[English] 日本語
Yorodumi
- PDB-9ejn: Crystal structure of magnesium-transporting ATPase MgtA in an E1-... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 9ejn
TitleCrystal structure of magnesium-transporting ATPase MgtA in an E1-like magnesium-bound state
ComponentsMagnesium-transporting ATPase, P-type 1
KeywordsMETAL TRANSPORT / Membrane protein / P-Type Atpase / Magnesium Ion
Function / homology
Function and homology information


P-type Mg2+ transporter / P-type magnesium transporter activity / ATP hydrolysis activity / ATP binding / plasma membrane
Similarity search - Function
P-type ATPase, subfamily IIIB / Cation-transporting P-type ATPase, C-terminal / Cation transporting ATPase, C-terminus / Cation transporter/ATPase, N-terminus / Cation-transporting P-type ATPase, N-terminal / Cation transporter/ATPase, N-terminus / E1-E2 ATPase / P-type ATPase, haloacid dehalogenase domain / P-type ATPase, phosphorylation site / P-type ATPase, cytoplasmic domain N ...P-type ATPase, subfamily IIIB / Cation-transporting P-type ATPase, C-terminal / Cation transporting ATPase, C-terminus / Cation transporter/ATPase, N-terminus / Cation-transporting P-type ATPase, N-terminal / Cation transporter/ATPase, N-terminus / E1-E2 ATPase / P-type ATPase, haloacid dehalogenase domain / P-type ATPase, phosphorylation site / P-type ATPase, cytoplasmic domain N / E1-E2 ATPases phosphorylation site. / P-type ATPase, A domain superfamily / P-type ATPase / P-type ATPase, transmembrane domain superfamily / haloacid dehalogenase-like hydrolase / HAD superfamily / HAD-like superfamily
Similarity search - Domain/homology
Magnesium-transporting ATPase, P-type 1
Similarity search - Component
Biological speciesLactococcus lactis subsp. lactis CV56 (lactic acid bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.55 Å
AuthorsKhan, M.B. / Primeau, J.O. / Basu, P.C. / Morth, J.P. / Lemieux, M.J. / Young, H.S.
Funding support Canada, 1items
OrganizationGrant numberCountry
Canadian Institutes of Health Research (CIHR) Canada
CitationJournal: To Be Published
Title: Crystal structure of magnesium-transporting ATPase MgtA in an E1-like magnesium-bound state
Authors: Khan, M.B. / Primeau, J.O. / Basu, P.C. / Morth, J.P. / Lemieux, M.J. / Young, H.S.
History
DepositionNov 28, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 26, 2025Provider: repository / Type: Initial release
Revision 1.1Mar 5, 2025Group: Database references / Structure summary / Category: audit_author / citation_author

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Magnesium-transporting ATPase, P-type 1
C: Magnesium-transporting ATPase, P-type 1
B: Magnesium-transporting ATPase, P-type 1
D: Magnesium-transporting ATPase, P-type 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)406,1138
Polymers406,0164
Non-polymers974
Water00
1
A: Magnesium-transporting ATPase, P-type 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)101,5282
Polymers101,5041
Non-polymers241
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: Magnesium-transporting ATPase, P-type 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)101,5282
Polymers101,5041
Non-polymers241
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
B: Magnesium-transporting ATPase, P-type 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)101,5282
Polymers101,5041
Non-polymers241
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Magnesium-transporting ATPase, P-type 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)101,5282
Polymers101,5041
Non-polymers241
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)180.403, 66.595, 218.666
Angle α, β, γ (deg.)90.000, 90.151, 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

-
Components

#1: Protein
Magnesium-transporting ATPase, P-type 1 / Mg(2+) transport ATPase / P-type 1


Mass: 101503.906 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lactococcus lactis subsp. lactis CV56 (lactic acid bacteria)
Gene: LL275_1350 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A1V0NGB6, P-type Mg2+ transporter
#2: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY
Has protein modificationN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.24 Å3/Da / Density % sol: 61.98 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 4% tert-butanol, 100 mM MgSo4, 14% 2000 MME, 10% Glycerol, 100 mM MOPS pH 6.8

