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- PDB-5wvn: Crystal structure of MBS-BaeS fusion protein -

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Basic information

Entry
Database: PDB / ID: 5wvn
TitleCrystal structure of MBS-BaeS fusion protein
ComponentsMaltose-binding periplasmic protein,Two-component system sensor kinase
KeywordsSUGAR BINDING PROTEIN / BaeS / sensor domain / Indole / two component system
Function / homology
Function and homology information


detection of maltose stimulus / maltose transport complex / carbohydrate transport / carbohydrate transmembrane transporter activity / maltose binding / maltose transport / maltodextrin transmembrane transport / ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing / ATP-binding cassette (ABC) transporter complex / cell chemotaxis ...detection of maltose stimulus / maltose transport complex / carbohydrate transport / carbohydrate transmembrane transporter activity / maltose binding / maltose transport / maltodextrin transmembrane transport / ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing / ATP-binding cassette (ABC) transporter complex / cell chemotaxis / outer membrane-bounded periplasmic space / periplasmic space / DNA damage response / membrane
Similarity search - Function
Maltose/Cyclodextrin ABC transporter, substrate-binding protein / Solute-binding family 1, conserved site / Bacterial extracellular solute-binding proteins, family 1 signature. / Bacterial extracellular solute-binding protein / Bacterial extracellular solute-binding protein
Similarity search - Domain/homology
: / Maltose/maltodextrin-binding periplasmic protein
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
Serratia marcescens subsp. marcescens Db11 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsWang, W. / Zhang, Y. / Ran, T. / Xu, D.
Funding support China, 3items
OrganizationGrant numberCountry
Natural Science Foundation of China31170686 China
Natural Science Foundation of China31400055 China
the Natural Science Foundation of Jiangsu ProvinceBK20140690 China
CitationJournal: Proteins / Year: 2017
Title: Crystal structure of the sensor domain of BaeS from Serratia marcescens FS14
Authors: Zhang, Y. / Qiu, S. / Jia, S. / Xu, D. / Ran, T. / Wang, W.
History
DepositionDec 26, 2016Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 3, 2018Provider: repository / Type: Initial release
Revision 1.1Jan 16, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Mar 20, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
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: Maltose-binding periplasmic protein,Two-component system sensor kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,6355
Polymers57,2501
Non-polymers3844
Water1629
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area190 Å2
ΔGint-12 kcal/mol
Surface area22190 Å2
MethodPISA
Unit cell
Length a, b, c (Å)119.084, 119.084, 147.011
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein Maltose-binding periplasmic protein,Two-component system sensor kinase / MBP / MMBP / Maltodextrin-binding protein


Mass: 57250.363 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli), (gene. exp.) Serratia marcescens subsp. marcescens Db11 (bacteria)
Strain: K12 / Gene: malE, b4034, JW3994, baeS, SMDB11_2949 / Production host: Escherichia coli (E. coli) / References: UniProt: P0AEX9, UniProt: A0A0N1UYP9
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 9 / 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: 4.55 Å3/Da / Density % sol: 72.98 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / Details: Citric Acid: NaOH , Ammonium Sulfate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.9785 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: AREA DETECTOR / Date: Jun 30, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9785 Å / Relative weight: 1
ReflectionResolution: 2.8→33.684 Å / Num. obs: 25337 / % possible obs: 99.9 % / Redundancy: 10.1 % / Net I/σ(I): 39.3
Reflection shellResolution: 2.8→2.9 Å / Redundancy: 9.8 % / Mean I/σ(I) obs: 3.2 / % possible all: 99.8

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.8→33.68 Å / SU ML: 0.4 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 27.2
RfactorNum. reflection% reflection
Rfree0.27 1229 4.85 %
Rwork0.228 --
obs0.23 25337 95 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.8→33.68 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3815 0 20 9 3844
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.013946
X-RAY DIFFRACTIONf_angle_d1.1485370
X-RAY DIFFRACTIONf_dihedral_angle_d16.5822323
X-RAY DIFFRACTIONf_chiral_restr0.056573
X-RAY DIFFRACTIONf_plane_restr0.007701
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.8001-2.91220.36821120.32151905X-RAY DIFFRACTION70
2.9122-3.04460.37631220.28792459X-RAY DIFFRACTION89
3.0446-3.2050.34121390.27522688X-RAY DIFFRACTION97
3.205-3.40560.33721270.26562796X-RAY DIFFRACTION100
3.4056-3.66830.28241490.23542782X-RAY DIFFRACTION100
3.6683-4.03690.29341410.20922802X-RAY DIFFRACTION100
4.0369-4.61980.24151380.19052833X-RAY DIFFRACTION100
4.6198-5.81560.20981700.2082831X-RAY DIFFRACTION100
5.8156-33.68650.21651310.21533012X-RAY DIFFRACTION99

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