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- PDB-5j4n: Crystal structure of the L-arginine/agmatine antiporter AdiC in c... -

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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 / L-arginine transmembrane transporter activity / amino acid transmembrane transport / intracellular pH elevation / amino acid transport / antiporter activity / 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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

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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 / Agmatine


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


Mass: 18.015 Da / Num. of mol.: 12 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

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

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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

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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

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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

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