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- PDB-3ip5: Structure of Atu2422-GABA receptor in complex with alanine -

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Basic information

Entry
Database: PDB / ID: 3ip5
TitleStructure of Atu2422-GABA receptor in complex with alanine
ComponentsABC transporter, substrate binding protein (Amino acid)
KeywordsTRANSPORT PROTEIN / VENUS FLYTRAP DOMAIN
Function / homology
Function and homology information


amino acid transport / metal ion binding
Similarity search - Function
Leu/Ile/Val-binding protein / Leucine-binding protein domain / Periplasmic binding protein / Response regulator / Periplasmic binding protein-like I / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ALANINE / DI(HYDROXYETHYL)ETHER / ABC transporter, substrate binding protein (Amino acid)
Similarity search - Component
Biological speciesAgrobacterium tumefaciens (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.35 Å
AuthorsMorera, S. / Planamente, S. / Vigouroux, A.
CitationJournal: J.Biol.Chem. / Year: 2010
Title: A conserved mechanism of GABA binding and antagonism is revealed by structure-function analysis of the periplasmic binding protein Atu2422 in Agrobacterium tumefaciens.
Authors: Planamente, S. / Vigouroux, A. / Mondy, S. / Nicaise, M. / Faure, D. / Morera, S.
History
DepositionAug 17, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 14, 2010Provider: 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_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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)37,7093
Polymers37,5141
Non-polymers1952
Water8,377465
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)116.250, 38.940, 71.630
Angle α, β, γ (deg.)90.00, 95.68, 90.00
Int Tables number5
Space group name H-MC121

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Components

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


Mass: 37514.070 Da / Num. of mol.: 1 / Fragment: UNP residues 24-372
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Agrobacterium tumefaciens (bacteria) / Strain: C58 / Gene: AGR_C_4394, Atu2422 / Plasmid: pET-9aSN1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)* / References: UniProt: Q7CX36
#2: Chemical ChemComp-ALA / ALANINE


Type: L-peptide linking / Mass: 89.093 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H7NO2
#3: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 465 / 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: 2.15 Å3/Da / Density % sol: 42.8 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 35% PEG 4000, 100 mM CACL2, 0.1 M Tris-HCl, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.9 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 16, 2008 / Details: kirkpatrick baez
RadiationMonochromator: si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 1.35→30 Å / Num. all: 69760 / Num. obs: 69760 / % possible obs: 99 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 1 / Redundancy: 4 % / Rsym value: 0.104 / Net I/σ(I): 13
Reflection shellResolution: 1.35→1.42 Å / Redundancy: 4 % / Num. unique all: 9671 / Rsym value: 0.509 / % possible all: 98.2

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Processing

Software
NameVersionClassification
JDirectordata collection
PHASERphasing
PHENIX(phenix.refine)refinement
XDSdata reduction
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1USK

1usk


Resolution: 1.35→30 Å / SU ML: 0.14 / σ(F): 1.99 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1862 3486 5 %random
Rwork0.1617 ---
obs0.1629 69735 98.97 %-
all-69760 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 53.965 Å2 / ksol: 0.387 e/Å3
Refinement stepCycle: LAST / Resolution: 1.35→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2574 0 10 465 3049
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0052637
X-RAY DIFFRACTIONf_angle_d0.9893569
X-RAY DIFFRACTIONf_dihedral_angle_d15.657940
X-RAY DIFFRACTIONf_chiral_restr0.064393
X-RAY DIFFRACTIONf_plane_restr0.004473
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.35-1.36850.27671370.25342615X-RAY DIFFRACTION99
1.3685-1.38810.26941370.24482605X-RAY DIFFRACTION97
1.3881-1.40880.26781370.23232595X-RAY DIFFRACTION99
1.4088-1.43080.21831380.22512628X-RAY DIFFRACTION98
1.4308-1.45420.24991360.21092583X-RAY DIFFRACTION98
1.4542-1.47930.2181360.2032589X-RAY DIFFRACTION99
1.4793-1.50620.22661400.18462653X-RAY DIFFRACTION98
1.5062-1.53520.19691390.17652633X-RAY DIFFRACTION99
1.5352-1.56650.18121370.16732613X-RAY DIFFRACTION98
1.5665-1.60060.16611390.15792632X-RAY DIFFRACTION99
1.6006-1.63780.1951380.16142633X-RAY DIFFRACTION98
1.6378-1.67880.17621390.15582631X-RAY DIFFRACTION99
1.6788-1.72420.18031380.14682632X-RAY DIFFRACTION99
1.7242-1.77490.17391390.14962630X-RAY DIFFRACTION99
1.7749-1.83220.1841420.14752697X-RAY DIFFRACTION100
1.8322-1.89760.17421380.1472624X-RAY DIFFRACTION99
1.8976-1.97360.17111400.14852659X-RAY DIFFRACTION99
1.9736-2.06340.17111400.14552670X-RAY DIFFRACTION99
2.0634-2.17220.14651410.13722677X-RAY DIFFRACTION100
2.1722-2.30820.1811410.1432676X-RAY DIFFRACTION100
2.3082-2.48640.18941410.15072669X-RAY DIFFRACTION100
2.4864-2.73650.19581420.16472704X-RAY DIFFRACTION100
2.7365-3.13220.1891420.15422704X-RAY DIFFRACTION100
3.1322-3.9450.15921430.13992715X-RAY DIFFRACTION100
3.945-31.78770.16731460.15352782X-RAY DIFFRACTION99

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