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- PDB-6epy: Structure of the PBP MelB (Atu4661) in complex with raffinose fro... -

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Basic information

Entry
Database: PDB / ID: 6epy
TitleStructure of the PBP MelB (Atu4661) in complex with raffinose from A.fabrum C58
ComponentsPeriplasmic alpha-galactoside-binding protein
KeywordsTRANSPORT PROTEIN / Periplasmic binding protein
Function / homology
Function and homology information


Dipeptide-binding Protein; domain 3 / Dipeptide-binding Protein; Domain 3 / Solute-binding protein family 5 domain / Solute-binding protein family 5 / Bacterial extracellular solute-binding proteins, family 5 Middle / Roll / Alpha Beta
Similarity search - Domain/homology
raffinose / Periplasmic alpha-galactoside-binding protein
Similarity search - Component
Biological speciesRhizobium radiobacter (Agrobacterium genomosp. 4)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.04 Å
AuthorsMorera, S. / Vigouroux, A.
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 / pdbx_struct_special_symmetry / 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.occupancy / _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.id / _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_asym_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.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_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_symmetry / _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 / _pdbx_struct_special_symmetry.label_asym_id / _struct_asym.entity_id / _struct_conn_type.id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Nov 20, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
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
C: Periplasmic alpha-galactoside-binding protein
D: Periplasmic alpha-galactoside-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)315,528137
Polymers308,2524
Non-polymers7,276133
Water21,2401179
1
A: Periplasmic alpha-galactoside-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)79,65553
Polymers77,0631
Non-polymers2,59252
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Periplasmic alpha-galactoside-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)79,01038
Polymers77,0631
Non-polymers1,94737
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Periplasmic alpha-galactoside-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)78,71230
Polymers77,0631
Non-polymers1,64929
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Periplasmic alpha-galactoside-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)78,15116
Polymers77,0631
Non-polymers1,08815
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)354.300, 74.270, 108.220
Angle α, β, γ (deg.)90.00, 105.50, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-731-

CA

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Components

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


Mass: 77063.047 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rhizobium radiobacter (Agrobacterium genomosp. 4)
Gene: SY94_4618 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A083ZM57
#2: Polysaccharide
alpha-D-galactopyranose-(1-6)-alpha-D-glucopyranose-(1-2)-beta-D-fructofuranose / raffinose


Type: oligosaccharide, Oligosaccharide / Class: Nutrient / Mass: 504.438 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Details: oligosaccharide with reducing-end-to-reducing-end glycosidic bond
References: raffinose
DescriptorTypeProgram
DGalpa1-6DGlcpa1-2DFrufbGlycam Condensed SequenceGMML 1.0
WURCS=2.0/3,3,2/[ha122h-2b_2-5][a2122h-1a_1-5][a2112h-1a_1-5]/1-2-3/a2-b1_b6-c1WURCSPDB2Glycan 1.1.0
[][b-D-Fruf]{[(2+1)][a-D-Glcp]{[(6+1)][a-D-Galp]{}}}LINUCSPDB-CARE
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


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


Mass: 40.078 Da / Num. of mol.: 125 / Source method: obtained synthetically / Formula: Ca
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1179 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.25 Å3/Da / Density % sol: 45.24 %
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 PILATUS 6M / Detector: PIXEL / Date: Feb 5, 2015
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.04→45.14 Å / Num. obs: 333472 / % possible obs: 98.8 % / Redundancy: 3.4 % / Biso Wilson estimate: 39.76 Å2 / CC1/2: 0.998 / Rsym value: 0.07 / Net I/σ(I): 10.84
Reflection shellResolution: 2.04→2.17 Å / CC1/2: 0.801 / Rsym value: 0.528 / % possible all: 94.4

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Processing

Software
NameVersionClassification
BUSTER2.10.2refinement
XDSdata reduction
XSCALEdata scaling
SHELXCDphasing
RefinementMethod to determine structure: SAD / Resolution: 2.04→45.14 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.95 / Rfactor Rfree error: 0 / SU R Cruickshank DPI: 0.188 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.185 / SU Rfree Blow DPI: 0.146 / SU Rfree Cruickshank DPI: 0.148
RfactorNum. reflection% reflectionSelection details
Rfree0.2 8544 5 %RANDOM
Rwork0.174 ---
obs0.175 170869 98.9 %-
Displacement parametersBiso mean: 44.74 Å2
Baniso -1Baniso -2Baniso -3
1-4.7209 Å20 Å21.149 Å2
2--3.5578 Å20 Å2
3----8.2787 Å2
Refine analyzeLuzzati coordinate error obs: 0.23 Å
Refinement stepCycle: 1 / Resolution: 2.04→45.14 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms21085 0 277 1179 22541
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0121886HARMONIC2
X-RAY DIFFRACTIONt_angle_deg129797HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d7318SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes581HARMONIC2
X-RAY DIFFRACTIONt_gen_planes3136HARMONIC5
X-RAY DIFFRACTIONt_it21886HARMONIC20
X-RAY DIFFRACTIONt_nbd3SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion3.36
X-RAY DIFFRACTIONt_other_torsion17.63
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion2737SEMIHARMONIC5
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_contact24967SEMIHARMONIC4
LS refinement shellResolution: 2.04→2.09 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.251 546 5 %
Rwork0.232 10375 -
all0.233 10921 -
obs--86.07 %
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)
11.56580.0294-0.10780.5933-0.08080.3740.03230.08590.0349-0.0662-0.01350.07580.0046-0.0635-0.0188-0.2934-0.00770.0101-0.3403-0.0034-0.31135.756713.175372.3689
21.1339-0.1053-0.02860.63590.0420.44870.02850.05270.0552-0.0789-0.06270.0663-0.0526-0.10380.0342-0.23840.0404-0.0145-0.2895-0.0252-0.2675148.616549.987119.9057
31.3755-0.16740.45371.2873-0.10590.86920.05870.0661-0.096-0.1427-0.0446-0.16210.11080.1976-0.0142-0.26220.02730.0087-0.30630.0058-0.235992.9717-26.403462.3847
42.22330.14270.60990.89620.00791.02470.0360.4452-0.1488-0.06370.0993-0.12720.06970.2992-0.1354-0.25770.0507-0.0065-0.0362-0.0624-0.1946106.828910.484711.048
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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