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- PDB-5l9p: Crystal structure of the PBP MotA from A. tumefaciens B6 -

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Basic information

Entry
Database: PDB / ID: 5l9p
TitleCrystal structure of the PBP MotA 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 / :
Function and homology information
Biological speciesAgrobacterium tumefaciens str. B6 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.54 Å
AuthorsMorera, S. / Marty, L.
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)78,06514
Polymers76,9122
Non-polymers1,15312
Water68538
1
A: periplasmic binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,0327
Polymers38,4561
Non-polymers5766
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: periplasmic binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,0327
Polymers38,4561
Non-polymers5766
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)64.400, 118.980, 111.210
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#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
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 38 / 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: 2.77 Å3/Da / Density % sol: 55.59 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4.6 / Details: 2 M AS, 0.1M sodium acetate

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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: 2.54→50 Å / Num. obs: 28729 / % possible obs: 99.3 % / Redundancy: 5.6 % / Biso Wilson estimate: 67.95 Å2 / Rsym value: 0.17 / Net I/σ(I): 7.35
Reflection shellResolution: 2.54→2.69 Å / Rsym value: 1.119

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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: 2.54→31.56 Å / Cor.coef. Fo:Fc: 0.918 / Cor.coef. Fo:Fc free: 0.895 / Rfactor Rfree error: 0 / SU R Cruickshank DPI: 0.416 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.412 / SU Rfree Blow DPI: 0.247 / SU Rfree Cruickshank DPI: 0.251
RfactorNum. reflection% reflectionSelection details
Rfree0.229 1435 5 %RANDOM
Rwork0.192 ---
obs0.194 28693 99.2 %-
Displacement parametersBiso mean: 60.07 Å2
Baniso -1Baniso -2Baniso -3
1-20.582 Å20 Å20 Å2
2---14.6428 Å20 Å2
3----5.9392 Å2
Refine analyzeLuzzati coordinate error obs: 0.36 Å
Refinement stepCycle: LAST / Resolution: 2.54→31.56 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5244 0 60 38 5342
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.015432HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.147393HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1783SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes140HARMONIC2
X-RAY DIFFRACTIONt_gen_planes784HARMONIC5
X-RAY DIFFRACTIONt_it5432HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion2.85
X-RAY DIFFRACTIONt_other_torsion21.09
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion697SEMIHARMONIC5
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_contact5958SEMIHARMONIC4
LS refinement shellResolution: 2.54→2.64 Å / Rfactor Rfree error: 0 / Total num. of bins used: 14
RfactorNum. reflection% reflection
Rfree0.307 141 5 %
Rwork0.268 2678 -
all0.27 2819 -
obs--94.25 %
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)
11.113-0.10660.10141.1574-0.59341.2534-0.0087-0.01860.132-0.0904-0.0641-0.0642-0.0158-0.0060.0727-0.05960.04390.011-0.0590.0809-0.10935.17432.595214.2449
22.5756-0.5266-1.07450.74020.18871.5071-0.07360.1155-0.27490.1016-0.08780.07630.0122-0.00450.1614-0.0679-0.03050.0247-0.19930.0334-0.032526.726315.740350.9037
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{ A|* }
2X-RAY DIFFRACTION2{ B|* }

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