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- PDB-7mzq: Crystal structure of the UcaD lectin-binding domain in complex wi... -

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Basic information

Entry
Database: PDB / ID: 7mzq
TitleCrystal structure of the UcaD lectin-binding domain in complex with fucose
ComponentsFimbrial adhesin UcaD
KeywordsSUGAR BINDING PROTEIN / lectin / cell adhesion
Function / homologyFimbrial-type adhesion domain / Fimbrial protein / Fimbrial-type adhesion domain superfamily / Adhesion domain superfamily / pilus / cell adhesion / beta-L-fucopyranose / Fimbrial adhesin
Function and homology information
Biological speciesProteus mirabilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsVe, T. / Lo, A.W. / Schembri, M.A. / Kobe, B.
Funding support Australia, 1items
OrganizationGrant numberCountry
National Health and Medical Research Council (NHMRC, Australia) Australia
CitationJournal: Plos Pathog. / Year: 2022
Title: Ucl fimbriae regulation and glycan receptor specificity contribute to gut colonisation by extra-intestinal pathogenic Escherichia coli.
Authors: Hancock, S.J. / Lo, A.W. / Ve, T. / Day, C.J. / Tan, L. / Mendez, A.A. / Phan, M.D. / Nhu, N.T.K. / Peters, K.M. / Richards, A.C. / Fleming, B.A. / Chang, C. / Ngu, D.H.Y. / Forde, B.M. / ...Authors: Hancock, S.J. / Lo, A.W. / Ve, T. / Day, C.J. / Tan, L. / Mendez, A.A. / Phan, M.D. / Nhu, N.T.K. / Peters, K.M. / Richards, A.C. / Fleming, B.A. / Chang, C. / Ngu, D.H.Y. / Forde, B.M. / Haselhorst, T. / Goh, K.G.K. / Beatson, S.A. / Jennings, M.P. / Mulvey, M.A. / Kobe, B. / Schembri, M.A.
History
DepositionMay 24, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 6, 2022Provider: repository / Type: Initial release
Revision 1.1Jan 25, 2023Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _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 / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Apr 3, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Fimbrial adhesin UcaD
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,3638
Polymers21,9861
Non-polymers3777
Water3,513195
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1100 Å2
ΔGint-48 kcal/mol
Surface area8910 Å2
Unit cell
Length a, b, c (Å)79.472, 79.472, 70.227
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number79
Space group name H-MI4
Space group name HallI4
Symmetry operation#1: x,y,z
#2: -y,x,z
#3: y,-x,z
#4: -x,-y,z
#5: x+1/2,y+1/2,z+1/2
#6: -y+1/2,x+1/2,z+1/2
#7: y+1/2,-x+1/2,z+1/2
#8: -x+1/2,-y+1/2,z+1/2
Components on special symmetry positions
IDModelComponents
11A-595-

HOH

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Components

#1: Protein Fimbrial adhesin UcaD


Mass: 21985.908 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Proteus mirabilis (bacteria) / Gene: NCTC10975_02625 / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: A0A2X2BLR9
#2: Sugar ChemComp-FUL / beta-L-fucopyranose / beta-L-fucose / 6-deoxy-beta-L-galactopyranose / L-fucose / fucose / 6-DEOXY-BETA-L-GALACTOSE / Fucose


Type: L-saccharide, beta linking / Mass: 164.156 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H12O5 / Feature type: SUBJECT OF INVESTIGATION
IdentifierTypeProgram
LFucpbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
b-L-fucopyranoseCOMMON NAMEGMML 1.0
b-L-FucpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
FucSNFG CARBOHYDRATE SYMBOLGMML 1.0
#3: Chemical
ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 195 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.52 Å3/Da / Density % sol: 51.22 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 0.1 M sodium citrate buffer pH 4.5-5.5, 2-3 M NaCl / PH range: 4.5-5.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9537 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Sep 22, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 1.5→39.74 Å / Num. obs: 34590 / % possible obs: 99.8 % / Redundancy: 13.8 % / Biso Wilson estimate: 17.65 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.064 / Rpim(I) all: 0.018 / Rrim(I) all: 0.066 / Net I/σ(I): 18.3
Reflection shellResolution: 1.5→1.53 Å / Rmerge(I) obs: 0.667 / Mean I/σ(I) obs: 2.5 / Num. unique obs: 1653 / CC1/2: 0.895 / Rpim(I) all: 0.187 / Rrim(I) all: 0.694

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Processing

Software
NameVersionClassification
PHENIX1.19.1_4122refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: UcaD

Resolution: 1.5→39.74 Å / SU ML: 0.1382 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 18.1504
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1761 1999 5.78 %
Rwork0.1626 32588 -
obs0.1634 34587 99.77 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 21.22 Å2
Refinement stepCycle: LAST / Resolution: 1.5→39.74 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1450 0 17 195 1662
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0081512
X-RAY DIFFRACTIONf_angle_d0.93612070
X-RAY DIFFRACTIONf_chiral_restr0.0622244
X-RAY DIFFRACTIONf_plane_restr0.0089268
X-RAY DIFFRACTIONf_dihedral_angle_d11.4473543
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5-1.540.23191370.19712266X-RAY DIFFRACTION97.01
1.54-1.580.2091400.1692317X-RAY DIFFRACTION100
1.58-1.630.19821460.17082332X-RAY DIFFRACTION99.96
1.63-1.680.18631380.16692298X-RAY DIFFRACTION100
1.68-1.740.23431460.1772349X-RAY DIFFRACTION100
1.74-1.810.20281460.16522311X-RAY DIFFRACTION100
1.81-1.90.19731430.15862335X-RAY DIFFRACTION100
1.9-20.1751410.14742309X-RAY DIFFRACTION100
2-2.120.16151420.15842327X-RAY DIFFRACTION99.96
2.12-2.280.17271420.15532345X-RAY DIFFRACTION100
2.28-2.510.22561450.17782319X-RAY DIFFRACTION100
2.51-2.880.20641410.17772341X-RAY DIFFRACTION100
2.88-3.620.15671440.15942360X-RAY DIFFRACTION99.96
3.63-39.740.14121480.15282379X-RAY DIFFRACTION99.92

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