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

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Basic information

Entry
Database: PDB / ID: 7mzr
TitleCrystal structure of the UcaD lectin-binding domain in complex with glucose
ComponentsFimbrial adhesin UcaD
KeywordsSUGAR BINDING PROTEIN / Lectin / Cell adhesion
Function / homologyFimbrial-type adhesion domain / Fimbrial protein / cell adhesion involved in single-species biofilm formation / Fimbrial-type adhesion domain superfamily / Adhesion domain superfamily / pilus / beta-D-glucopyranose / Fimbrial adhesin
Function and homology information
Biological speciesProteus mirabilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.78 Å
AuthorsVe, T. / Lo, A.W. / Schembri, M.A. / Kobe, B.
Funding support Australia, 3items
OrganizationGrant numberCountry
National Health and Medical Research Council (NHMRC, Australia)1071659 Australia
National Health and Medical Research Council (NHMRC, Australia)1110971 Australia
National Health and Medical Research Council (NHMRC, Australia)1180826 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)22,3798
Polymers21,9861
Non-polymers3937
Water3,675204
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1130 Å2
ΔGint-48 kcal/mol
Surface area8810 Å2
Unit cell
Length a, b, c (Å)79.075, 79.075, 70.183
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-601-

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-BGC / beta-D-glucopyranose / beta-D-glucose / D-glucose / glucose / Glucose


Type: D-saccharide, beta linking / Mass: 180.156 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H12O6 / Feature type: SUBJECT OF INVESTIGATION
IdentifierTypeProgram
DGlcpbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
b-D-glucopyranoseCOMMON NAMEGMML 1.0
b-D-GlcpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcSNFG 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.: 204 / 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: 2.68 Å3/Da / Density % sol: 54.07 %
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: Oct 23, 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: 15.5 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: 1.78→39.54 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 19.8595
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1968 2023 9.73 %
Rwork0.1617 18760 -
obs0.1651 20783 99.82 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 18.89 Å2
Refinement stepCycle: LAST / Resolution: 1.78→39.54 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1445 0 18 204 1667
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00821508
X-RAY DIFFRACTIONf_angle_d0.9362064
X-RAY DIFFRACTIONf_chiral_restr0.062243
X-RAY DIFFRACTIONf_plane_restr0.0092267
X-RAY DIFFRACTIONf_dihedral_angle_d11.0873549
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.78-1.820.30141400.2581305X-RAY DIFFRACTION97.83
1.82-1.870.23711390.19221313X-RAY DIFFRACTION100
1.87-1.930.19591450.14951363X-RAY DIFFRACTION99.87
1.93-1.990.18051420.14661333X-RAY DIFFRACTION99.93
1.99-2.060.19291450.14871333X-RAY DIFFRACTION100
2.06-2.140.21011470.15061315X-RAY DIFFRACTION100
2.14-2.240.19131440.15281358X-RAY DIFFRACTION100
2.24-2.360.20911400.16351349X-RAY DIFFRACTION100
2.36-2.510.21531420.16581333X-RAY DIFFRACTION99.93
2.51-2.70.2221460.17871334X-RAY DIFFRACTION100
2.7-2.970.24411480.18691345X-RAY DIFFRACTION100
2.97-3.40.17621470.16551348X-RAY DIFFRACTION100
3.4-4.280.161430.13561348X-RAY DIFFRACTION100
4.29-39.540.17461550.15531383X-RAY DIFFRACTION99.87

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