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- PDB-6eq8: Structure of the periplasmic binding protein (PBP) MelB (Atu4661)... -

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Basic information

Entry
Database: PDB / ID: 6eq8
TitleStructure of the periplasmic binding protein (PBP) MelB (Atu4661) in complex with galactinol from agrobacterium fabrum C58
ComponentsPeriplasmic alpha-galactoside-binding protein
KeywordsTRANSPORT 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
galactinol / 1-ETHOXY-2-(2-ETHOXYETHOXY)ETHANE / DI(HYDROXYETHYL)ETHER / Periplasmic alpha-galactoside-binding protein
Similarity search - Component
Biological speciesRhizobium radiobacter (Agrobacterium genomosp. 4)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.19 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 18, 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 1.2Jan 17, 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
Revision 1.3Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)313,015110
Polymers305,4384
Non-polymers7,576106
Water15,529862
1
D: Periplasmic alpha-galactoside-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)78,09922
Polymers76,3601
Non-polymers1,74021
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Periplasmic alpha-galactoside-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)77,62922
Polymers76,3601
Non-polymers1,26921
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Periplasmic alpha-galactoside-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)78,84937
Polymers76,3601
Non-polymers2,48936
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
A: Periplasmic alpha-galactoside-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)78,43829
Polymers76,3601
Non-polymers2,07828
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)355.260, 73.660, 108.080
Angle α, β, γ (deg.)90.00, 105.49, 90.00
Int Tables number5
Space group name H-MC121

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Components

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Protein , 1 types, 4 molecules DBCA

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


Mass: 76359.602 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

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Non-polymers , 8 types, 968 molecules

#2: Chemical...
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 39 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical
ChemComp-BQZ / galactinol


Mass: 342.296 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C12H22O11
#4: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 13 / Source method: obtained synthetically / Formula: Ca
#5: Chemical
ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C4H10O3
#6: Chemical ChemComp-P4G / 1-ETHOXY-2-(2-ETHOXYETHOXY)ETHANE


Mass: 162.227 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C8H18O3
#7: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#8: Chemical...
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 35 / Source method: obtained synthetically / Formula: Cl
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 862 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.23 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 1 / Wavelength: 0.98 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 8, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.19→50 Å / Num. obs: 137636 / % possible obs: 98.7 % / Redundancy: 5.2 % / Biso Wilson estimate: 49.64 Å2 / CC1/2: 0.993 / Rsym value: 0.171 / Net I/σ(I): 7.5
Reflection shellResolution: 2.19→2.3 Å / Mean I/σ(I) obs: 1.5 / CC1/2: 0.579 / Rsym value: 1.125 / % possible all: 92.6

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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: 2.19→32.06 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.924 / Rfactor Rfree error: 0.01 / SU R Cruickshank DPI: 0.276 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.269 / SU Rfree Blow DPI: 0.188 / SU Rfree Cruickshank DPI: 0.192
RfactorNum. reflection% reflectionSelection details
Rfree0.217 6879 5 %RANDOM
Rwork0.184 ---
obs0.186 137582 99.1 %-
Displacement parametersBiso mean: 45.66 Å2
Baniso -1Baniso -2Baniso -3
1-9.8392 Å20 Å2-1.275 Å2
2---5.3257 Å20 Å2
3----4.5135 Å2
Refine analyzeLuzzati coordinate error obs: 0.28 Å
Refinement stepCycle: 1 / Resolution: 2.19→32.06 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms21149 0 432 862 22443
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0122095HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.0929940HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d7415SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes583HARMONIC2
X-RAY DIFFRACTIONt_gen_planes3138HARMONIC5
X-RAY DIFFRACTIONt_it22095HARMONIC20
X-RAY DIFFRACTIONt_nbd3SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion3.29
X-RAY DIFFRACTIONt_other_torsion18.34
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion2721SEMIHARMONIC5
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_contact25061SEMIHARMONIC4
LS refinement shellResolution: 2.19→2.25 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.282 450 5 %
Rwork0.274 8555 -
all0.274 9005 -
obs--88.25 %
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)
12.80090.487-0.09270.71770.00360.4858-0.04470.14250.156-0.06070.02360.0256-0.0336-0.06620.021-0.1982-0.0258-0.0186-0.22720.0229-0.2226135.917513.192372.3495
22.6699-0.2836-0.19440.510.12490.40860.07340.14190.1465-0.0499-0.0935-0.1098-0.017-0.02240.0201-0.18840.03810.0267-0.2340.0045-0.201148.749349.994719.8363
30.44070.092-0.02610.47830.01140.7147-0.0025-0.0523-0.0741-0.0180.0035-0.11910.05680.2035-0.001-0.15180.01750.0062-0.12820.0077-0.223292.8145-26.208562.0801
40.8784-0.1179-0.03080.69830.1880.6795-0.0276-0.0384-0.01070.02190.0744-0.1480.06730.165-0.0468-0.16720.0083-0.0002-0.1997-0.027-0.235106.747210.237611.1327
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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