support Portugal, 1items
OrganizationGrant numberCountry
Fundacao para a Ciencia e a TecnologiaPOCI-01-0145-FEDER-029863(PTDC/BIA-BQM/29863/2017) Portugal
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2021
Title: c-di-AMP, a likely master regulator of bacterial K + homeostasis machinery, activates a K + exporter.
Authors: Cereija, T.B. / Guerra, J.P.L. / Jorge, J.M.P. / Morais-Cabral, J.H.
History
DepositionSep 23, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 31, 2021Provider: repository / Type: Initial release
Revision 1.1Apr 7, 2021Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Apr 14, 2021Group: Database references / Category: citation / Item: _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.3Jan 31, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: K(+)/H(+) antiporter subunit KhtT
B: K(+)/H(+) antiporter subunit KhtT


Theoretical massNumber of molelcules
Total (without water)16,0142
Polymers16,0142
Non-polymers00
Water1,35175
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2800 Å2
ΔGint-18 kcal/mol
Surface area7680 Å2
MethodPISA
Unit cell
Length a, b, c (Å)35.197, 63.594, 64.568
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein K(+)/H(+) antiporter subunit KhtT


Mass: 8006.892 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (strain 168) (bacteria)
Strain: 168 / Gene: khtT, yhaT, BSU09860 / Production host: Escherichia coli (E. coli) / References: UniProt: O07535
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 75 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.27 Å3/Da / Density % sol: 45.8 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 100 mM Bis-Tris propane pH 8.5 200 mM KNa tartrate 20% PEG 3350

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.978566 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 17, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.978566 Å / Relative weight: 1
ReflectionResolution: 1.54→45.31 Å / Num. obs: 22120 / % possible obs: 99.8 % / Redundancy: 12.9 % / CC1/2: 0.999 / Rmerge(I) obs: 0.051 / Rpim(I) all: 0.015 / Rrim(I) all: 0.053 / Net I/σ(I): 20.7
Reflection shellResolution: 1.54→1.57 Å / Rmerge(I) obs: 1.048 / Mean I/σ(I) obs: 1.6 / Num. unique obs: 1075 / CC1/2: 0.91 / Rpim(I) all: 0.295 / Rrim(I) all: 1.089

-
Processing

Software
NameVersionClassification
PHENIX1.8.2_1309refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7AGV

7agv


Resolution: 1.54→32.284 Å / SU ML: 0.16 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 33.28 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2338 1028 4.67 %
Rwork0.2247 20997 -
obs0.2252 22025 99.58 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 134.62 Å2 / Biso mean: 48.7163 Å2 / Biso min: 25.17 Å2
Refinement stepCycle: final / Resolution: 1.54→32.284 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1114 0 0 75 1189
Biso mean---50.41 -
Num. residues----140
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0061183
X-RAY DIFFRACTIONf_angle_d0.9831596
X-RAY DIFFRACTIONf_chiral_restr0.07173
X-RAY DIFFRACTIONf_plane_restr0.003220
X-RAY DIFFRACTIONf_dihedral_angle_d14.436472
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.54-1.62120.321410.28312943100
1.6212-1.72280.32861550.27182935100
1.7228-1.85580.29961590.25482961100
1.8558-2.04250.25821210.24512985100
2.0425-2.3380.26551430.23643018100
2.338-2.94530.26721470.26083039100
2.9453-32.2840.20541620.1999311699
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
13.5472-2.31081.77212.96-0.90949.6564-0.05690.29680.0524-0.9010.17950.32680.10590.1891-0.08820.3702-0.0238-0.05560.2767-0.00920.2822-6.9035-7.16624.5466
28.63290.83680.39883.4366-1.06758.7356-0.23350.45880.9011-0.39820.0866-0.4253-1.25710.48450.19870.4136-0.1011-0.03490.36210.01580.2877-2.79920.13098.0288
34.2892.52393.02358.66843.10098.03790.5853-0.4513-0.38350.7996-0.14630.00690.65220.3361-0.47330.2806-0.0359-0.00020.2509-0.0090.2483-2.585-6.966914.5604
45.0884-4.82073.91355.4082-2.36625.3232-0.4686-0.78342.5358-1.8512-0.4385-4.1119-1.00823.38970.95970.7851-0.12570.22350.785-0.17261.19579.9410.13035.2801
54.98863.9169-6.18724.531-3.06739.1807-0.67510.0833-0.51910.05930.6409-0.76461.06330.1387-0.04720.31110.0513-0.02350.3345-0.06740.39281.1636-4.477718.0152
68.9531-1.5198-0.67242.7647-2.70858.7411-0.377-0.9218-0.04050.66020.70040.6660.3463-1.1031-0.35970.2583-0.07670.09270.4102-0.01930.3155-12.0041-0.177721.343
72.92272.22940.88633.1015-2.99029.32060.0126-0.17920.18350.67190.07530.039-0.52590.3208-0.13040.40860.00530.05870.2959-0.01530.2532-5.86129.676128.4179
83.8305-1.04111.83092.5592-1.81084.87730.0539-0.0042-0.44220.2690.12480.21140.59070.6297-0.0760.37040.09660.00030.3915-0.03150.2456-2.76973.630123.9117
98.33141.9636-2.43379.73424.26667.1157-0.21360.17050.2810.33350.329-0.9031-0.36590.3862-0.14890.2703-0.00380.03440.187-0.09090.20581.82977.868618.9291
103.36841.4163-1.5434.8834-5.28248.2848-0.36650.3732-0.0903-2.1070.64880.95010.4784-0.8-0.27930.35510.0415-0.10060.4-0.05810.3975-11.95393.030211.5762
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 0 through 18 )A0 - 18
2X-RAY DIFFRACTION2chain 'A' and (resid 19 through 30 )A19 - 30
3X-RAY DIFFRACTION3chain 'A' and (resid 31 through 40 )A31 - 40
4X-RAY DIFFRACTION4chain 'A' and (resid 41 through 47 )A41 - 47
5X-RAY DIFFRACTION5chain 'A' and (resid 48 through 55 )A48 - 55
6X-RAY DIFFRACTION6chain 'A' and (resid 56 through 68 )A56 - 68
7X-RAY DIFFRACTION7chain 'B' and (resid -2 through 18 )B-2 - 18
8X-RAY DIFFRACTION8chain 'B' and (resid 19 through 30 )B19 - 30
9X-RAY DIFFRACTION9chain 'B' and (resid 31 through 55 )B31 - 55
10X-RAY DIFFRACTION10chain 'B' and (resid 56 through 68 )B56 - 68

+
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