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- PDB-6epz: Structure of the periplasmic binding protein MelB (Atu4661) in co... -

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Basic information

Entry
Database: PDB / ID: 6epz
TitleStructure of the periplasmic binding protein MelB (Atu4661) in complex with melibiose from Agrobacterium fabrum C58
ComponentsPeriplasmic alpha-galactoside-binding protein
KeywordsTRANSPORT PROTEIN / protein transporter
Function / homologySolute-binding protein family 5 domain / Solute-binding protein family 5 / Bacterial extracellular solute-binding proteins, family 5 Middle / periplasmic space / alpha-melibiose / DI(HYDROXYETHYL)ETHER / Periplasmic alpha-galactoside-binding protein
Function and homology information
Biological speciesRhizobium radiobacter (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 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 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Non-polymer description / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp / entity / entity_name_com / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_molecule_features / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_struct_conn_angle / struct_asym / struct_conn / struct_conn_type / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.pdbx_formal_charge / _atom_site.type_symbol / _atom_site_anisotrop.U[1][1] / _atom_site_anisotrop.U[1][2] / _atom_site_anisotrop.U[1][3] / _atom_site_anisotrop.U[2][2] / _atom_site_anisotrop.U[2][3] / _atom_site_anisotrop.U[3][3] / _atom_site_anisotrop.pdbx_auth_asym_id / _atom_site_anisotrop.pdbx_auth_atom_id / _atom_site_anisotrop.pdbx_auth_comp_id / _atom_site_anisotrop.pdbx_auth_seq_id / _atom_site_anisotrop.pdbx_label_atom_id / _atom_site_anisotrop.pdbx_label_comp_id / _atom_site_anisotrop.type_symbol / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.pdbx_synonyms / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.type / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_asym.entity_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Jan 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
D: Periplasmic alpha-galactoside-binding protein
C: Periplasmic alpha-galactoside-binding protein
B: Periplasmic alpha-galactoside-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)308,27352
Polymers305,4384
Non-polymers2,83548
Water24,7171372
1
A: Periplasmic alpha-galactoside-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)77,11213
Polymers76,3601
Non-polymers75312
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Periplasmic alpha-galactoside-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)77,05714
Polymers76,3601
Non-polymers69813
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Periplasmic alpha-galactoside-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)77,01914
Polymers76,3601
Non-polymers66013
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Periplasmic alpha-galactoside-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)77,08411
Polymers76,3601
Non-polymers72410
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)351.610, 73.730, 107.580
Angle α, β, γ (deg.)90.00, 105.38, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-1161-

HOH

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Components

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Protein / Sugars , 2 types, 8 molecules ADCB

#1: Protein
Periplasmic alpha-galactoside-binding protein


Mass: 76359.602 Da / Num. of mol.: 4
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: Polysaccharide
alpha-D-galactopyranose-(1-6)-alpha-D-glucopyranose / alpha-melibiose


Type: oligosaccharide, Oligosaccharide / Class: Metabolism / Mass: 342.297 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Details: oligosaccharide / References: alpha-melibiose
DescriptorTypeProgram
DGalpa1-6DGlcpa1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,2,1/[a2122h-1a_1-5][a2112h-1a_1-5]/1-2/a6-b1WURCSPDB2Glycan 1.1.0
[][a-D-Glcp]{[(6+1)][a-D-Galp]{}}LINUCSPDB-CARE

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Non-polymers , 6 types, 1416 molecules

#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Mg
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical...
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 28 / Source method: obtained synthetically / Formula: Na
#6: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#7: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1372 / 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: 2.2 Å3/Da / Density % sol: 44.12 %
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 1 / Wavelength: 0.98 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: May 18, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.8→49 Å / Num. obs: 246319 / % possible obs: 99.4 % / Redundancy: 6.6 % / Biso Wilson estimate: 30.42 Å2 / CC1/2: 0.998 / Rsym value: 0.1 / Net I/σ(I): 11.4
Reflection shellResolution: 1.8→1.9 Å / Mean I/σ(I) obs: 1.9 / CC1/2: 0.8 / Rsym value: 0.772 / % possible all: 97.1

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Processing

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

6epy


Resolution: 1.8→48.85 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.948 / Rfactor Rfree error: 0 / SU R Cruickshank DPI: 0.122 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.122 / SU Rfree Blow DPI: 0.106 / SU Rfree Cruickshank DPI: 0.107
RfactorNum. reflection% reflectionSelection details
Rfree0.195 12285 5 %RANDOM
Rwork0.177 ---
obs0.178 245683 99.9 %-
Displacement parametersBiso mean: 33.82 Å2
Baniso -1Baniso -2Baniso -3
1-2.817 Å20 Å2-1.2496 Å2
2--4.0799 Å20 Å2
3----6.8969 Å2
Refine analyzeLuzzati coordinate error obs: 0.24 Å
Refinement stepCycle: 1 / Resolution: 1.8→48.85 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms21207 0 169 1372 22748
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0121975HARMONIC2
X-RAY DIFFRACTIONt_angle_deg129893HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d7341SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes585HARMONIC2
X-RAY DIFFRACTIONt_gen_planes3154HARMONIC5
X-RAY DIFFRACTIONt_it21975HARMONIC20
X-RAY DIFFRACTIONt_nbd9SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion3.48
X-RAY DIFFRACTIONt_other_torsion17.47
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion2733SEMIHARMONIC5
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_contact26180SEMIHARMONIC4
LS refinement shellResolution: 1.8→1.85 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.312 902 5 %
Rwork0.285 17129 -
all0.286 18031 -
obs--99.7 %
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)
11.4376-0.0289-0.29090.4325-0.06790.25090.04110.064-0.01410.0044-0.01530.0798-0.0216-0.0608-0.0258-0.2639-0.01040.0097-0.24110.0016-0.2316136.488412.789772.18
20.9011-0.1521-0.19550.35040.04920.3526-0.0120.04590.0248-0.0248-0.0268-0.0159-0.0012-0.05920.0388-0.21940.0179-0.0098-0.2256-0.026-0.1918149.477949.902419.6411
30.63750.02420.15920.3902-0.06970.44370.02520.0091-0.0632-0.0152-0.0325-0.09870.02050.06710.0073-0.28080.00750.0195-0.23620.0057-0.215893.0402-26.603462.0985
40.9266-0.0593-0.08430.40130.12760.8856-0.0255-0.0699-0.00620.00280.1087-0.12410.06370.2561-0.0831-0.23940.03390.0028-0.1501-0.0439-0.2405106.947611.167110.6794
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{ A|* }
2X-RAY DIFFRACTION2{ B|* }
3X-RAY DIFFRACTION3{ C|* }
4X-RAY DIFFRACTION4{ D|* }

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