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- PDB-5l9i: Crystal structure of the periplasmic binding protein MotA in comp... -

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Basic information

Entry
Database: PDB / ID: 5l9i
TitleCrystal structure of the periplasmic binding protein MotA in complex with DFG from A. tumefaciens B6
Componentsperiplasmic binding protein
KeywordsTRANSPORT PROTEIN / Periplasmic binding protein
Function / homologyPeriplasmic binding protein-like II / D-Maltodextrin-Binding Protein; domain 2 / 3-Layer(aba) Sandwich / Alpha Beta / DI(HYDROXYETHYL)ETHER / Deoxyfructosylglutamine / :
Function and homology information
Biological speciesAgrobacterium tumefaciens str. B6 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsMarty, L. / Morera, S.
Funding support France, 1items
OrganizationGrant numberCountry
French National Research AgencyANR-12-BSV8-0003-01 France
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
DepositionJun 10, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 21, 2016Provider: repository / Type: Initial release
Revision 1.1Nov 16, 2016Group: Database references
Revision 1.2Sep 6, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
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: periplasmic binding protein
B: periplasmic binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)78,33916
Polymers76,9122
Non-polymers1,42814
Water5,188288
1
A: periplasmic binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,1378
Polymers38,4561
Non-polymers6817
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: periplasmic binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,2038
Polymers38,4561
Non-polymers7477
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)71.390, 71.390, 134.060
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number76
Space group name H-MP41

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein periplasmic binding protein


Mass: 38455.945 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Agrobacterium tumefaciens str. B6 (bacteria)
Gene: ASB65_13110 / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / References: UniProt: A0A109C781

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Non-polymers , 5 types, 302 molecules

#2: Chemical ChemComp-SNW / Deoxyfructosylglutamine / santhopine


Mass: 308.285 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C11H20N2O8
#3: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C4H10O3
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Ca
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 288 / 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: 2.22 Å3/Da / Density % sol: 44.62 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5 / Details: 24% PEG 4K, 0.1 M MES, 0.2 M CaCl2

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.97 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Feb 6, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 1.9→50 Å / Num. obs: 52621 / % possible obs: 99.7 % / Redundancy: 4.48 % / Biso Wilson estimate: 44.47 Å2 / Rsym value: 0.064 / Net I/σ(I): 11.9
Reflection shellResolution: 1.9→2.01 Å / Rsym value: 0.888

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Processing

Software
NameVersionClassification
BUSTER2.10.2refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5L9G

5l9g


Resolution: 1.9→38 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.949 / Rfactor Rfree error: 0 / SU R Cruickshank DPI: 0.14 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.138 / SU Rfree Blow DPI: 0.123 / SU Rfree Cruickshank DPI: 0.125
RfactorNum. reflection% reflectionSelection details
Rfree0.206 2629 5 %RANDOM
Rwork0.177 ---
obs0.179 52588 99.8 %-
Displacement parametersBiso mean: 52.47 Å2
Baniso -1Baniso -2Baniso -3
1-1.8693 Å20 Å20 Å2
2--1.8693 Å20 Å2
3----3.7387 Å2
Refine analyzeLuzzati coordinate error obs: 0.24 Å
Refinement stepCycle: 1 / Resolution: 1.9→38 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5007 0 90 288 5385
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.015216HARMONIC2
X-RAY DIFFRACTIONt_angle_deg17076HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1741SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes140HARMONIC2
X-RAY DIFFRACTIONt_gen_planes746HARMONIC5
X-RAY DIFFRACTIONt_it5216HARMONIC20
X-RAY DIFFRACTIONt_nbd0SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion3.02
X-RAY DIFFRACTIONt_other_torsion18.33
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion672SEMIHARMONIC5
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_contact6145SEMIHARMONIC4
LS refinement shellResolution: 1.9→1.95 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.252 194 4.99 %
Rwork0.249 3692 -
all0.249 3886 -
obs--99.41 %
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)
12.8202-0.62410.97940.9068-0.66922.04360.34750.6276-0.4398-0.0891-0.1740.11380.15010.362-0.1735-0.49740.0801-0.0525-0.3413-0.119-0.426615.137848.5118-0.1823
20.57570.13850.13622.327-0.44052.40640.0431-0.01180.07090.31120.16930.4438-0.2615-0.15-0.2125-0.47310.04860.1079-0.5170.0432-0.368246.602783.5112-12.7351
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{ A|* }
2X-RAY DIFFRACTION2{ B|* }

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