[English] 日本語
Yorodumi
- PDB-5j4n: Crystal structure of the L-arginine/agmatine antiporter AdiC in c... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5j4n
TitleCrystal structure of the L-arginine/agmatine antiporter AdiC in complex with agmatine at 2.6 Angstroem resolution
ComponentsArginine/agmatine antiporter
KeywordsTRANSPORT PROTEIN / Membrane Protein / Exchanger / Transporter / AdiC-agmatine complex
Function / homology
Function and homology information


arginine:agmatine antiporter activity / cellular stress response to acidic pH / antiporter activity / amino acid transport / identical protein binding / plasma membrane
Similarity search - Function
: / Amino acid/polyamine transporter I / Amino acid permease
Similarity search - Domain/homology
AGMATINE / Arginine/agmatine antiporter / Arginine/agmatine antiporter
Similarity search - Component
Biological speciesEscherichia coli O157:H7 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.594 Å
AuthorsJeckelmann, J.M. / Ilgue, H. / Fotiadis, D.
Funding support Switzerland, 1items
OrganizationGrant numberCountry
Swiss National Science Foundation31003A_162581 Switzerland
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2016
Title: Insights into the molecular basis for substrate binding and specificity of the wild-type L-arginine/agmatine antiporter AdiC.
Authors: Ilgu, H. / Jeckelmann, J.M. / Gapsys, V. / Ucurum, Z. / de Groot, B.L. / Fotiadis, D.
History
DepositionApr 1, 2016Deposition site: RCSB / Processing site: PDBE
Revision 1.0Aug 31, 2016Provider: repository / Type: Initial release
Revision 1.1Sep 14, 2016Group: Database references
Revision 1.2Sep 21, 2016Group: Database references
Revision 1.3Sep 6, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Jan 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Arginine/agmatine antiporter
B: Arginine/agmatine antiporter
hetero molecules


Theoretical massNumber of molelcules
Total (without water)95,9434
Polymers95,6832
Non-polymers2602
Water21612
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5970 Å2
ΔGint-49 kcal/mol
Surface area32070 Å2
MethodPISA
Unit cell
Length a, b, c (Å)104.765, 175.635, 72.868
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

-
Components

#1: Protein Arginine/agmatine antiporter


Mass: 47841.387 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: in complex with agmatine / Source: (gene. exp.) Escherichia coli O157:H7 (bacteria) / Gene: adiC, Z5717, ECs5097 / Plasmid: pET21 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P60063, UniProt: P60061*PLUS
#2: Chemical ChemComp-AG2 / AGMATINE / (4-AMINOBUTYL)GUANIDINE


Mass: 130.191 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C5H14N4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 12 / 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: 3.35 Å3/Da / Density % sol: 63.3 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: PEG 400; NaCl

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Aug 23, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.594→49.44 Å / Num. obs: 41837 / % possible obs: 98.7 % / Redundancy: 6.7 % / CC1/2: 0.999 / Rmerge(I) obs: 0.0109 / Net I/σ(I): 12
Reflection shellResolution: 2.594→2.73 Å / Redundancy: 6.7 % / Rmerge(I) obs: 1.17 / Mean I/σ(I) obs: 1.6 / % possible all: 94.9

-
Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
XDS(VERSION Jun 17, 2015)data reduction
XSCALE(VERSION Jun 17, 2015)data scaling
PHASER2.5.6phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5J4I

5j4i


Resolution: 2.594→49.44 Å / SU ML: 0.33 / Cross valid method: FREE R-VALUE / σ(F): 1.31 / Phase error: 26.51
RfactorNum. reflection% reflection
Rfree0.2507 3952 5.01 %
Rwork0.2209 --
obs0.2224 41795 97.97 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 68.8 Å2
Refinement stepCycle: LAST / Resolution: 2.594→49.44 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6475 0 18 12 6505
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0076663
X-RAY DIFFRACTIONf_angle_d0.9229115
X-RAY DIFFRACTIONf_dihedral_angle_d10.8172237
X-RAY DIFFRACTIONf_chiral_restr0.0461095
X-RAY DIFFRACTIONf_plane_restr0.0041109
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.594-2.62560.3351140.34312181X-RAY DIFFRACTION80
2.6256-2.65880.3351410.32192663X-RAY DIFFRACTION98
2.6588-2.69380.32071440.31932724X-RAY DIFFRACTION98
2.6938-2.73070.30951410.30172628X-RAY DIFFRACTION99
2.7307-2.76970.28161430.28712720X-RAY DIFFRACTION98
2.7697-2.81110.28911450.28192702X-RAY DIFFRACTION99
2.8111-2.8550.33221410.28072711X-RAY DIFFRACTION98
2.855-2.90180.31571370.28332638X-RAY DIFFRACTION97
2.9018-2.95180.28531400.26572660X-RAY DIFFRACTION99
2.9518-3.00550.29621400.26312715X-RAY DIFFRACTION99
3.0055-3.06330.2871420.25682740X-RAY DIFFRACTION100
3.0633-3.12580.30961410.25622681X-RAY DIFFRACTION99
3.1258-3.19380.29191330.26912745X-RAY DIFFRACTION99
3.1938-3.2680.26021470.26512708X-RAY DIFFRACTION99
3.268-3.34970.30751440.24182664X-RAY DIFFRACTION99
3.3497-3.44030.2161480.2382712X-RAY DIFFRACTION98
3.4403-3.54150.22071360.20762633X-RAY DIFFRACTION97
3.5415-3.65580.25911400.21122678X-RAY DIFFRACTION97
3.6558-3.78640.21861460.21522680X-RAY DIFFRACTION99
3.7864-3.93790.25061450.21672719X-RAY DIFFRACTION99
3.9379-4.11710.26631450.2182714X-RAY DIFFRACTION99
4.1171-4.3340.20361430.19082732X-RAY DIFFRACTION99
4.334-4.60540.23191400.182663X-RAY DIFFRACTION98
4.6054-4.96060.19661370.18152672X-RAY DIFFRACTION98
4.9606-5.45930.32381450.20782721X-RAY DIFFRACTION100
5.4593-6.24790.23321430.23272695X-RAY DIFFRACTION99
6.2479-7.86660.2111440.18962672X-RAY DIFFRACTION98
7.8666-49.4490.23061470.19782682X-RAY DIFFRACTION98

+
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