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- PDB-6eq0: Structure of the periplasmic binding protein (PBP) MelB (atu4661)... -

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Basic information

Entry
Database: PDB / ID: 6eq0
TitleStructure of the periplasmic binding protein (PBP) MelB (atu4661) in complex with galactose from agrobacterium tumefacien C58
ComponentsPeriplasmic alpha-galactoside-binding protein
KeywordsTRANSPORT PROTEIN / Protein transport associated to ABC transporter
Function / homologySolute-binding protein family 5 domain / Solute-binding protein family 5 / Bacterial extracellular solute-binding proteins, family 5 Middle / periplasmic space / alpha-D-galactopyranose / DI(HYDROXYETHYL)ETHER / Periplasmic alpha-galactoside-binding protein
Function and homology information
Biological speciesRhizobium radiobacter (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.45 Å
AuthorsVigouroux, A. / Morera, S.
Funding support France, 1items
OrganizationGrant numberCountry
CNRSMI France
CitationJournal: J. Biol. Chem. / Year: 2018
Title: The plant defense signal galactinol is specifically used as a nutrient by the bacterial pathogenAgrobacterium fabrum.
Authors: Meyer, T. / Vigouroux, A. / Aumont-Nicaise, M. / Comte, G. / Vial, L. / Lavire, C. / Morera, S.
History
DepositionOct 12, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 11, 2018Provider: repository / Type: Initial release
Revision 1.1Jun 6, 2018Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp / citation ...chem_comp / citation / entity / pdbx_entity_nonpoly
Item: _chem_comp.name / _citation.journal_volume ..._chem_comp.name / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _entity.pdbx_description / _pdbx_entity_nonpoly.name
Revision 1.2Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_conn / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.3Jan 17, 2024Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Periplasmic alpha-galactoside-binding protein
B: Periplasmic alpha-galactoside-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)155,84460
Polymers152,7192
Non-polymers3,12558
Water4,558253
1
A: Periplasmic alpha-galactoside-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)78,23536
Polymers76,3601
Non-polymers1,87535
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Periplasmic alpha-galactoside-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)77,60924
Polymers76,3601
Non-polymers1,24923
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)107.840, 73.920, 171.100
Angle α, β, γ (deg.)90.00, 92.55, 90.00
Int Tables number5
Space group name H-MC121

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Components

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Protein / Sugars , 2 types, 4 molecules AB

#1: Protein Periplasmic alpha-galactoside-binding protein / MelB


Mass: 76359.602 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rhizobium radiobacter (bacteria) / Gene: SY94_4618 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A083ZM57
#2: Sugar ChemComp-GLA / alpha-D-galactopyranose / alpha-D-galactose / D-galactose / galactose / ALPHA D-GALACTOSE / Galactose


Type: D-saccharide, alpha linking / Mass: 180.156 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C6H12O6
IdentifierTypeProgram
DGalpaCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
a-D-galactopyranoseCOMMON NAMEGMML 1.0
a-D-GalpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GalSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 5 types, 309 molecules

#3: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3
#4: Chemical...
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 21 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical
ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: Cl
#6: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 17 / Source method: obtained synthetically / Formula: Ca
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 253 / 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: 2.23 Å3/Da / Density % sol: 44.86 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop
Details: 25% PEG 4000, 0.6 M NaCl, 0.2 M CaCl2 and 0.1 M Mes pH 6.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 2 / Wavelength: 0.98 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Jun 6, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.45→50 Å / Num. obs: 49700 / % possible obs: 99.2 % / Redundancy: 6.3 % / Biso Wilson estimate: 63.81 Å2 / CC1/2: 0.991 / Rsym value: 0.182 / Net I/σ(I): 9
Reflection shellResolution: 2.45→2.59 Å / Mean I/σ(I) obs: 1.6 / CC1/2: 0.512 / Rsym value: 1 / % possible all: 95.7

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Processing

Software
NameVersionClassification
BUSTER2.10.2refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6EPZ

6epz


Resolution: 2.45→46.51 Å / Cor.coef. Fo:Fc: 0.921 / Cor.coef. Fo:Fc free: 0.891 / Rfactor Rfree error: 0 / SU R Cruickshank DPI: 0.665 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.598 / SU Rfree Blow DPI: 0.27 / SU Rfree Cruickshank DPI: 0.278
RfactorNum. reflection% reflectionSelection details
Rfree0.241 2480 5 %RANDOM
Rwork0.194 ---
obs0.196 49589 99.7 %-
Displacement parametersBiso mean: 65.47 Å2
Baniso -1Baniso -2Baniso -3
1--3.2643 Å20 Å20.0529 Å2
2--8.6244 Å20 Å2
3----5.3601 Å2
Refine analyzeLuzzati coordinate error obs: 0.34 Å
Refinement stepCycle: 1 / Resolution: 2.45→46.51 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10590 0 155 253 10998
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0110995HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.1614912HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d3689SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes292HARMONIC2
X-RAY DIFFRACTIONt_gen_planes1572HARMONIC5
X-RAY DIFFRACTIONt_it10995HARMONIC20
X-RAY DIFFRACTIONt_nbd8SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion3
X-RAY DIFFRACTIONt_other_torsion20.74
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion1354SEMIHARMONIC5
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_contact12523SEMIHARMONIC4
LS refinement shellResolution: 2.45→2.51 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.314 182 5 %
Rwork0.258 3460 -
all0.261 3642 -
obs--98.2 %
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)
10.77820.0675-0.24192.56810.01092.19310.00910.1343-0.0825-0.873-0.07370.02180.0565-0.46270.0646-0.31460.03-0.0183-0.303-0.0371-0.472828.577621.864465.1284
20.6399-0.05140.53423.46590.27681.9208-0.09970.04780.0570.3656-0.05160.9237-0.1868-0.09890.1513-0.29480.00290.0882-0.5464-0.0228-0.343326.5789-12.593721.2025
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{ A|* }
2X-RAY DIFFRACTION2{ B|* }

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