[English] 日本語
Yorodumi
- PDB-8vqk: YcjN from Escherichia coli -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8vqk
TitleYcjN from Escherichia coli
ComponentsPutative ABC transporter periplasmic-binding protein YcjN
KeywordsUNKNOWN FUNCTION / Substrate binding protein / ABC transporter cognate binding protein / ligand binding protein
Function / homology
Function and homology information


ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing / transmembrane transport / outer membrane-bounded periplasmic space / membrane / plasma membrane
Similarity search - Function
: / Bacterial extracellular solute-binding protein / Bacterial extracellular solute-binding protein / Prokaryotic membrane lipoprotein lipid attachment site profile.
Similarity search - Domain/homology
: / : / DI(HYDROXYETHYL)ETHER / Putative ABC transporter periplasmic-binding protein YcjN
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å
AuthorsTrevino, M.A. / Fernandez, D. / Sharaf, N.G.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: J.Biol.Chem. / Year: 2024
Title: Expression, purification, and characterization of diacylated Lipo-YcjN from Escherichia coli.
Authors: Trevino, M.A. / Amankwah, K.A. / Fernandez, D. / Weston, S.A. / Stewart, C.J. / Gallardo, J.M. / Shahgholi, M. / Sharaf, N.G.
History
DepositionJan 18, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 9, 2024Provider: repository / Type: Initial release
Revision 1.1Oct 16, 2024Group: Database references / Category: citation
Item: _citation.page_first / _citation.page_last ..._citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Nov 13, 2024Group: Database references / Category: citation / Item: _citation.journal_volume

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Putative ABC transporter periplasmic-binding protein YcjN
B: Putative ABC transporter periplasmic-binding protein YcjN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)97,45114
Polymers96,4672
Non-polymers98412
Water5,747319
1
A: Putative ABC transporter periplasmic-binding protein YcjN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,6066
Polymers48,2341
Non-polymers3725
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Putative ABC transporter periplasmic-binding protein YcjN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,8458
Polymers48,2341
Non-polymers6117
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)63.216, 63.290, 74.314
Angle α, β, γ (deg.)110.01, 91.09, 118.66
Int Tables number1
Space group name H-MP1

-
Components

-
Protein , 1 types, 2 molecules AB

#1: Protein Putative ABC transporter periplasmic-binding protein YcjN


Mass: 48233.605 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: ycjN, b1310, JW1303 / Production host: Escherichia coli (E. coli) / References: UniProt: P76042

-
Non-polymers , 6 types, 331 molecules

#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C3H8O3
#4: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C4H10O3
#5: Chemical
ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: K
#6: Chemical ChemComp-CD / CADMIUM ION


Mass: 112.411 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cd
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 319 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestN
Has protein modificationN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.48 Å3/Da / Density % sol: 50.36 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop
Details: 0.01 M CdCl2, 0.2 M NH4SO4, 0.1 M HEPES pH 7.5, and 25 % PSM

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-1 / Wavelength: 0.97946 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 8, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97946 Å / Relative weight: 1
ReflectionResolution: 1.95→38.4 Å / Num. obs: 61761 / % possible obs: 91.4 % / Redundancy: 3.9 % / Rpim(I) all: 0.088 / Net I/σ(I): 3.9
Reflection shellResolution: 1.95→2.06 Å / Num. unique obs: 6203 / CC1/2: 0.293

-
Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.95→35.65 Å / SU ML: 0.32 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 31.06 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.264 3085 5.01 %
Rwork0.2152 --
obs0.2177 61593 91.2 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.95→35.65 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6139 0 43 319 6501
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0076276
X-RAY DIFFRACTIONf_angle_d0.8058518
X-RAY DIFFRACTIONf_dihedral_angle_d14.9962301
X-RAY DIFFRACTIONf_chiral_restr0.048995
X-RAY DIFFRACTIONf_plane_restr0.0061096
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.95-1.980.4231260.40422708X-RAY DIFFRACTION91
1.98-2.010.44531370.382588X-RAY DIFFRACTION90
2.01-2.050.37951220.35092650X-RAY DIFFRACTION90
2.05-2.080.33261340.33312575X-RAY DIFFRACTION89
2.08-2.120.38111100.29822474X-RAY DIFFRACTION84
2.12-2.170.37871320.27282382X-RAY DIFFRACTION82
2.17-2.220.30551840.26062686X-RAY DIFFRACTION94
2.22-2.270.29831680.24532792X-RAY DIFFRACTION95
2.27-2.320.28861260.24242751X-RAY DIFFRACTION94
2.32-2.390.30091150.23632738X-RAY DIFFRACTION94
2.39-2.460.26731340.22562734X-RAY DIFFRACTION93
2.46-2.540.29471510.2182735X-RAY DIFFRACTION93
2.54-2.630.27311580.21942692X-RAY DIFFRACTION93
2.63-2.730.2791660.20082658X-RAY DIFFRACTION92
2.73-2.860.25721560.20082624X-RAY DIFFRACTION91
2.86-3.010.29281270.21462552X-RAY DIFFRACTION87
3.01-3.190.27941270.21462453X-RAY DIFFRACTION84
3.19-3.440.23521480.20562795X-RAY DIFFRACTION96
3.44-3.790.25271300.18372835X-RAY DIFFRACTION96
3.79-4.330.21521470.17932746X-RAY DIFFRACTION95
4.33-5.460.21511560.17472648X-RAY DIFFRACTION92
5.46-35.650.2511310.2152692X-RAY DIFFRACTION92

+
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