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- PDB-2xwx: Vibrio cholerae colonization factor GbpA crystal structure -

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Basic information

Entry
Database: PDB / ID: 2xwx
TitleVibrio cholerae colonization factor GbpA crystal structure
ComponentsGLCNAC-BINDING PROTEIN A
KeywordsCHITIN-BINDING PROTEIN
Function / homology
Function and homology information


chitin binding / extracellular region
Similarity search - Function
Immunoglobulin-like - #2550 / Alpha-Beta Plaits - #2150 / N-acetylglucosamine-binding protein A / N-acetylglucosamine binding protein A domain 2 / N-acetylglucosamine binding protein domain 2 / chitin-binding protein cbp21 / Cellulose/chitin-binding protein, N-terminal / Lytic polysaccharide mono-oxygenase, cellulose-degrading / Coagulation Factor XIII; Chain A, domain 1 / Distorted Sandwich ...Immunoglobulin-like - #2550 / Alpha-Beta Plaits - #2150 / N-acetylglucosamine-binding protein A / N-acetylglucosamine binding protein A domain 2 / N-acetylglucosamine binding protein domain 2 / chitin-binding protein cbp21 / Cellulose/chitin-binding protein, N-terminal / Lytic polysaccharide mono-oxygenase, cellulose-degrading / Coagulation Factor XIII; Chain A, domain 1 / Distorted Sandwich / Immunoglobulin E-set / Alpha-Beta Plaits / Immunoglobulin-like / Sandwich / 2-Layer Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
GlcNAc-binding protein A
Similarity search - Component
Biological speciesVIBRIO CHOLERAE (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.8 Å
AuthorsWong, E. / Vaaje-Kolstad, G. / Ghosh, A. / Guerrero, R.H. / Konarev, P.V. / Ibrahim, A.F.M. / Svergun, D.I. / Eijsink, V.G.H. / Chatterjee, N.S. / van Aalten, D.M.F.
CitationJournal: PLoS Pathog / Year: 2012
Title: The Vibrio cholerae colonization factor GbpA possesses a modular structure that governs binding to different host surfaces.
Authors: Edmond Wong / Gustav Vaaje-Kolstad / Avishek Ghosh / Ramon Hurtado-Guerrero / Peter V Konarev / Adel F M Ibrahim / Dmitri I Svergun / Vincent G H Eijsink / Nabendu S Chatterjee / Daan M F van Aalten /
Abstract: Vibrio cholerae is a bacterial pathogen that colonizes the chitinous exoskeleton of zooplankton as well as the human gastrointestinal tract. Colonization of these different niches involves an N- ...Vibrio cholerae is a bacterial pathogen that colonizes the chitinous exoskeleton of zooplankton as well as the human gastrointestinal tract. Colonization of these different niches involves an N-acetylglucosamine binding protein (GbpA) that has been reported to mediate bacterial attachment to both marine chitin and mammalian intestinal mucin through an unknown molecular mechanism. We report structural studies that reveal that GbpA possesses an unusual, elongated, four-domain structure, with domains 1 and 4 showing structural homology to chitin binding domains. A glycan screen revealed that GbpA binds to GlcNAc oligosaccharides. Structure-guided GbpA truncation mutants show that domains 1 and 4 of GbpA interact with chitin in vitro, whereas in vivo complementation studies reveal that domain 1 is also crucial for mucin binding and intestinal colonization. Bacterial binding studies show that domains 2 and 3 bind to the V. cholerae surface. Finally, mouse virulence assays show that only the first three domains of GbpA are required for colonization. These results explain how GbpA provides structural/functional modular interactions between V. cholerae, intestinal epithelium and chitinous exoskeletons.
History
DepositionNov 6, 2010Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 16, 2011Provider: repository / Type: Initial release
Revision 1.1Aug 29, 2012Group: Database references / Structure summary
Revision 1.2Apr 15, 2015Group: Source and taxonomy / Structure summary

