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- PDB-7mzo: Crystal structure of the UcaD lectin-binding domain -

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Basic information

Entry
Database: PDB / ID: 7mzo
TitleCrystal structure of the UcaD lectin-binding domain
ComponentsFimbrial adhesin UcaD
KeywordsSUGAR BINDING PROTEIN / lectin / cell adhesion
Function / homologyFimbrial-type adhesion domain / Fimbrial protein / Fimbrial-type adhesion domain superfamily / cell adhesion involved in single-species biofilm formation / Adhesion domain superfamily / pilus / Fimbrial adhesin
Function and homology information
Biological speciesProteus mirabilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.62 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)22,1636
Polymers21,9861
Non-polymers1775
Water4,450247
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area600 Å2
ΔGint-43 kcal/mol
Surface area8920 Å2
Unit cell
Length a, b, c (Å)77.390, 77.390, 70.910
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-639-

HOH

21A-640-

HOH

31A-647-

HOH

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Components

#1: Protein Fimbrial adhesin UcaD


Mass: 21985.908 Da / Num. of mol.: 1 / Fragment: lectin-binding domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Proteus mirabilis (bacteria) / Gene: NCTC10975_02625 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A2X2BLR9
#2: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Cl
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 247 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.41 Å3/Da / Density % sol: 49.06 %
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

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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: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 30, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 1.62→54.72 Å / Num. obs: 26588 / % possible obs: 99.9 % / Redundancy: 7 % / Biso Wilson estimate: 16.68 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.11 / Rpim(I) all: 0.045 / Rrim(I) all: 0.119 / Net I/σ(I): 11.6
Reflection shellResolution: 1.62→1.65 Å / Rmerge(I) obs: 1.443 / Mean I/σ(I) obs: 1.4 / Num. unique obs: 1305 / CC1/2: 0.634 / Rpim(I) all: 0.584 / Rrim(I) all: 1.559

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Processing

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

Resolution: 1.62→38.7 Å / SU ML: 0.1728 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 21.0098
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1922 1312 4.94 %
Rwork0.1688 25263 -
obs0.1699 26575 99.87 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 20.82 Å2
Refinement stepCycle: LAST / Resolution: 1.62→38.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1449 0 5 247 1701
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0091491
X-RAY DIFFRACTIONf_angle_d0.95662038
X-RAY DIFFRACTIONf_chiral_restr0.0621237
X-RAY DIFFRACTIONf_plane_restr0.0104265
X-RAY DIFFRACTIONf_dihedral_angle_d11.0138539
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.62-1.680.28091630.25072787X-RAY DIFFRACTION99.9
1.69-1.760.26581430.23322791X-RAY DIFFRACTION99.86
1.76-1.850.23041640.19512769X-RAY DIFFRACTION99.93
1.85-1.970.18931390.17412811X-RAY DIFFRACTION99.97
1.97-2.120.20321590.15732768X-RAY DIFFRACTION99.93
2.12-2.340.18681390.16442828X-RAY DIFFRACTION99.93
2.34-2.670.17661210.1732819X-RAY DIFFRACTION99.93
2.67-3.370.19821430.17062826X-RAY DIFFRACTION99.76
3.37-38.70.15981410.14472864X-RAY DIFFRACTION99.6

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