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- PDB-5l9o: Crystal structure of Agrobacterium tumefaciens C58 strain PBP Soc... -

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Basic information

Entry
Database: PDB / ID: 5l9o
TitleCrystal structure of Agrobacterium tumefaciens C58 strain PBP SocA in complex with glucopine
ComponentsDeoxyfructosyl-amino Acid Transporter Periplasmic Binding Protein
KeywordsTRANSPORT PROTEIN / periplasmic binding protein / ABC transporter / synthetic opine
Function / homology
Function and homology information


ligand-gated monoatomic ion channel activity / periplasmic space / membrane
Similarity search - Function
Bacterial periplasmic substrate-binding proteins / Bacterial extracellular solute-binding proteins, family 3 / Solute-binding protein family 3/N-terminal domain of MltF / Ionotropic glutamate receptor / Eukaryotic homologues of bacterial periplasmic substrate binding proteins. / Periplasmic binding protein-like II / D-Maltodextrin-Binding Protein; domain 2 / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Glucopine / Deoxyfructosyl-amino Acid Transporter Periplasmic Binding Protein
Similarity search - Component
Biological speciesAgrobacterium fabrum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.84 Å
AuthorsMarty, L. / Morera, S.
CitationJournal: J.Biol.Chem. / Year: 2016
Title: Structural Basis for High Specificity of Amadori Compound and Mannopine Opine Binding in Bacterial Pathogens.
Authors: Marty, L. / Vigouroux, A. / Aumont-Nicaise, M. / Dessaux, Y. / Faure, D. / Morera, S.
History
DepositionJun 10, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 21, 2016Provider: repository / Type: Initial release
Revision 1.1Nov 16, 2016Group: Database references
Revision 1.2Jan 10, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Deoxyfructosyl-amino Acid Transporter Periplasmic Binding Protein
B: Deoxyfructosyl-amino Acid Transporter Periplasmic Binding Protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,08016
Polymers57,7592
Non-polymers1,32114
Water3,837213
1
A: Deoxyfructosyl-amino Acid Transporter Periplasmic Binding Protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,6029
Polymers28,8791
Non-polymers7238
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Deoxyfructosyl-amino Acid Transporter Periplasmic Binding Protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,4787
Polymers28,8791
Non-polymers5996
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)39.600, 62.290, 84.230
Angle α, β, γ (deg.)90.00, 101.40, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Deoxyfructosyl-amino Acid Transporter Periplasmic Binding Protein


Mass: 28879.453 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Agrobacterium fabrum (strain C58 / ATCC 33970) (bacteria)
Gene: socA, Atu5006 / Production host: Escherichia coli (E. coli) / References: UniProt: Q7D447
#2: Chemical ChemComp-GOP / Glucopine


Mass: 310.301 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C11H22N2O8
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 213 / 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

Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 36% PEG 4K, 0.1 M HEPES pH 7.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 2 / Wavelength: 0.98 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: May 29, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.84→50 Å / Num. obs: 33762 / % possible obs: 96.3 % / Redundancy: 4.8 % / Biso Wilson estimate: 31.16 Å2 / Rsym value: 0.072 / Net I/σ(I): 12.74
Reflection shellResolution: 1.84→1.9 Å / Rsym value: 0.53

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Processing

Software
NameVersionClassification
BUSTER2.10.2refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4YMX

4ymx


Resolution: 1.84→33.83 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.931 / Rfactor Rfree error: 0 / SU R Cruickshank DPI: 0.19 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.189 / SU Rfree Blow DPI: 0.158 / SU Rfree Cruickshank DPI: 0.16
RfactorNum. reflection% reflectionSelection details
Rfree0.252 1687 5 %RANDOM
Rwork0.218 ---
obs0.219 33754 96.5 %-
Displacement parametersBiso mean: 42.77 Å2
Baniso -1Baniso -2Baniso -3
1-4.82 Å20 Å2-0.6537 Å2
2---9.3012 Å20 Å2
3---4.4812 Å2
Refine analyzeLuzzati coordinate error obs: 0.29 Å
Refinement stepCycle: 1 / Resolution: 1.84→33.83 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3647 0 84 213 3944
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0093797HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.025123HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1263SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes90HARMONIC2
X-RAY DIFFRACTIONt_gen_planes554HARMONIC5
X-RAY DIFFRACTIONt_it3797HARMONIC20
X-RAY DIFFRACTIONt_nbd0SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion2.8
X-RAY DIFFRACTIONt_other_torsion17.54
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion488SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact4745SEMIHARMONIC4
LS refinement shellResolution: 1.84→1.9 Å / Rfactor Rfree error: 0 / Total num. of bins used: 17
RfactorNum. reflection% reflection
Rfree0.242 105 4.96 %
Rwork0.246 2010 -
all0.246 2115 -
obs--69.71 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.740.2723-0.34682.8828-0.8632.83280.07940.0723-0.12360.02610.0110.0833-0.0622-0.1387-0.0904-0.03910.0058-0.0559-0.1452-0.0246-0.1874-18.414-7.858-46.6831
21.9069-0.4458-1.33934.7967-2.57725.00650.16480.4265-0.12120.07290.02610.4542-0.1341-0.4692-0.1908-0.13620.0288-0.0328-0.1152-0.0211-0.2459-6.9549-7.5904-5.6459
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{ A|* }
2X-RAY DIFFRACTION2{ B|* }

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