[English] 日本語
Yorodumi
- PDB-3w62: MamM-CTD E289A -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3w62
TitleMamM-CTD E289A
ComponentsMagnetosome protein MamM
KeywordsMETAL TRANSPORT / cation diffusion diffusion (CDF) / divalent metal cation / METAL ION TRANSPORT
Function / homology
Function and homology information


magnetosome membrane / monoatomic cation transmembrane transporter activity / iron ion transport / metal ion binding / plasma membrane
Similarity search - Function
: / Cation efflux protein, cytoplasmic domain / Cation efflux protein, cytoplasmic domain / : / Cation efflux protein, cytoplasmic domain / Cation efflux protein, cytoplasmic domain superfamily / Cation efflux protein / Cation efflux transmembrane domain superfamily / Cation efflux transmembrane domain / Alpha-Beta Plaits ...: / Cation efflux protein, cytoplasmic domain / Cation efflux protein, cytoplasmic domain / : / Cation efflux protein, cytoplasmic domain / Cation efflux protein, cytoplasmic domain superfamily / Cation efflux protein / Cation efflux transmembrane domain superfamily / Cation efflux transmembrane domain / Alpha-Beta Plaits / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Magnetosome protein MamM / Magnetosome protein MamM
Similarity search - Component
Biological speciesMagnetospirillum gryphiswaldense (magnetotactic)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.64 Å
AuthorsZeytuni, N. / Davidov, G. / Zarivach, R.
CitationJournal: Plos One / Year: 2014
Title: Cation diffusion facilitators transport initiation and regulation is mediated by cation induced conformational changes of the cytoplasmic domain
Authors: Zeytuni, N. / Uebe, R. / Maes, M. / Davidov, G. / Baram, M. / Raschdorf, O. / Nadav-Tsubery, M. / Kolusheva, S. / Bitton, R. / Goobes, G. / Friedler, A. / Miller, Y. / Schuler, D. / Zarivach, R.
History
DepositionFeb 10, 2013Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 16, 2014Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.2Nov 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 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Magnetosome protein MamM
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,1213
Polymers11,9281
Non-polymers1922
Water1,38777
1
A: Magnetosome protein MamM
hetero molecules

A: Magnetosome protein MamM
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,2416
Polymers23,8572
Non-polymers3844
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_554-x,y,-z-1/21
Buried area720 Å2
ΔGint-6 kcal/mol
Surface area9010 Å2
MethodPISA
Unit cell
Length a, b, c (Å)36.719, 94.912, 53.683
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-402-

SO4

-
Components

#1: Protein Magnetosome protein MamM / Magnetosome protein MamM / Cation efflux protein family / MamM protein


Mass: 11928.480 Da / Num. of mol.: 1 / Fragment: UNP residues 215-318 / Mutation: E289A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Magnetospirillum gryphiswaldense (magnetotactic)
Strain: MSR-1 / Gene: mamM, mgI491, MGR_4095 / Plasmid: pET28 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosseta / References: UniProt: Q6NE57, UniProt: V6F235*PLUS
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 77 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 1.96 Å3/Da / Density % sol: 37.26 % / Mosaicity: 0.371 °
Crystal growMethod: vapor diffusion, sitting drop / pH: 8
Details: 33% PEG 4000, 0.25M AmSO4, pH 8, VAPOR DIFFUSION, SITTING DROP

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.873 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Sep 10, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.873 Å / Relative weight: 1
ReflectionResolution: 1.64→50 Å / Num. obs: 11843 / % possible obs: 99.5 % / Redundancy: 5.9 % / Rmerge(I) obs: 0.043 / Χ2: 0.971 / Net I/σ(I): 15.5
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
1.64-1.675.80.2645870.7241100
1.67-1.760.2165750.7561100
1.7-1.7360.2255890.9281100
1.73-1.7760.1545740.7971100
1.77-1.816.10.1295880.7731100
1.81-1.8560.1195960.841100
1.85-1.8960.1055721.0451100
1.89-1.945.70.1025921.515199.8
1.94-260.0735741.0311100
2-2.075.80.0565960.854199.2
2.07-2.145.80.0535850.915199.8
2.14-2.2360.0445970.9331100
2.23-2.335.80.0485931.0271100
2.33-2.4560.0375980.851100
2.45-2.660.0345880.894199.7
2.6-2.85.80.0395971.13199.7
2.8-3.0960.0535981.2061100
3.09-3.535.80.0586061.264199.8
3.53-4.455.60.0356191.071199.4
4.45-505.20.0246190.895192.7

-
Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACT3.11data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3W5X

3w5x


Resolution: 1.64→47.46 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.956 / WRfactor Rfree: 0.2139 / WRfactor Rwork: 0.1911 / Occupancy max: 1 / Occupancy min: 0.34 / FOM work R set: 0.8614 / SU B: 3.695 / SU ML: 0.059 / SU R Cruickshank DPI: 0.0894 / SU Rfree: 0.0872 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.089 / ESU R Free: 0.087 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES: WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2041 564 4.8 %RANDOM
Rwork0.1798 ---
obs0.181 11803 99.18 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 65.54 Å2 / Biso mean: 26.1651 Å2 / Biso min: 9.27 Å2
Baniso -1Baniso -2Baniso -3
1-1.25 Å20 Å20 Å2
2---0.73 Å20 Å2
3----0.52 Å2
Refinement stepCycle: LAST / Resolution: 1.64→47.46 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms613 0 10 77 700
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0250.021671
X-RAY DIFFRACTIONr_bond_other_d0.0020.02453
X-RAY DIFFRACTIONr_angle_refined_deg1.8551.95915
X-RAY DIFFRACTIONr_angle_other_deg1.01731101
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.568589
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.19122.64734
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.59915113
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.289159
X-RAY DIFFRACTIONr_chiral_restr0.120.2102
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.02755
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02137
X-RAY DIFFRACTIONr_mcbond_it1.3881.5409
X-RAY DIFFRACTIONr_mcbond_other0.4361.5166
X-RAY DIFFRACTIONr_mcangle_it2.5032664
X-RAY DIFFRACTIONr_scbond_it4.2413262
X-RAY DIFFRACTIONr_scangle_it7.1544.5245
LS refinement shellResolution: 1.639→1.682 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.311 40 -
Rwork0.266 815 -
all-855 -
obs--98.84 %
Refinement TLS params.Method: refined / Origin x: -0.0419 Å / Origin y: 14.6151 Å / Origin z: -0.2182 Å
111213212223313233
T0.0398 Å2-0.0004 Å2-0.0208 Å2-0.0447 Å2-0.0354 Å2--0.0581 Å2
L-0.046 °2-0.4726 °20.0809 °2-1.7635 °21.0366 °2--1.7747 °2
S0.0463 Å °-0.022 Å °0.0467 Å °0.0612 Å °0.0643 Å °0.0276 Å °0.1907 Å °0.0529 Å °-0.1106 Å °

+
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