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- PDB-3ipc: Structure of ATU2422-GABA F77A mutant receptor in complex with leucine -

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Basic information

Entry
Database: PDB / ID: 3ipc
TitleStructure of ATU2422-GABA F77A mutant receptor in complex with leucine
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
LEUCINE / ABC transporter, substrate binding protein (Amino acid)
Similarity search - Component
Biological speciesAgrobacterium tumefaciens (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.3 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 1.2Oct 13, 2021Group: Database references / Derived calculations / Category: database_2 / 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 1.3Sep 6, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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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)37,6653
Polymers37,4381
Non-polymers2272
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)119.770, 43.030, 66.460
Angle α, β, γ (deg.)90.00, 109.76, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-405-

HOH

21A-720-

HOH

31A-787-

HOH

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Components

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


Mass: 37437.977 Da / Num. of mol.: 1 / Fragment: UNP residues 24-372 / Mutation: F77A
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-LEU / LEUCINE


Type: L-peptide linking / Mass: 131.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H13NO2
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#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: 42.86 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 0.1 M Tris-HCl, 6% 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: Jun 26, 2009 / 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: 1.3→32.1 Å / Num. all: 68599 / Num. obs: 68599 / % possible obs: 89 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 1 / Redundancy: 3.5 % / Rsym value: 0.045 / Net I/σ(I): 17.3
Reflection shellResolution: 1.3→1.39 Å / Redundancy: 1.8 % / Num. unique all: 6206 / Rsym value: 0.337 / % possible all: 50

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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 3IP5,3IP6,3IP7,3IP9,3IPA

3ip5

3ip6

3ip7

3ip9

3ipa


Resolution: 1.3→32.1 Å / SU ML: 0.02 / σ(F): 1.99 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1862 3429 5 %RANDOM
Rwork0.1575 ---
obs0.1589 68579 88.97 %-
all-68599 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 47.231 Å2 / ksol: 0.389 e/Å3
Refinement stepCycle: LAST / Resolution: 1.3→32.1 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2568 0 14 465 3047
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0062652
X-RAY DIFFRACTIONf_angle_d1.0493598
X-RAY DIFFRACTIONf_dihedral_angle_d16.246952
X-RAY DIFFRACTIONf_chiral_restr0.068397
X-RAY DIFFRACTIONf_plane_restr0.006478
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.3-1.32690.3017420.2999799X-RAY DIFFRACTION26
1.3269-1.34670.2594800.2511520X-RAY DIFFRACTION50
1.3467-1.36780.2558930.22611765X-RAY DIFFRACTION59
1.3678-1.39020.24251070.20942031X-RAY DIFFRACTION66
1.3902-1.41420.21351170.19792225X-RAY DIFFRACTION73
1.4142-1.43990.2191280.19442434X-RAY DIFFRACTION81
1.4399-1.46750.20911410.18282680X-RAY DIFFRACTION88
1.4675-1.49750.18391520.17162896X-RAY DIFFRACTION96
1.4975-1.530.18641590.15863018X-RAY DIFFRACTION100
1.53-1.56560.17181600.15153031X-RAY DIFFRACTION100
1.5656-1.60480.16951610.14553066X-RAY DIFFRACTION100
1.6048-1.64810.17971600.14593039X-RAY DIFFRACTION100
1.6481-1.69660.17761590.14453017X-RAY DIFFRACTION100
1.6966-1.75130.18771590.14913031X-RAY DIFFRACTION100
1.7513-1.81390.19131610.15073064X-RAY DIFFRACTION100
1.8139-1.88650.19241610.14543055X-RAY DIFFRACTION100
1.8865-1.97220.15451600.15013028X-RAY DIFFRACTION100
1.9722-2.07610.16591610.14163058X-RAY DIFFRACTION100
2.0761-2.2060.16871610.14383060X-RAY DIFFRACTION100
2.206-2.37610.20121610.14863074X-RAY DIFFRACTION100
2.3761-2.61480.17681610.1543043X-RAY DIFFRACTION100
2.6148-2.9920.19621610.16353075X-RAY DIFFRACTION100
2.992-3.76550.17531630.14083099X-RAY DIFFRACTION100
3.7655-19.97130.17511610.153042X-RAY DIFFRACTION96

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