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- PDB-3ob6: Structure of AdiC(N101A) in the open-to-out Arg+ bound conformation -

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Basic information

Entry
Database: PDB / ID: 3ob6
TitleStructure of AdiC(N101A) in the open-to-out Arg+ bound conformation
ComponentsAdiC arginine:agmatine antiporter
KeywordsMEMBRANE PROTEIN / Amino acid antiporter / Arginine / Membrane / Transmembrane Antiporter / APC-T / 5+5 Inverted Repeat
Function / homologyarginine:agmatine antiporter activity / : / cellular stress response to acidic pH / Amino acid/polyamine transporter I / Amino acid permease / plasma membrane / ARGININE / : / Arginine/agmatine antiporter
Function and homology information
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsCarpena, X. / Kowalczyk, L. / Ratera, M. / Valencia, E. / Vazquez-lbar, J.L. / Fita, I. / Palacin, M.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2011
Title: Molecular basis of substrate-induced permeation by an amino acid antiporter.
Authors: Kowalczyk, L. / Ratera, M. / Paladino, A. / Bartoccioni, P. / Errasti-Murugarren, E. / Valencia, E. / Portella, G. / Bial, S. / Zorzano, A. / Fita, I. / Orozco, M. / Carpena, X. / Vazquez- ...Authors: Kowalczyk, L. / Ratera, M. / Paladino, A. / Bartoccioni, P. / Errasti-Murugarren, E. / Valencia, E. / Portella, G. / Bial, S. / Zorzano, A. / Fita, I. / Orozco, M. / Carpena, X. / Vazquez-Ibar, J.L. / Palacin, M.
History
DepositionAug 6, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 16, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Sep 6, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / 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 / struct_ref_seq_dif / struct_site
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 / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: AdiC arginine:agmatine antiporter
B: AdiC arginine:agmatine antiporter
hetero molecules


Theoretical massNumber of molelcules
Total (without water)94,0034
Polymers93,6522
Non-polymers3502
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5150 Å2
ΔGint-44 kcal/mol
Surface area32100 Å2
MethodPISA
Unit cell
Length a, b, c (Å)86.071, 77.204, 104.451
Angle α, β, γ (deg.)90.00, 106.79, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22B
13A
23B
14A
24B
15A
25B

NCS domain segments:

Component-ID: 1

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDRefine codeAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11ALAALATRPTRP3AA5 - 1705 - 170
21ALAALATRPTRP3BB5 - 1705 - 170
12GLYGLYLEULEU3AA275 - 339275 - 339
22GLYGLYLEULEU3BB275 - 339275 - 339
13SERSERALAALA3AA355 - 440355 - 440
23SERSERALAALA3BB355 - 440355 - 440
14ALAALAALAALA3AA181 - 265181 - 265
24ALAALAALAALA3BB181 - 265181 - 265
15ARGARGARGARG4AC450
25ARGARGARGARG4BD450

NCS ensembles :
ID
1
2
3
4
5

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Components

#1: Protein AdiC arginine:agmatine antiporter / AdiC


Mass: 46826.234 Da / Num. of mol.: 2 / Mutation: N101A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: adiC, B21_03947 / Plasmid: pTTQ18-His6-AdiC / Production host: Escherichia coli (E. coli) / References: UniProt: C5WBZ6, UniProt: P60061*PLUS
#2: Chemical ChemComp-ARG / ARGININE


Type: L-peptide linking / Mass: 175.209 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H15N4O2

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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: 3.54 Å3/Da / Density % sol: 65.3 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 24-28% PEG400, 2mM Cymal-5, 1mM LDAO, 0.1M TRIS, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.9791 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD
RadiationMonochromator: Si 111 Channel / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 3→30 Å / Num. all: 25006 / Num. obs: 24681 / % possible obs: 93.3 % / Observed criterion σ(F): 1.5 / Observed criterion σ(I): 1.5 / Redundancy: 3.3 % / Net I/σ(I): 6.8
Reflection shellResolution: 3→3.11 Å / Redundancy: 2.6 % / Mean I/σ(I) obs: 2.4 / % possible all: 73.4

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Processing

Software
NameVersionClassification
MOLREPphasing
REFMAC5.5.0102refinement
DNAdata collection
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3LRB

3lrb


Resolution: 3→25 Å / Cor.coef. Fo:Fc: 0.926 / Cor.coef. Fo:Fc free: 0.915 / SU B: 51.527 / SU ML: 0.41 / Cross valid method: THROUGHOUT / ESU R Free: 0.447 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.27202 1255 5.1 %RANDOM
Rwork0.24328 ---
obs0.24473 23349 92.96 %-
all-23349 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 47.695 Å2
Baniso -1Baniso -2Baniso -3
1--7.01 Å20 Å2-1.97 Å2
2--7.67 Å20 Å2
3----1.79 Å2
Refinement stepCycle: LAST / Resolution: 3→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6411 0 24 0 6435
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0226601
X-RAY DIFFRACTIONr_bond_other_d0.0040.024226
X-RAY DIFFRACTIONr_angle_refined_deg1.4181.9599030
X-RAY DIFFRACTIONr_angle_other_deg1.063310346
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6655863
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.6722.011189
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.65615975
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.2451522
X-RAY DIFFRACTIONr_chiral_restr0.0940.21089
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0217282
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021386
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.3811.54287
X-RAY DIFFRACTIONr_mcbond_other0.071.51784
X-RAY DIFFRACTIONr_mcangle_it0.74526885
X-RAY DIFFRACTIONr_scbond_it1.02432314
X-RAY DIFFRACTIONr_scangle_it1.6944.52145
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Refine-ID: X-RAY DIFFRACTION

Ens-IDNumberTypeRms dev position (Å)Weight position
1967tight positional0.040.05
2377tight positional0.030.05
3507tight positional0.040.05
4497tight positional0.040.05
525medium positional0.760.5
11099loose positional0.055
2367loose positional0.035
3605loose positional0.075
4486loose positional0.065
1967tight thermal0.070.5
2377tight thermal0.060.5
3507tight thermal0.070.5
4497tight thermal0.070.5
525medium thermal0.132
11099loose thermal0.0610
2367loose thermal0.0610
3605loose thermal0.0710
4486loose thermal0.0710
LS refinement shellResolution: 3→3.077 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.409 70 -
Rwork0.37 1239 -
obs--67.86 %
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)
13.1436-0.41460.94861.0561-0.81362.2160.09490.3265-0.20690.1277-0.1219-0.09590.00430.37770.0270.27340.02370.03970.1079-0.09090.263338.9334-6.172327.6921
23.1774-0.20710.50292.13360.5031.9682-0.02770.1270.04570.1273-0.1790.2645-0.2501-0.55340.20670.26050.0155-0.03040.2712-0.1180.17690.79276.587721.4669
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A5 - 440
2X-RAY DIFFRACTION1A450
3X-RAY DIFFRACTION2B5 - 440
4X-RAY DIFFRACTION2B450

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