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: GLCNAC-BINDING PROTEIN A
B: GLCNAC-BINDING PROTEIN A


Theoretical massNumber of molelcules
Total (without water)86,5862
Polymers86,5862
Non-polymers00
Water11,349630
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6240 Å2
ΔGint-20.2 kcal/mol
Surface area32650 Å2
MethodPISA
Unit cell
Length a, b, c (Å)55.955, 120.182, 67.177
Angle α, β, γ (deg.)90.00, 108.41, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection details
111CHAIN A AND (RESSEQ 24:202 OR RESSEQ 209:313 OR RESSEQ 315:414)
211CHAIN B AND (RESSEQ 24:202 OR RESSEQ 209:313 OR RESSEQ 315:414)

NCS oper: (Code: given
Matrix: (0.773047, -0.183263, 0.6073), (-0.182617, -0.981124, -0.063613), (0.607494, -0.061728, -0.791922)
Vector: -39.8101, 97.5974, 145.5364)

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Components

#1: Protein GLCNAC-BINDING PROTEIN A / GBPA


Mass: 43292.984 Da / Num. of mol.: 2 / Fragment: RESIDUES 24-414
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) VIBRIO CHOLERAE (bacteria) / Description: CLONED FROM GENOMIC DNA OF V. CHOLERAE / Plasmid: PGEX6P GBPA / Production host: ESCHERICHIA COLI BL21(DE3) (bacteria) / Strain (production host): C43 / References: UniProt: Q9KLD5
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 630 / 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: 1.9 Å3/Da / Density % sol: 40 % / Description: NONE
Crystal growpH: 7.5
Details: 0.2 M MG(HCO3)2, 50% (W/V) PEG 3350, 3.33% (W/V) D-SORBITOL, PH 7.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.933
DetectorType: MARRESEARCH / Detector: CCD / Date: Oct 20, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.933 Å / Relative weight: 1
ReflectionResolution: 1.8→20 Å / Num. obs: 73728 / % possible obs: 96.1 % / Observed criterion σ(I): 2 / Redundancy: 3 % / Biso Wilson estimate: 28.69 Å2 / Rmerge(I) obs: 0.05 / Net I/σ(I): 14.4
Reflection shellResolution: 1.8→1.9 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.33 / Mean I/σ(I) obs: 3 / % possible all: 91.6

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE: 1.5_2)refinement
DENZOdata reduction
SCALEPACKdata scaling
SOLVEphasing
RefinementMethod to determine structure: SAD
Starting model: NONE

Resolution: 1.8→19.94 Å / SU ML: 0.24 / σ(F): 1.34 / Phase error: 26.1 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.246 738 1 %
Rwork0.207 --
obs0.207 72993 95.2 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 53.25 Å2 / ksol: 0.34 e/Å3
Displacement parametersBiso mean: 36.3 Å2
Baniso -1Baniso -2Baniso -3
1-0.5197 Å20 Å20.4001 Å2
2---0.4323 Å20 Å2
3----0.0875 Å2
Refinement stepCycle: LAST / Resolution: 1.8→19.94 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6014 0 0 630 6644
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0086160
X-RAY DIFFRACTIONf_angle_d1.1248382
X-RAY DIFFRACTIONf_dihedral_angle_d18.7612220
X-RAY DIFFRACTIONf_chiral_restr0.079908
X-RAY DIFFRACTIONf_plane_restr0.0061114
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11A3000X-RAY DIFFRACTIONPOSITIONAL
12B3000X-RAY DIFFRACTIONPOSITIONAL0.852
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8026-1.94160.30511490.283513389X-RAY DIFFRACTION88
1.9416-2.13680.29441420.247414292X-RAY DIFFRACTION93
2.1368-2.44550.2611500.230514748X-RAY DIFFRACTION96
2.4455-3.07930.27481460.212215230X-RAY DIFFRACTION99
3.0793-19.9430.21451510.182815331X-RAY DIFFRACTION99
Refinement TLS params.Method: refined / Origin x: -6.6131 Å / Origin y: 47.1343 Å / Origin z: 77.2633 Å
111213212223313233
T0.1138 Å2-0.0203 Å2-0.0292 Å2-0.1653 Å20.0333 Å2--0.1862 Å2
L0.5306 °20.1314 °2-0.4831 °2-0.8288 °2-0.1535 °2--1.1203 °2
S0.0298 Å °0.0148 Å °0.0021 Å °0.0351 Å °0.0438 Å °0.1188 Å °-0.0735 Å °0.0119 Å °-0 Å °
Refinement TLS groupSelection details: ALL

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