[English] 日本語
Yorodumi
- PDB-5lj8: Structure of the E. coli MacB periplasmic domain (P21) -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5lj8
TitleStructure of the E. coli MacB periplasmic domain (P21)
ComponentsMacrolide export ATP-binding/permease protein MacB
KeywordsTRANSPORT PROTEIN / Membrane Protein ABC Transporter
Function / homology
Function and homology information


polymyxin transport / polymyxin transmembrane transporter activity / MacAB-TolC complex / xenobiotic detoxification by transmembrane export across the plasma membrane / Translocases; Catalysing the translocation of other compounds; Linked to the hydrolysis of a nucleoside triphosphate / ABC-type xenobiotic transporter activity / transmembrane transporter activity / response to antibiotic / protein homodimerization activity / ATP hydrolysis activity ...polymyxin transport / polymyxin transmembrane transporter activity / MacAB-TolC complex / xenobiotic detoxification by transmembrane export across the plasma membrane / Translocases; Catalysing the translocation of other compounds; Linked to the hydrolysis of a nucleoside triphosphate / ABC-type xenobiotic transporter activity / transmembrane transporter activity / response to antibiotic / protein homodimerization activity / ATP hydrolysis activity / ATP binding / identical protein binding / membrane / plasma membrane
Similarity search - Function
Macrolide export ATP-binding/permease protein macB family profile. / : / MacB-like periplasmic core domain / MacB-like periplasmic core domain / MacB, ATP-binding domain / ABC3 transporter permease protein domain / FtsX-like permease C-terminal / ABC transporter-like, conserved site / ABC transporters family signature. / ABC transporter ...Macrolide export ATP-binding/permease protein macB family profile. / : / MacB-like periplasmic core domain / MacB-like periplasmic core domain / MacB, ATP-binding domain / ABC3 transporter permease protein domain / FtsX-like permease C-terminal / ABC transporter-like, conserved site / ABC transporters family signature. / ABC transporter / ABC transporter-like, ATP-binding domain / ATP-binding cassette, ABC transporter-type domain profile. / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Macrolide export ATP-binding/permease protein MacB
Similarity search - Component
Biological speciesEscherichia coli K-12 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å
AuthorsCrow, A.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Medical Research Council (United Kingdom)MR/N000994/1 United Kingdom
CitationJournal: Proc. Natl. Acad. Sci. U.S.A. / Year: 2017
Title: Structure and mechanotransmission mechanism of the MacB ABC transporter superfamily.
Authors: Crow, A. / Greene, N.P. / Kaplan, E. / Koronakis, V.
History
DepositionJul 18, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 15, 2017Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2017Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Jan 24, 2018Group: Source and taxonomy / Category: entity_src_gen
Item: _entity_src_gen.pdbx_host_org_ncbi_taxonomy_id / _entity_src_gen.pdbx_host_org_scientific_name ..._entity_src_gen.pdbx_host_org_ncbi_taxonomy_id / _entity_src_gen.pdbx_host_org_scientific_name / _entity_src_gen.pdbx_host_org_strain / _entity_src_gen.pdbx_host_org_variant
Revision 1.3Jan 10, 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 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Macrolide export ATP-binding/permease protein MacB
B: Macrolide export ATP-binding/permease protein MacB


Theoretical massNumber of molelcules
Total (without water)47,2292
Polymers47,2292
Non-polymers00
Water1,78399
1
A: Macrolide export ATP-binding/permease protein MacB


Theoretical massNumber of molelcules
Total (without water)23,6141
Polymers23,6141
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Macrolide export ATP-binding/permease protein MacB


Theoretical massNumber of molelcules
Total (without water)23,6141
Polymers23,6141
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)50.110, 54.860, 66.890
Angle α, β, γ (deg.)90.00, 92.86, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: THR / Beg label comp-ID: THR / End auth comp-ID: ASN / End label comp-ID: ASN / Refine code: _ / Auth seq-ID: 311 - 506 / Label seq-ID: 4 - 199

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

-
Components

#1: Protein Macrolide export ATP-binding/permease protein MacB


Mass: 23614.443 Da / Num. of mol.: 2 / Fragment: UNP residues 309-508
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli K-12 (bacteria) / Gene: macB, ybjZ, b0879, JW0863 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): C43
References: UniProt: P75831, Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to catalyse transmembrane movement of substances
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 99 / 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: 1.94 Å3/Da / Density % sol: 36.74 %
Crystal growTemperature: 288 K / Method: vapor diffusion, sitting drop
Details: 30% Pentaerythritol ethoxylate (15/4 EO/OH), 6% polyvinylpyrrolidone, 100mM HEPES pH 7.5

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.96861 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Sep 9, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.96861 Å / Relative weight: 1
ReflectionResolution: 1.95→66.81 Å / Num. obs: 25260 / % possible obs: 99.8 % / Redundancy: 3.4 % / Rsym value: 0.089 / Net I/σ(I): 8.1
Reflection shellRsym value: 0.542

-
Processing

Software
NameVersionClassification
REFMAC5.8.0069refinement
iMOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3ftj

3ftj


Resolution: 1.95→32.87 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.92 / SU B: 4.376 / SU ML: 0.122 / Cross valid method: THROUGHOUT / ESU R: 0.189 / ESU R Free: 0.165 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22772 1309 4.9 %RANDOM
Rwork0.17796 ---
obs0.18043 25260 99.76 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 25.77 Å2
Baniso -1Baniso -2Baniso -3
1-2.24 Å20 Å2-
2---0.89 Å20 Å2
3----1.3 Å2
Refinement stepCycle: 1 / Resolution: 1.95→32.87 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3181 0 0 99 3280
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0193345
X-RAY DIFFRACTIONr_bond_other_d0.0060.023112
X-RAY DIFFRACTIONr_angle_refined_deg1.6591.9284551
X-RAY DIFFRACTIONr_angle_other_deg1.23437125
X-RAY DIFFRACTIONr_dihedral_angle_1_deg
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0950.2487
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.023968
X-RAY DIFFRACTIONr_gen_planes_other0.0050.02843
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_it2.2872.3121656
X-RAY DIFFRACTIONr_mcbond_other2.2872.3111655
X-RAY DIFFRACTIONr_mcangle_it3.4263.4532084
X-RAY DIFFRACTIONr_mcangle_other3.4273.4552085
X-RAY DIFFRACTIONr_scbond_it3.1882.7491689
X-RAY DIFFRACTIONr_scbond_other3.1882.7511690
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.9313.9552468
X-RAY DIFFRACTIONr_long_range_B_refined6.74424.652739
X-RAY DIFFRACTIONr_long_range_B_other6.66224.6432724
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Number: 11366 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.14 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 1.95→2.001 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.258 92 -
Rwork0.248 1872 -
obs--99.59 %

+
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