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- PDB-5lom: Crystal structure of the PBP SocA from Agrobacterium tumefaciens ... -

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Basic information

Entry
Database: PDB / ID: 5lom
TitleCrystal structure of the PBP SocA from Agrobacterium tumefaciens C58 in complex with DFG at 1.5 A resolution
ComponentsDeoxyfructosyl-amino Acid Transporter Periplasmic Binding Protein
KeywordsTRANSPORT PROTEIN / Periplasmic Binding Protein / Amadori compound / opine / DFG
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
Deoxyfructosylglutamine / Deoxyfructosyl-amino Acid Transporter Periplasmic Binding Protein
Similarity search - Component
Biological speciesAgrobacterium fabrum str. C58 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsMarty, L. / Vigouroux, A. / 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
DepositionAug 9, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 21, 2016Provider: repository / Type: Initial release
Revision 1.1Nov 16, 2016Group: Database references
Revision 1.2Nov 29, 2017Group: Database references / Category: pdbx_database_related
Revision 1.3Jan 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)58,8247
Polymers58,0212
Non-polymers8035
Water9,170509
1
A: Deoxyfructosyl-amino Acid Transporter Periplasmic Binding Protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,4434
Polymers29,0111
Non-polymers4323
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)29,3813
Polymers29,0111
Non-polymers3702
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)39.620, 62.030, 84.890
Angle α, β, γ (deg.)90.00, 101.27, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Deoxyfructosyl-amino Acid Transporter Periplasmic Binding Protein / bacterial periplasmic binding protein SocA


Mass: 29010.648 Da / Num. of mol.: 2 / Fragment: UNP residues 36-278
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Agrobacterium fabrum str. C58 (bacteria)
Gene: socA, Atu5006 / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: Q7D447
#2: Chemical ChemComp-SNW / Deoxyfructosylglutamine / santhopine


Mass: 308.285 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C11H20N2O8
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 509 / 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: 1.76 Å3/Da / Density % sol: 30.24 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 8.5 / Details: 30% PEG 4K, 100mM Tris

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 2 / Wavelength: 0.9798 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 29, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9798 Å / Relative weight: 1
ReflectionResolution: 1.5→50 Å / Num. obs: 64331 / % possible obs: 99.2 % / Redundancy: 6.71 % / Biso Wilson estimate: 18.27 Å2 / CC1/2: 0.997 / Rsym value: 0.01 / Net I/σ(I): 11.5
Reflection shellResolution: 1.5→1.59 Å / Redundancy: 6 % / Rmerge(I) obs: 0.706 / Mean I/σ(I) obs: 2.1 / CC1/2: 0.856 / % possible all: 97.2

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Processing

Software
NameVersionClassification
BUSTER2.10.2refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5L9M

5l9m
PDB Unreleased entry


Resolution: 1.5→41.63 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.939 / Rfactor Rfree error: 0 / SU R Cruickshank DPI: 0.087 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.091 / SU Rfree Blow DPI: 0.089 / SU Rfree Cruickshank DPI: 0.087
RfactorNum. reflection% reflectionSelection details
Rfree0.224 3213 5 %RANDOM
Rwork0.191 ---
obs0.192 64244 99.4 %-
Displacement parametersBiso mean: 19.96 Å2
Baniso -1Baniso -2Baniso -3
1-3.2079 Å20 Å2-1.2138 Å2
2---4.5476 Å20 Å2
3---1.3397 Å2
Refine analyzeLuzzati coordinate error obs: 0.21 Å
Refinement stepCycle: LAST / Resolution: 1.5→41.63 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3722 0 54 509 4285
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.013867HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.015240HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1285SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes92HARMONIC2
X-RAY DIFFRACTIONt_gen_planes570HARMONIC5
X-RAY DIFFRACTIONt_it3867HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion3.29
X-RAY DIFFRACTIONt_other_torsion16.02
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion496SEMIHARMONIC5
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_contact5272SEMIHARMONIC4
LS refinement shellResolution: 1.5→1.54 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.383 233 5 %
Rwork0.329 4423 -
all0.331 4656 -
obs--98.4 %
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)
10.9180.045-0.14180.4781-0.04621.04070.0177-0.0311-0.05780.0014-0.02140.02480.0195-0.0150.0036-0.03030.0039-0.0028-0.1313-0.0036-0.0338-18.414-7.8584-46.6825
20.5217-0.0587-0.12890.4590.0110.39910.01490.0379-0.0274-0.0128-0.01590.02930-0.00980.001-0.04770.00120.0031-0.1348-0.0016-0.05-6.9548-7.5928-5.6426
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{ A|* }
2X-RAY DIFFRACTION2{ B|* }

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