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- PDB-3lrc: Structure of E. coli AdiC (P1) -

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Basic information

Entry
Database: PDB / ID: 3lrc
TitleStructure of E. coli AdiC (P1)
ComponentsArginine/agmatine antiporter
KeywordsTRANSPORT PROTEIN / AdiC / transporter / antiporter / 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 / MOLECULAR REPLACEMENT / Resolution: 4.004 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 11, 2010Deposition site: RCSB / Processing site: PDBJ
SupersessionFeb 23, 2010ID: 3H6B
Revision 1.0Feb 23, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 2023Group: 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 / 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

Downloads & links

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Assembly

Deposited unit
A: Arginine/agmatine antiporter
B: Arginine/agmatine antiporter
C: Arginine/agmatine antiporter
D: Arginine/agmatine antiporter


Theoretical massNumber of molelcules
Total (without water)187,4774
Polymers187,4774
Non-polymers00
Water0
1
A: Arginine/agmatine antiporter
B: Arginine/agmatine antiporter


Theoretical massNumber of molelcules
Total (without water)93,7392
Polymers93,7392
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4250 Å2
ΔGint-43 kcal/mol
Surface area34660 Å2
MethodPISA
2
C: Arginine/agmatine antiporter
D: Arginine/agmatine antiporter


Theoretical massNumber of molelcules
Total (without water)93,7392
Polymers93,7392
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4200 Å2
ΔGint-43 kcal/mol
Surface area34680 Å2
MethodPISA
Unit cell
Length a, b, c (Å)81.88, 111.67, 113.76
Angle α, β, γ (deg.)80.03, 74.34, 68.83
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D

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
31ASPASPASNASNchain C and (resseq 6:252 or resseq 273:435 )CC6 - 2526 - 252
32THRTHRPROPROchain C and (resseq 6:252 or resseq 273:435 )CC273 - 435273 - 435
41ASPASPASNASNchain D and (resseq 6:252 or resseq 273:435 )DD6 - 2526 - 252
42THRTHRPROPROchain D and (resseq 6:252 or resseq 273:435 )DD273 - 435273 - 435

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Components

#1: Protein
Arginine/agmatine antiporter


Mass: 46869.258 Da / Num. of mol.: 4
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: 4.96 Å3/Da / Density % sol: 75.22 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 20% PEG 400, 100mM Tris pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 20, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 4→30 Å / Num. all: 64533 / Num. obs: 58157 / % possible obs: 95.6 % / Redundancy: 1.1 % / Biso Wilson estimate: 297 Å2 / Rmerge(I) obs: 0.042
Reflection shellResolution: 4→4.2 Å / Redundancy: 1.1 % / Rmerge(I) obs: 0.153 / Mean I/σ(I) obs: 1.48 / Num. unique all: 3097 / Rsym value: 0.213 / % possible all: 94.8

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Processing

Software
NameVersionClassification
BSSdata collection
PHASERphasing
PHENIX(phenix.refine)refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3H5M

3h5m
PDB Unreleased entry


Resolution: 4.004→30 Å / SU ML: 0.64 / Isotropic thermal model: Isotropic / σ(F): 1.65 / Phase error: 43.84 / Stereochemistry target values: ML
Details: Friedel pairs exist in SF file under I_Plus/minus and F_Plus/minus columns.
RfactorNum. reflection% reflectionSelection details
Rfree0.3312 2908 5.01 %Thin Shell
Rwork0.3194 ---
obs0.32 58026 95.73 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 190.45 Å2 / ksol: 0.23 e/Å3
Displacement parametersBiso mean: 301.049 Å2
Baniso -1Baniso -2Baniso -3
1-35.891 Å240.789 Å2-0.487 Å2
2---32.932 Å20.123 Å2
3----2.959 Å2
Refinement stepCycle: LAST / Resolution: 4.004→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12144 0 0 0 12144
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.03213132
X-RAY DIFFRACTIONf_angle_d1.73117728
X-RAY DIFFRACTIONf_dihedral_angle_d24.6387340
X-RAY DIFFRACTIONf_chiral_restr0.0932072
X-RAY DIFFRACTIONf_plane_restr0.012056
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11A3036X-RAY DIFFRACTIONPOSITIONAL0.044
12B3036X-RAY DIFFRACTIONPOSITIONAL0.044
13C3036X-RAY DIFFRACTIONPOSITIONAL0.046
14D3036X-RAY DIFFRACTIONPOSITIONAL0.025
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
4.0041-4.069600.39632557X-RAY DIFFRACTION89
4.0696-4.139700.37212833X-RAY DIFFRACTION97
4.1397-4.214800.34722771X-RAY DIFFRACTION97
4.2148-4.295700.34582852X-RAY DIFFRACTION97
4.2957-4.383200.33362776X-RAY DIFFRACTION98
4.3832-4.47820.345713200.34881524X-RAY DIFFRACTION97
4.4782-4.582100.3082795X-RAY DIFFRACTION98
4.5821-4.696400.28082799X-RAY DIFFRACTION97
4.6964-4.822900.30452775X-RAY DIFFRACTION96
4.8229-4.964400.30142792X-RAY DIFFRACTION98
4.9644-5.12400.30832819X-RAY DIFFRACTION97
5.124-5.306300.32382754X-RAY DIFFRACTION97
5.3063-5.517800.37012867X-RAY DIFFRACTION97
5.5178-5.76760.3849690.34881857X-RAY DIFFRACTION97
5.7676-6.06970.3456500.31172747X-RAY DIFFRACTION98
6.0697-6.447200.26832824X-RAY DIFFRACTION98
6.4472-6.940400.28332844X-RAY DIFFRACTION98
6.9404-7.630400.28342809X-RAY DIFFRACTION97
7.6304-8.715300.24252838X-RAY DIFFRACTION98
8.7153-10.9090.2565690.22172179X-RAY DIFFRACTION96
10.909-32.201700.31962106X-RAY DIFFRACTION73
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)
1-1.3478-2.55550.94422.35851.1861.946-1.0215-1.1659-0.29913.0881.3855-0.8676-0.12030.652-0.0312.18570.2941-0.61871.8053-0.20041.334125.640372.447664.2806
2-1.1774-3.789-0.02436.01940.97651.9941.00450.10710.7458-2.0066-0.6393-2.0332-0.93311.43540.04040.3384-0.55850.28941.0476-0.14460.926229.945163.798424.8815
3-0.5709-4.1015-0.84343.5622-0.75312.057-0.8008-0.28370.76021.66310.834-1.2814-0.46151.53690.08390.4564-0.4471-0.2791.2186-0.21131.230447.51615.615843.8101
4-1.3824-3.0072-1.89591.4928-1.25811.87320.68710.6090.9898-2.1589-0.7397-0.36-0.07280.5494-0.12811.94960.12870.32581.51770.27121.104254.25468.23734.4761
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain AA6 - 435
2X-RAY DIFFRACTION2chain BB6 - 435
3X-RAY DIFFRACTION3chain CC6 - 435
4X-RAY DIFFRACTION4chain DD6 - 435

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