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- PDB-4eq7: Structure of Atu4243-GABA receptor -

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Basic information

Entry
Database: PDB / ID: 4eq7
TitleStructure of Atu4243-GABA receptor
ComponentsABC transporter, substrate binding protein (Polyamine)
KeywordsTRANSPORT PROTEIN / class D of PBP
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 / ABC transporter, substrate binding protein (Polyamine)
Function and homology information
Biological speciesAgrobacterium tumefaciens (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.91 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 18, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 21, 2012Provider: repository / Type: Initial release
Revision 1.1Dec 19, 2012Group: Database references
Revision 1.2Oct 16, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn / 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_conn.pdbx_leaving_atom_flag / _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: ABC transporter, substrate binding protein (Polyamine)
B: ABC transporter, substrate binding protein (Polyamine)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,27816
Polymers70,9532
Non-polymers1,32514
Water11,764653
1
A: ABC transporter, substrate binding protein (Polyamine)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,1418
Polymers35,4771
Non-polymers6657
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: ABC transporter, substrate binding protein (Polyamine)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,1378
Polymers35,4771
Non-polymers6617
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6020 Å2
ΔGint-128 kcal/mol
Surface area25830 Å2
MethodPISA
Unit cell
Length a, b, c (Å)104.280, 104.280, 286.710
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122

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Components

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


Mass: 35476.613 Da / Num. of mol.: 2
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-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: SO4
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 653 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 3.17 Å3/Da / Density % sol: 61.21 %
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
RadiationMonochromator: SI 111 / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.9→43 Å / Num. all: 131000 / Num. obs: 130795 / % possible obs: 97.4 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Biso Wilson estimate: 23.57 Å2
Reflection shellResolution: 1.9→2.03 Å / % possible all: 95.7

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Processing

Software
NameVersionClassification
DNAdata collection
SHELXSphasing
BUSTER2.10.0refinement
XDSdata reduction
XDSdata scaling
RefinementMethod to determine structure: SAD / Resolution: 1.91→43.07 Å / Cor.coef. Fo:Fc: 0.9542 / Cor.coef. Fo:Fc free: 0.9419 / SU R Cruickshank DPI: 0.112 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.1915 3477 5 %RANDOM
Rwork0.1657 ---
all0.167 70000 --
obs0.167 69545 96.16 %-
Displacement parametersBiso mean: 23.63 Å2
Baniso -1Baniso -2Baniso -3
1--0.1124 Å20 Å20 Å2
2---0.1124 Å20 Å2
3---0.2248 Å2
Refine analyzeLuzzati coordinate error obs: 0.181 Å
Refinement stepCycle: LAST / Resolution: 1.91→43.07 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4958 0 75 653 5686
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.015147HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.986997HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1700SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes134HARMONIC2
X-RAY DIFFRACTIONt_gen_planes732HARMONIC5
X-RAY DIFFRACTIONt_it5147HARMONIC20
X-RAY DIFFRACTIONt_omega_torsion3.67
X-RAY DIFFRACTIONt_other_torsion16.17
X-RAY DIFFRACTIONt_chiral_improper_torsion660SEMIHARMONIC5
X-RAY DIFFRACTIONt_ideal_dist_contact6434SEMIHARMONIC4
LS refinement shellResolution: 1.91→1.96 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2 224 5.01 %
Rwork0.1721 4245 -
all0.1735 4469 -
obs--96.16 %

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