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- PDB-3lrb: Structure of E. coli AdiC -

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Basic information

Entry
Database: PDB / ID: 3lrb
TitleStructure of E. coli AdiC
ComponentsArginine/agmatine antiporter
KeywordsTRANSPORT PROTEIN / transporter / antiporter / AdiC / Amino-acid transport / Antiport / Cell inner membrane / Cell membrane / Membrane / Transmembrane / Transport
Function / homologyAmino acid/polyamine transporter I / Amino acid permease / amino acid transport / antiporter activity / identical protein binding / plasma membrane / Arginine/agmatine antiporter
Function and homology information
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 3.61 Å
AuthorsGao, X. / Lu, F. / Zhou, L. / Shi, Y.
CitationJournal: Science / Year: 2009
Title: Structure and mechanism of an amino acid antiporter
Authors: Gao, X. / Lu, F. / Zhou, L. / Dang, S. / Sun, L. / Li, X. / Wang, J. / Shi, Y.
History
DepositionFeb 10, 2010Deposition site: RCSB / Processing site: PDBJ
SupersessionFeb 23, 2010ID: 3H5M
Revision 1.0Feb 23, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 20, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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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


Theoretical massNumber of molelcules
Total (without water)93,7392
Polymers93,7392
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4370 Å2
ΔGint-47 kcal/mol
Surface area33430 Å2
MethodPISA
Unit cell
Length a, b, c (Å)92.810, 108.300, 138.110
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11ASPASPASNASNchain A and (resseq 6:252 or resseq 273:435 )AA6 - 2526 - 252
12THRTHRPROPROchain A and (resseq 6:252 or resseq 273:435 )AA273 - 435273 - 435
21ASPASPASNASNchain B and (resseq 6:252 or resseq 273:435 )BB6 - 2526 - 252
22THRTHRPROPROchain B and (resseq 6:252 or resseq 273:435 )BB273 - 435273 - 435

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Components

#1: Protein Arginine/agmatine antiporter


Mass: 46869.258 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: O157:H7 / Gene: adiC, Z5717, ECs5097 / Plasmid: pET15b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P60063

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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: 3.7 Å3/Da / Density % sol: 66.78 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 0.4% NG, 0.1mM Tris, 22% (w/v) PEG 400, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K , temperature 291.0K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jul 14, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.61→50 Å / Num. obs: 16598 / Redundancy: 10.8 % / Biso Wilson estimate: 152.36 Å2 / Rmerge(I) obs: 0.083
Reflection shellResolution: 3.61→3.75 Å / Redundancy: 5.3 % / Rmerge(I) obs: 0.463 / % possible all: 99.9

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Processing

Software
NameVersionClassification
BSSdata collection
PHASERphasing
PHENIX(phenix.refine)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: SAD / Resolution: 3.61→49.323 Å / SU ML: 0.58 / Isotropic thermal model: Isotropic / σ(F): 1.33 / Phase error: 36.94 / Stereochemistry target values: MLHL
RfactorNum. reflection% reflectionSelection details
Rfree0.3184 873 5.28 %Thin Shell
Rwork0.2952 ---
obs0.2965 16519 99.57 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 150 Å2 / ksol: 0.273 e/Å3
Displacement parametersBiso mean: 188.562 Å2
Baniso -1Baniso -2Baniso -3
1-24.767 Å20 Å2-0 Å2
2--14.205 Å20 Å2
3----38.972 Å2
Refinement stepCycle: LAST / Resolution: 3.61→49.323 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6072 0 0 0 6072
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0316508
X-RAY DIFFRACTIONf_angle_d1.8578806
X-RAY DIFFRACTIONf_dihedral_angle_d24.5653670
X-RAY DIFFRACTIONf_chiral_restr0.0991036
X-RAY DIFFRACTIONf_plane_restr0.0111028
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11A3036X-RAY DIFFRACTIONPOSITIONAL0.033
12B3036X-RAY DIFFRACTIONPOSITIONAL0.033
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.607-3.83290.41912790.3962411X-RAY DIFFRACTION99
3.8329-4.128700.31272697X-RAY DIFFRACTION100
4.1287-4.54390.30942660.25772446X-RAY DIFFRACTION100
4.5439-5.200800.23632769X-RAY DIFFRACTION100
5.2008-6.55010.40782010.30822570X-RAY DIFFRACTION100
6.5501-49.32740.22181270.26182753X-RAY DIFFRACTION99
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)
11.88550.1386-0.4433-1.2986-0.2971.9485-0.192-0.043-0.56680.0708-0.2510.05850.46310.42970.29811.2827-0.1804-0.08411.2452-0.09281.298486.270260.4805-1.3537
20.4676-0.6706-0.7050.45620.24191.0224-0.17190.0972-0.71720.1758-0.1683-0.32640.4933-0.29520.26731.1683-0.222-0.13831.1479-0.1051.28456.889242.394620.3353
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain AA6 - 435
2X-RAY DIFFRACTION2chain BB6 - 435

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