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- PDB-4euo: Structure of Atu4243-GABA sensor -

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Basic information

Entry
Database: PDB / ID: 4euo
TitleStructure of Atu4243-GABA sensor
ComponentsABC transporter, substrate binding protein (Polyamine)
KeywordsTRANSPORT PROTEIN / class D of PBP / GABA-binding
Function / homologyBacterial extracellular solute-binding protein / Bacterial extracellular solute-binding protein / Periplasmic binding protein-like II / D-Maltodextrin-Binding Protein; domain 2 / periplasmic space / 3-Layer(aba) Sandwich / Alpha Beta / GAMMA-AMINO-BUTANOIC ACID / ABC transporter, substrate binding protein (Polyamine)
Function and homology information
Biological speciesAgrobacterium tumefaciens (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.28 Å
AuthorsMorera, S. / Planamente, S.
CitationJournal: Mol.Microbiol. / Year: 2012
Title: Structural basis for selective GABA binding in bacterial pathogens.
Authors: Planamente, S. / Mondy, S. / Hommais, F. / Vigouroux, A. / Morera, S. / Faure, D.
History
DepositionApr 25, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 21, 2012Provider: repository / Type: Initial release
Revision 1.1Dec 19, 2012Group: Database references
Revision 1.2Sep 13, 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_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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 2.0Nov 15, 2023Group: Atomic model / Data collection / Category: atom_site / chem_comp_atom / chem_comp_bond
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_1 / _chem_comp_bond.atom_id_2

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: ABC transporter, substrate binding protein (Polyamine)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,6246
Polymers35,1481
Non-polymers4755
Water6,846380
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)59.090, 59.090, 150.500
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221
Components on special symmetry positions
IDModelComponents
11A-508-

HOH

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Components

#1: Protein ABC transporter, substrate binding protein (Polyamine)


Mass: 35148.355 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Agrobacterium tumefaciens (bacteria) / Strain: C58 / ATCC 33970 / Gene: Atu4243 / Production host: Escherichia coli (E. coli) / References: UniProt: A9CGA5
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-ABU / GAMMA-AMINO-BUTANOIC ACID / GAMMA(AMINO)-BUTYRIC ACID


Mass: 103.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H9NO2
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 380 / 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: 2.16 Å3/Da / Density % sol: 43 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: AS, Tris-HCl 8.5 and 10% glycerol, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.9795 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Feb 10, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.28→42 Å / Num. all: 78000 / Num. obs: 77296 / % possible obs: 97.7 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Biso Wilson estimate: 13.46 Å2
Reflection shellResolution: 1.28→1.36 Å / % possible all: 88.5

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Processing

Software
NameVersionClassification
DNAdata collection
SHELXSphasing
BUSTER2.10.0refinement
XDSdata reduction
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4EQ7

4eq7


Resolution: 1.28→18.74 Å / Cor.coef. Fo:Fc: 0.9649 / Cor.coef. Fo:Fc free: 0.9589 / SU R Cruickshank DPI: 0.044 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.1814 3863 5 %RANDOM
Rwork0.1648 ---
all0.167 78000 --
obs0.1657 77265 97.36 %-
Displacement parametersBiso mean: 17.85 Å2
Baniso -1Baniso -2Baniso -3
1--1.3521 Å20 Å20 Å2
2---1.3521 Å20 Å2
3---2.7041 Å2
Refine analyzeLuzzati coordinate error obs: 0.134 Å
Refinement stepCycle: LAST / Resolution: 1.28→18.74 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2410 0 30 380 2820
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.012512HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.043412HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d849SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes65HARMONIC2
X-RAY DIFFRACTIONt_gen_planes359HARMONIC5
X-RAY DIFFRACTIONt_it2512HARMONIC20
X-RAY DIFFRACTIONt_omega_torsion4.6
X-RAY DIFFRACTIONt_other_torsion16.21
X-RAY DIFFRACTIONt_chiral_improper_torsion326SEMIHARMONIC5
X-RAY DIFFRACTIONt_ideal_dist_contact3340SEMIHARMONIC4
LS refinement shellResolution: 1.28→1.31 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2374 237 5.01 %
Rwork0.218 4498 -
all0.219 4735 -
obs--97.36 %

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