[English] 日本語
Yorodumi
- PDB-6li5: Crystal structure of apo-MCR-1-S -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6li5
TitleCrystal structure of apo-MCR-1-S
ComponentsProbable phosphatidylethanolamine transferase Mcr-1
KeywordsTRANSFERASE / MCR-1-S / ANTIBIOTIC
Function / homology
Function and homology information


transferase activity, transferring phosphorus-containing groups / Transferases; Transferring phosphorus-containing groups / response to antibiotic / plasma membrane
Similarity search - Function
Phosphoethanolamine transferase, N-terminal / Phosphoethanolamine transferase EptA/EptB / Phosphoethanolamine transferase / Sulfatase, N-terminal / Sulfatase / Alkaline-phosphatase-like, core domain superfamily
Similarity search - Domain/homology
Probable phosphatidylethanolamine transferase Mcr-1
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SAD / Resolution: 1.82 Å
AuthorsZhang, Q. / Wang, M. / Sun, H.
CitationJournal: Nat Commun / Year: 2020
Title: Resensitizing carbapenem- and colistin-resistant bacteria to antibiotics using auranofin.
Authors: Sun, H. / Zhang, Q. / Wang, R. / Wang, H. / Wong, Y.T. / Wang, M. / Hao, Q. / Yan, A. / Kao, R.Y. / Ho, P.L. / Li, H.
History
DepositionDec 10, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 16, 2020Provider: repository / Type: Initial release
Revision 1.1Oct 28, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Probable phosphatidylethanolamine transferase Mcr-1
B: Probable phosphatidylethanolamine transferase Mcr-1


Theoretical massNumber of molelcules
Total (without water)72,2332
Polymers72,2332
Non-polymers00
Water1,33374
1
A: Probable phosphatidylethanolamine transferase Mcr-1


Theoretical massNumber of molelcules
Total (without water)36,1161
Polymers36,1161
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Probable phosphatidylethanolamine transferase Mcr-1


Theoretical massNumber of molelcules
Total (without water)36,1161
Polymers36,1161
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)47.162, 84.045, 81.416
Angle α, β, γ (deg.)90.000, 98.510, 90.000
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein Probable phosphatidylethanolamine transferase Mcr-1 / Polymyxin resistance protein MCR-1


Mass: 36116.320 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: mcr1, mcr-1, APZ14_31440 / Production host: Escherichia coli (E. coli)
References: UniProt: A0A0R6L508, Transferases; Transferring phosphorus-containing groups
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 74 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.21 Å3/Da / Density % sol: 44.32 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 100mM KSCN, 32% PEG 3350, 100mM Tris-HON3, 10mM EDTA, PH 8.0

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: LIQUID ANODE / Site: SSRF / Beamline: BL17U / Wavelength: 0.97915 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 4, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97915 Å / Relative weight: 1
ReflectionResolution: 1.82→42.02 Å / Num. obs: 51159 / % possible obs: 91 % / Redundancy: 3.9 % / CC1/2: 0.999 / Rmerge(I) obs: 0.03 / Rpim(I) all: 0.018 / Rrim(I) all: 0.035 / Net I/σ(I): 19.2 / Num. measured all: 197944 / Scaling rejects: 29
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
1.82-1.9240.49267880.9290.2770.56683.1
5.75-103.70.02616090.9970.0150.0387.6

-
Processing

Software
NameVersionClassification
Aimless0.7.2data scaling
PHENIX1.15_3459refinement
PDB_EXTRACT3.25data extraction
HKL-2000data reduction
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 1.82→40.783 Å / SU ML: 0.24 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 30.54
RfactorNum. reflection% reflection
Rfree0.2427 2482 4.86 %
Rwork0.2003 --
obs0.2023 51048 90.61 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 110.89 Å2 / Biso mean: 50.4801 Å2 / Biso min: 25.43 Å2
Refinement stepCycle: final / Resolution: 1.82→40.783 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5064 0 0 74 5138
Biso mean---43.56 -
Num. residues----646
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.82-1.85480.36631420.3158292498
1.8548-1.89270.31551460.2929282296
1.8927-1.93380.4098580.2891124742
1.9338-1.97880.32381410.2577284496
1.9788-2.02830.30811390.2556288097
2.0283-2.08310.29131400.252224976
2.0831-2.14440.26231480.2478287896
2.1444-2.21370.28211440.2409290899
2.2137-2.29280.31161250.2416240781
2.2928-2.38460.27731590.2436286796
2.3846-2.49310.28861480.2459269891
2.4931-2.62450.31011540.2485275293
2.6245-2.78890.30481590.2331292499
2.7889-3.00410.24471620.2204292799
3.0041-3.30630.2581250.2049294499
3.3063-3.78450.23071370.1869284294
3.7845-4.76690.19211150.15269389
4.7669-100.1891400.1695276090

+
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