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-1 / Wavelength: 0.97946 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 19, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97946 Å / Relative weight: 1
ReflectionResolution: 3.2→25 Å / Num. obs: 85323 / % possible obs: 99 % / Redundancy: 1.8 % / CC1/2: 0.85 / Net I/σ(I): 2
Reflection shellResolution: 3.21→3.25 Å / Num. unique obs: 7632 / CC1/2: 0.31

-
Processing

Software
NameVersionClassification
PHENIX1.21.2_5419refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.55→24.91 Å / SU ML: 0.5861 / Cross valid method: FREE R-VALUE / σ(F): 1.99 / Phase error: 39.6881
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.339 3123 4.97 %
Rwork0.288 59678 -
obs0.2905 62801 98.55 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 98.1 Å2
Refinement stepCycle: LAST / Resolution: 3.55→24.91 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms27348 0 4 0 27352
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.001927824
X-RAY DIFFRACTIONf_angle_d0.474337704
X-RAY DIFFRACTIONf_chiral_restr0.03864564
X-RAY DIFFRACTIONf_plane_restr0.00384704
X-RAY DIFFRACTIONf_dihedral_angle_d12.635710200
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.55-3.610.38511660.3762643X-RAY DIFFRACTION99.29
3.61-3.660.4431360.37922751X-RAY DIFFRACTION99.93
3.66-3.730.41061270.36282729X-RAY DIFFRACTION99.1
3.73-3.790.43941600.35142660X-RAY DIFFRACTION99.75
3.79-3.870.38691830.33272686X-RAY DIFFRACTION98.79
3.87-3.950.33461210.30742769X-RAY DIFFRACTION99.62
3.95-4.030.37591340.29762645X-RAY DIFFRACTION99.5
4.03-4.120.30691100.28752820X-RAY DIFFRACTION99.63
4.13-4.230.33191590.28112675X-RAY DIFFRACTION98.99
4.23-4.340.34581280.27632713X-RAY DIFFRACTION99.3
4.34-4.470.34151730.26262680X-RAY DIFFRACTION97.94
4.47-4.610.3131590.26672577X-RAY DIFFRACTION97.06
4.61-4.780.32181370.25912606X-RAY DIFFRACTION93.91
4.78-4.970.28731460.25032713X-RAY DIFFRACTION99.27
4.97-5.190.27871470.25472763X-RAY DIFFRACTION99.59
5.19-5.460.32161460.2682712X-RAY DIFFRACTION99.44
5.46-5.80.34911130.27092760X-RAY DIFFRACTION99.45
5.8-6.240.33711340.28192769X-RAY DIFFRACTION99.49
6.24-6.860.32251260.30112756X-RAY DIFFRACTION98.73
6.86-7.820.31291440.26872772X-RAY DIFFRACTION99.08
7.82-9.750.25691290.23482672X-RAY DIFFRACTION94.15
9.75-24.910.36691450.31152807X-RAY DIFFRACTION96.47
Refinement TLS params.Method: refined / Origin x: -33.8549210642 Å / Origin y: -38.8854656566 Å / Origin z: -42.5361815016 Å
111213212223313233
T0.45703540038 Å2-0.0500227559867 Å20.0910159532009 Å2-0.413852000217 Å20.0766353837672 Å2--1.44483569538 Å2
L0.0118972369659 °20.0158413493282 °2-0.0934796054652 °2-0.0213783274418 °2-0.0137764065852 °2--0.203508778541 °2
S0.00204959926425 Å °-0.0789770143542 Å °0.031539537899 Å °0.13229511278 Å °0.00964812212038 Å °0.0174036093892 Å °-0.0604595653055 Å °0.000306326680849 Å °-0.0269621435351 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