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- PDB-5nwp: Crystal Structure of the Lectin Domain From the F17-like Adhesin, UclD -

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Basic information

Entry
Database: PDB / ID: 5nwp
TitleCrystal Structure of the Lectin Domain From the F17-like Adhesin, UclD
ComponentsAdhesin
KeywordsCELL ADHESION / F17-like / UclD / Lectin / Adhesin / UPEC
Function / homology
Function and homology information


cell adhesion involved in single-species biofilm formation / pilus / RNA-directed DNA polymerase activity
Similarity search - Function
Fimbrial-type adhesion domain / Fimbrial protein / : / Fimbrial-type adhesion domain superfamily / Adhesion domain superfamily
Similarity search - Domain/homology
Putative F17-like fimbril adhesin subunit / Adhesin
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.05 Å
AuthorsRuer, S. / Remaut, H.
Funding support Belgium, 1items
OrganizationGrant numberCountry
FWOG030411N Belgium
CitationJournal: Nature / Year: 2017
Title: Selective depletion of uropathogenic E. coli from the gut by a FimH antagonist.
Authors: Spaulding, C.N. / Klein, R.D. / Ruer, S. / Kau, A.L. / Schreiber, H.L. / Cusumano, Z.T. / Dodson, K.W. / Pinkner, J.S. / Fremont, D.H. / Janetka, J.W. / Remaut, H. / Gordon, J.I. / Hultgren, S.J.
History
DepositionMay 8, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 21, 2017Provider: repository / Type: Initial release
Revision 1.1Jun 28, 2017Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_id_ASTM ..._citation.country / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.2Jul 5, 2017Group: Database references / Category: citation
Item: _citation.country / _citation.journal_id_ASTM ..._citation.country / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3May 1, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Adhesin
B: Adhesin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,0723
Polymers42,9762
Non-polymers961
Water11,638646
1
A: Adhesin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,5842
Polymers21,4881
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Adhesin


Theoretical massNumber of molelcules
Total (without water)21,4881
Polymers21,4881
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)30.089, 91.871, 64.932
Angle α, β, γ (deg.)90.00, 96.46, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Adhesin / F17-like Adhesin / UclD / F17 fimbril adhesin subunit / Putative F17-like fimbril adhesin subunit


Mass: 21488.193 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: OK10_24545, WM48_23800 / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: Q8GA71, UniProt: Q1R2V7*PLUS
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 646 / 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: 2.08 Å3/Da / Density % sol: 40.72 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 16% PEG 4000, 0.1M Tris HCl pH 8.5, 0.2M MgCl2

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 1.008 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jan 22, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.008 Å / Relative weight: 1
ReflectionResolution: 1.05→91.87 Å / Num. obs: 144393 / % possible obs: 88.8 % / Redundancy: 5 % / Biso Wilson estimate: 5.7 Å2 / Rmerge(I) obs: 0.079 / Rpim(I) all: 0.034 / Net I/σ(I): 11.9
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsRpim(I) all% possible all
1.05-1.1120.3362.1103540.30843.8
3.32-37.437.20.05431.152340.02299.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0124refinement
XDSdata reduction
SCALAdata scaling
SHELXDphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Se-SAD model

Resolution: 1.05→91.87 Å / Cor.coef. Fo:Fc: 0.982 / Cor.coef. Fo:Fc free: 0.975 / SU B: 0.738 / SU ML: 0.016 / Cross valid method: THROUGHOUT / ESU R: 0.025 / ESU R Free: 0.026 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.14252 7242 5 %RANDOM
Rwork0.11711 ---
obs0.11839 137073 88.7 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 11.786 Å2
Baniso -1Baniso -2Baniso -3
1-0.09 Å20 Å2-0.08 Å2
2---0.15 Å20 Å2
3---0.07 Å2
Refinement stepCycle: 1 / Resolution: 1.05→91.87 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2914 0 5 646 3565
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0270.0193193
X-RAY DIFFRACTIONr_bond_other_d0.0030.023043
X-RAY DIFFRACTIONr_angle_refined_deg2.2321.9624413
X-RAY DIFFRACTIONr_angle_other_deg1.41737030
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.4675455
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.31123.84125
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.30215478
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.3261519
X-RAY DIFFRACTIONr_chiral_restr0.1480.2510
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.0213776
X-RAY DIFFRACTIONr_gen_planes_other0.0080.02737
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.9170.8531660
X-RAY DIFFRACTIONr_mcbond_other1.9130.8521659
X-RAY DIFFRACTIONr_mcangle_it2.2661.2932095
X-RAY DIFFRACTIONr_mcangle_other2.2681.2932096
X-RAY DIFFRACTIONr_scbond_it3.9141.1681533
X-RAY DIFFRACTIONr_scbond_other3.9131.1691530
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.7911.6522287
X-RAY DIFFRACTIONr_long_range_B_refined5.41710.0984164
X-RAY DIFFRACTIONr_long_range_B_other4.7218.6123702
X-RAY DIFFRACTIONr_rigid_bond_restr7.12836236
X-RAY DIFFRACTIONr_sphericity_free28.6435108
X-RAY DIFFRACTIONr_sphericity_bonded10.84556688
LS refinement shellResolution: 1.05→1.077 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.297 221 -
Rwork0.295 3966 -
obs--34.81 %

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