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- PDB-7mzp: Crystal structure of the UclD lectin-binding domain -

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Basic information

Entry
Database: PDB / ID: 7mzp
TitleCrystal structure of the UclD lectin-binding domain
ComponentsF17-like fimbril adhesin subunit UclD
KeywordsSUGAR BINDING PROTEIN / lectin / cell adhesion
Function / homologyFimbrial-type adhesion domain / Fimbrial protein / Fimbrial-type adhesion domain superfamily / Adhesion domain superfamily / pilus / cell adhesion / IODIDE ION / F17-like fimbril adhesin subunit
Function and homology information
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 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: F17-like fimbril adhesin subunit UclD
B: F17-like fimbril adhesin subunit UclD
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,2708
Polymers44,5082
Non-polymers7616
Water2,324129
1
A: F17-like fimbril adhesin subunit UclD
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,8896
Polymers22,2541
Non-polymers6355
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: F17-like fimbril adhesin subunit UclD
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,3812
Polymers22,2541
Non-polymers1271
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)39.040, 58.120, 175.420
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

#1: Protein F17-like fimbril adhesin subunit UclD / Type 1 fimbrial protein


Mass: 22254.156 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: F11
Gene: AWF59_013360, EPS70_23860, EWK56_25230, HJO44_004566, HV098_04385, HVW98_02190, NCTC9075_01316
Production host: Escherichia coli BL21 (bacteria) / References: UniProt: A0A1X9VGE7
#2: Chemical
ChemComp-IOD / IODIDE ION / Iodide


Mass: 126.904 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: I
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 129 / 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: 2.52 Å3/Da / Density % sol: 51.19 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 20-25% w/v PEG 3350, 0.1 M Bis-Tris propane pH 6.5, 0.2 M sodium iodide

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX1 / Wavelength: 0.9537 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Aug 20, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 2.2→58.12 Å / Num. obs: 21160 / % possible obs: 100 % / Redundancy: 7 % / Biso Wilson estimate: 23.08 Å2 / CC1/2: 0.99 / Rmerge(I) obs: 0.257 / Rpim(I) all: 0.105 / Rrim(I) all: 0.278 / Net I/σ(I): 5.4
Reflection shellResolution: 2.2→2.27 Å / Rmerge(I) obs: 1.325 / Mean I/σ(I) obs: 1.5 / Num. unique obs: 1794 / CC1/2: 0.748 / Rpim(I) all: 0.532 / Rrim(I) all: 1.43

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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: 2.2→43.85 Å / SU ML: 0.275 / Cross valid method: FREE R-VALUE / σ(F): 1.75 / Phase error: 30.4537
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.3058 1068 5.07 %
Rwork0.248 19998 -
obs0.2508 21066 99.81 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 29.14 Å2
Refinement stepCycle: LAST / Resolution: 2.2→43.85 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2785 0 6 129 2920
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0022847
X-RAY DIFFRACTIONf_angle_d0.55313888
X-RAY DIFFRACTIONf_chiral_restr0.0456450
X-RAY DIFFRACTIONf_plane_restr0.0042507
X-RAY DIFFRACTIONf_dihedral_angle_d11.18491014
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2-2.30.32981490.29712428X-RAY DIFFRACTION99.88
2.3-2.420.34241280.2792479X-RAY DIFFRACTION99.92
2.42-2.570.30851300.28992433X-RAY DIFFRACTION99.92
2.57-2.770.31871230.27262493X-RAY DIFFRACTION99.81
2.77-3.050.31681310.2692488X-RAY DIFFRACTION99.77
3.05-3.490.32511470.23592468X-RAY DIFFRACTION99.85
3.49-4.40.25991150.19952554X-RAY DIFFRACTION99.89
4.4-43.850.2941450.24182655X-RAY DIFFRACTION99.47
Refinement TLS params.Method: refined / Origin x: 7.56169896251 Å / Origin y: 17.0778734298 Å / Origin z: 68.9396000023 Å
111213212223313233
T0.161053318199 Å20.00106429277766 Å2-0.0239999837766 Å2-0.212840347711 Å20.00361406686052 Å2--0.169698343419 Å2
L0.192741605574 °20.094391159562 °20.0275707880996 °2-0.618539787153 °2-0.00211283369458 °2--0.37999044617 °2
S-0.035299776774 Å °0.0281342632553 Å °0.000442736190183 Å °-0.0969948393574 Å °0.016380272416 Å °0.0588375551309 Å °-0.036153902352 Å °0.048249054798 Å °0.0100776108439 Å °
Refinement TLS groupSelection details: all

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