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- PDB-3ipa: Structure of ATU2422-GABA receptor in complex with alanine -

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Basic information

Entry
Database: PDB / ID: 3ipa
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 / ABC transporter, substrate binding protein (Amino acid)
Similarity search - Component
Biological speciesAgrobacterium tumefaciens (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.55 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)37,7954
Polymers37,5141
Non-polymers2813
Water6,215345
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)118.990, 42.990, 66.180
Angle α, β, γ (deg.)90.00, 109.63, 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-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 345 / 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: 2.12 Å3/Da / Density % sol: 42.12 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 0.1 M Tris-HCl, 6.5% glycerol, 2.5 M ammonium sulfate, 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: Dec 21, 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: 1.55→30 Å / Num. all: 45887 / Num. obs: 45887 / % possible obs: 99.5 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 1 / Redundancy: 3.3 % / Rsym value: 0.109 / Net I/σ(I): 9.4
Reflection shellResolution: 1.55→1.64 Å / Redundancy: 3.3 % / Num. unique all: 7312 / Rsym value: 0.66 / % possible all: 99

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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 entries 3IP5,3IP6,3IP7,3IP9

3ip5

3ip6

3ip7

3ip9


Resolution: 1.55→19.875 Å / SU ML: 0.15 / σ(F): 1.99 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2024 2292 5 %RANDOM
Rwork0.1705 ---
obs0.1721 45849 99.61 %-
all-45887 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 51.129 Å2 / ksol: 0.398 e/Å3
Refinement stepCycle: LAST / Resolution: 1.55→19.875 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2574 0 16 345 2935
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0042662
X-RAY DIFFRACTIONf_angle_d0.8883612
X-RAY DIFFRACTIONf_dihedral_angle_d16.398954
X-RAY DIFFRACTIONf_chiral_restr0.058397
X-RAY DIFFRACTIONf_plane_restr0.004478
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.55-1.58370.25281390.25042669X-RAY DIFFRACTION98
1.5837-1.62050.2751440.23532725X-RAY DIFFRACTION100
1.6205-1.6610.29151420.22312699X-RAY DIFFRACTION100
1.661-1.70590.22081420.21022702X-RAY DIFFRACTION100
1.7059-1.75610.23591430.1972715X-RAY DIFFRACTION100
1.7561-1.81270.25381420.18722703X-RAY DIFFRACTION100
1.8127-1.87750.23821420.17772699X-RAY DIFFRACTION100
1.8775-1.95260.2291440.17652721X-RAY DIFFRACTION100
1.9526-2.04140.18881430.15592722X-RAY DIFFRACTION100
2.0414-2.14890.1811420.14862711X-RAY DIFFRACTION100
2.1489-2.28330.18631440.15012720X-RAY DIFFRACTION100
2.2833-2.45930.18241430.15322723X-RAY DIFFRACTION100
2.4593-2.70630.17671440.15892736X-RAY DIFFRACTION100
2.7063-3.09660.18071430.16842725X-RAY DIFFRACTION100
3.0966-3.89660.18351460.15052763X-RAY DIFFRACTION99
3.8966-19.87710.18071490.15472824X-RAY DIFFRACTION100

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