[English] 日本語
Yorodumi
- PDB-5yk2: The complex structure of Rv3197-erythromycin from Mycobacterium t... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5yk2
TitleThe complex structure of Rv3197-erythromycin from Mycobacterium tuberculosis
ComponentsProbable conserved ATP-binding protein ABC transporter
KeywordsTRANSPORT PROTEIN / Mycobacterium tuberculosis / macrolide antibiotic binding protein / non-canonical ABC protein
Function / homologyABC1 atypical kinase-like domain / ADCK3-like domain / ABC1 atypical kinase-like domain / peptidoglycan-based cell wall / Protein kinase-like domain superfamily / ATP binding / ERYTHROMYCIN A / Probable conserved ATP-binding protein ABC transporter
Function and homology information
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.807 Å
AuthorsRao, Z.H. / Zhang, Q.Q.
Funding support China, 3items
OrganizationGrant numberCountry
State Key Development Program for Basic Research of the Ministry of Science and Technology of China2014CB542800 China
National Natural Science Foundation of China81330036 China
National Natural Science Foundation of China81520108019 China
CitationJournal: Protein Cell / Year: 2018
Title: Discovery of the first macrolide antibiotic binding protein in Mycobacterium tuberculosis: a new antibiotic resistance drug target.
Authors: Zhang, Q. / Liu, H. / Liu, X. / Jiang, D. / Zhang, B. / Tian, H. / Yang, C. / Guddat, L.W. / Yang, H. / Mi, K. / Rao, Z.
History
DepositionOct 11, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 7, 2018Provider: repository / Type: Initial release
Revision 1.1Nov 21, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Nov 22, 2023Group: 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: Probable conserved ATP-binding protein ABC transporter
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,3332
Polymers49,5991
Non-polymers7341
Water0
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area920 Å2
ΔGint-7 kcal/mol
Surface area21850 Å2
MethodPISA
Unit cell
Length a, b, c (Å)187.238, 187.238, 67.205
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number182
Space group name H-MP6322

-
Components

#1: Protein Probable conserved ATP-binding protein ABC transporter / macrolide antibiotic binding protein


Mass: 49599.285 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv) (bacteria)
Strain: ATCC 25618 / H37Rv / Gene: Rv3197 / Plasmid: pGEX-6P-1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-Codon Plus (DE3) RIL / References: UniProt: O53343
#2: Chemical ChemComp-ERY / ERYTHROMYCIN A / Erythromycin


Mass: 733.927 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C37H67NO13 / Feature type: SUBJECT OF INVESTIGATION / Comment: antibiotic*YM

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.47 Å3/Da / Density % sol: 64.5 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 1.8M ammonium sulfate, 0.1M Bis-Tris (pH 6.5), 2% (v/v) polyethylene glycol monomethyl ether 550

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97855 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 9, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97855 Å / Relative weight: 1
ReflectionResolution: 2.8→50 Å / Num. obs: 17350 / % possible obs: 99.4 % / Redundancy: 13.2 % / Rmerge(I) obs: 0.079 / Net I/σ(I): 26.5
Reflection shellResolution: 2.8→2.9 Å / Redundancy: 13.4 % / Rmerge(I) obs: 0.723 / Mean I/σ(I) obs: 2.7 / Num. unique obs: 1686 / % possible all: 100

-
Processing

Software
NameVersionClassification
PHENIX1.8.4_1496refinement
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5YJZ

5yjz


Resolution: 2.807→34.712 Å / SU ML: 0.37 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 27.1
RfactorNum. reflection% reflection
Rfree0.2738 886 5.19 %
Rwork0.2294 --
obs0.2317 17071 97.82 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.807→34.712 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3042 0 51 0 3093
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0023157
X-RAY DIFFRACTIONf_angle_d0.7214284
X-RAY DIFFRACTIONf_dihedral_angle_d12.8611219
X-RAY DIFFRACTIONf_chiral_restr0.025490
X-RAY DIFFRACTIONf_plane_restr0.004553
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.8072-2.9830.33461540.29852442X-RAY DIFFRACTION92
2.983-3.21310.32791510.27482694X-RAY DIFFRACTION99
3.2131-3.53620.28481500.25782712X-RAY DIFFRACTION100
3.5362-4.04720.27461570.2222713X-RAY DIFFRACTION100
4.0472-5.09650.21991410.20142771X-RAY DIFFRACTION99
5.0965-34.71470.27111330.20892853X-RAY DIFFRACTION97
Refinement TLS params.Method: refined / Origin x: -74.8865 Å / Origin y: 23.6794 Å / Origin z: 9.7816 Å
111213212223313233
T0.5257 Å2-0.009 Å2-0.1726 Å2-0.3796 Å2-0.3295 Å2--0.502 Å2
L0.2303 °20.0895 °2-0.0971 °2-0.5451 °20.2364 °2--0.3158 °2
S-0.1275 Å °-0.0376 Å °0.0751 Å °0.0507 Å °0.186 Å °-0.0987 Å °0.2257 Å °0.1199 Å °0.0317 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