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- PDB-7o82: The L-arginine/agmatine antiporter from E. coli at 1.7 A resolution -

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Basic information

Entry
Database: PDB / ID: 7o82
TitleThe L-arginine/agmatine antiporter from E. coli at 1.7 A resolution
ComponentsArginine/agmatine antiporter
KeywordsTRANSPORT PROTEIN / AdiC / Transporter / Membrane Protein
Function / homology
Function and homology information


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
DECANE / HEXANE / N-OCTANE / Arginine/agmatine antiporter
Similarity search - Component
Biological speciesEscherichia coli O157:H7 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.69 Å
AuthorsJeckelmann, J.M. / Ilgue, H. / Kalbermatter, D. / Fotiadis, D.
Funding support Switzerland, 1items
OrganizationGrant numberCountry
Swiss National Science Foundation310030_184980 Switzerland
CitationJournal: Bmc Biol. / Year: 2021
Title: High-resolution structure of the amino acid transporter AdiC reveals insights into the role of water molecules and networks in oligomerization and substrate binding.
Authors: Ilgu, H. / Jeckelmann, J.M. / Kalbermatter, D. / Ucurum, Z. / Lemmin, T. / Fotiadis, D.
History
DepositionApr 14, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 8, 2021Provider: repository / Type: Initial release
Revision 1.1Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)97,76216
Polymers95,6832
Non-polymers2,07914
Water6,431357
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9510 Å2
ΔGint-1 kcal/mol
Surface area32560 Å2
MethodPISA
Unit cell
Length a, b, c (Å)104.708, 175.592, 73.275
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212

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Components

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Protein / Sugars , 2 types, 5 molecules AB

#1: Protein Arginine/agmatine antiporter


Mass: 47841.387 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli O157:H7 (bacteria) / Gene: adiC, Z5717, ECs5097
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: P60063
#2: Sugar ChemComp-BNG / nonyl beta-D-glucopyranoside / Beta-NONYLGLUCOSIDE / nonyl beta-D-glucoside / nonyl D-glucoside / nonyl glucoside


Type: D-saccharide / Mass: 306.395 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Formula: C15H30O6 / Comment: detergent*YM
IdentifierTypeProgram
b-nonylglucosideIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0

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Non-polymers , 5 types, 368 molecules

#3: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#4: Chemical
ChemComp-HEX / HEXANE


Mass: 86.175 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C6H14
#5: Chemical ChemComp-D10 / DECANE


Mass: 142.282 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H22
#6: Chemical ChemComp-OCT / N-OCTANE


Mass: 114.229 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 357 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN

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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: 3.66 Å3/Da / Density % sol: 66.42 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 8.5 / Details: Tris-HCl pH 8.5, PEG400, NG

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Sep 22, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.69→56.81 Å / Num. obs: 118568 / % possible obs: 96.4 % / Redundancy: 121.5 % / Biso Wilson estimate: 39.79 Å2 / CC1/2: 0.992 / Rpim(I) all: 0.02 / Rrim(I) all: 0.18 / Net I/σ(I): 52.2
Reflection shellResolution: 1.69→1.79 Å / Mean I/σ(I) obs: 1.4 / Num. unique obs: 5173 / CC1/2: 0.572 / Rpim(I) all: 0.7

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
Aimlessdata scaling
PHASERphasing
PHENIX1.13_2998refinement
PDB_EXTRACT3.25data extraction
XDS2018data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5j4i

5j4i


Resolution: 1.69→34.58 Å / SU ML: 0.16 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 27.11
RfactorNum. reflection% reflection
Rfree0.2031 1999 1.69 %
Rwork0.1949 --
obs0.195 118535 78.28 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 181.35 Å2 / Biso mean: 53.6007 Å2 / Biso min: 26.28 Å2
Refinement stepCycle: final / Resolution: 1.69→34.58 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6475 0 403 357 7235
Biso mean--96.87 61.36 -
Num. residues----873
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.6902-1.73250.399300.3775177317
1.7325-1.77930.3298470.3151268226
1.7793-1.83170.3397690.2827408139
1.8317-1.89080.28471000.2605575955
1.8908-1.95840.26311260.2473737170
1.9584-2.03680.27421590.2339928788
2.0368-2.12940.23161800.218710518100
2.1294-2.24170.23511830.200110585100
2.2417-2.38210.20411800.184410593100
2.3821-2.5660.20341830.187610608100
2.566-2.82410.17881830.179610678100
2.8241-3.23250.22391830.193310671100
3.2325-4.07160.21061850.184610806100
4.0716-34.580.18091910.196811124100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.4481-0.1980.25541.1374-0.42511.6826-0.0403-0.25260.05950.00080.0740.14460.2242-0.1611-0.0440.2830.0406-0.00780.3256-0.05420.2403-17.994124.2713-1.0478
21.7313-1.8319-0.00846.076-2.11941.4333-0.1447-0.2605-0.078-0.10060.35780.50210.1863-0.2305-0.17910.2940.0315-0.0580.432-0.05630.2466-16.380919.80135.7392
32.4327-0.3504-0.29930.8257-0.1650.7902-0.01190.01120.1774-0.12730.01490.0704-0.0342-0.06840.00140.29240.0174-0.03330.3124-0.02720.2562-8.034229.4345-10.3994
45.5015.26282.36135.27682.22443.56050.5603-0.3004-0.13660.4086-0.5939-0.32860.06280.2618-0.00990.2535-0.00660.06530.4425-0.00010.370727.607317.4119-26.765
51.3423-0.2240.28931.15350.52572.60890.03010.04640.206-0.027-0.0397-0.16490.3084-0.1319-0.01520.3033-0.10170.07070.2961-0.00250.27523.990219.6797-17.941
62.84881.56460.93762.82021.02031.53030.03750.37160.0018-0.30930.1249-0.27690.05590.2198-0.17540.3625-0.0330.070.47410.03050.235523.604814.0616-32.1728
75.01154.69611.94965.4932-0.93887.798-0.12820.1484-1.7490.13960.7269-2.01750.47910.3122-0.48770.50530.05060.02880.5704-0.21210.940226.0396-4.3087-30.7484
83.5275-0.80950.19741.14850.30951.92530.0066-0.09630.01740.0458-0.0085-0.16430.1766-0.00450.01710.2557-0.08610.03210.3098-0.03550.304224.620521.3624-13.5324
92.1031-0.3165-0.23123.42520.99833.66590.0257-0.00650.48410.00490.0443-0.1317-0.05230.3067-0.05030.0485-0.01860.00840.3198-0.00520.31927.641429.7059-15.096
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 5 through 188 )A5 - 188
2X-RAY DIFFRACTION2chain 'A' and (resid 189 through 271 )A189 - 271
3X-RAY DIFFRACTION3chain 'A' and (resid 272 through 441 )A272 - 441
4X-RAY DIFFRACTION4chain 'B' and (resid 6 through 39 )B6 - 39
5X-RAY DIFFRACTION5chain 'B' and (resid 40 through 143 )B40 - 143
6X-RAY DIFFRACTION6chain 'B' and (resid 144 through 249 )B144 - 249
7X-RAY DIFFRACTION7chain 'B' and (resid 250 through 271 )B250 - 271
8X-RAY DIFFRACTION8chain 'B' and (resid 272 through 379 )B272 - 379
9X-RAY DIFFRACTION9chain 'B' and (resid 380 through 441 )B380 - 441

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