[English] 日本語
Yorodumi
- PDB-6a83: Crystal structure of the C-terminal periplasmic domain of EcEptC ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6a83
TitleCrystal structure of the C-terminal periplasmic domain of EcEptC from Escherichia coli complex with Zn
ComponentsPhosphoethanolamine transferase EptC
KeywordsTRANSFERASE / phosphoethanolamine transferase
Function / homology
Function and homology information


phosphotransferase activity, phosphate group as acceptor / Transferases; Transferring phosphorus-containing groups / lipopolysaccharide core region biosynthetic process / plasma membrane
Similarity search - Function
: / Phosphoethanolamine transferase / Sulfatase, N-terminal / Sulfatase / Alkaline-phosphatase-like, core domain superfamily
Similarity search - Domain/homology
Phosphoethanolamine transferase EptC
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.602 Å
AuthorsZhao, Y.Q. / Gu, Y.J. / Cheng, W.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China31570842 China
CitationJournal: FEBS J. / Year: 2019
Title: Structural and mechanistic insights into polymyxin resistance mediated by EptC originating from Escherichia coli.
Authors: Zhao, Y. / Meng, Q. / Lai, Y. / Wang, L. / Zhou, D. / Dou, C. / Gu, Y. / Nie, C. / Wei, Y. / Cheng, W.
History
DepositionJul 6, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 26, 2018Provider: repository / Type: Initial release
Revision 1.1Mar 6, 2019Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation.year
Revision 1.2Nov 22, 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 / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Phosphoethanolamine transferase EptC
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,6253
Polymers45,5371
Non-polymers882
Water77543
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area130 Å2
ΔGint-12 kcal/mol
Surface area14770 Å2
MethodPISA
Unit cell
Length a, b, c (Å)103.568, 103.568, 122.294
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

-
Components

#1: Protein Phosphoethanolamine transferase EptC


Mass: 45536.520 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Gene: eptC, cptA, yijP, b3955, JW3927 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: P0CB39, Transferases; Transferring phosphorus-containing groups
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: Zn
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: Na
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 43 / 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: 4.16 Å3/Da / Density % sol: 70.42 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / Details: 0.2 M Ammonium formate (pH7.5), 20% (w/v) PEG3350

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97853 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Mar 20, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97853 Å / Relative weight: 1
ReflectionResolution: 2.6→47.69 Å / Num. obs: 23768 / % possible obs: 99.98 % / Redundancy: 19.3 % / CC1/2: 0.999 / Rmerge(I) obs: 0.125 / Rpim(I) all: 0.029 / Rrim(I) all: 0.129 / Net I/σ(I): 19.5
Reflection shellResolution: 2.6→2.9 Å / Rmerge(I) obs: 0.753 / Mean I/σ(I) obs: 4.7 / Num. unique obs: 1880 / CC1/2: 0.956 / Rpim(I) all: 0.172 / Rrim(I) all: 0.772 / % possible all: 100

-
Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
SHELXSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6A82

6a82


Resolution: 2.602→47.685 Å / SU ML: 0.38 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 25.04
RfactorNum. reflection% reflection
Rfree0.2368 1161 4.88 %
Rwork0.2124 --
obs0.2136 23768 99.92 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.602→47.685 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2915 0 2 43 2960
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0042995
X-RAY DIFFRACTIONf_angle_d0.664082
X-RAY DIFFRACTIONf_dihedral_angle_d12.141797
X-RAY DIFFRACTIONf_chiral_restr0.042434
X-RAY DIFFRACTIONf_plane_restr0.004540
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6018-2.72020.35971380.29012804X-RAY DIFFRACTION100
2.7202-2.86360.28271560.25262767X-RAY DIFFRACTION100
2.8636-3.0430.26341550.24472769X-RAY DIFFRACTION100
3.043-3.27790.26051510.23912783X-RAY DIFFRACTION100
3.2779-3.60770.26011190.21592836X-RAY DIFFRACTION100
3.6077-4.12950.24941460.18992819X-RAY DIFFRACTION100
4.1295-5.20170.19431590.1792849X-RAY DIFFRACTION100
5.2017-47.69320.22241370.22322980X-RAY DIFFRACTION100

+
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