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- PDB-9n4g: YehD Receptor Binding Domain -

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Basic information

Entry
Database: PDB / ID: 9n4g
TitleYehD Receptor Binding Domain
ComponentsYehD protein
KeywordsCELL ADHESION / Adhesin / CUP pili
Function / homologyUncharacterised conserved protein UCP030811 / Fimbrial-type adhesion domain / Fimbrial protein / Fimbrial-type adhesion domain superfamily / cell adhesion involved in single-species biofilm formation / Adhesion domain superfamily / pilus / Uncharacterized fimbrial-like protein YehA
Function and homology information
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.7 Å
AuthorsKlein, R.D. / Tamadonfar, K.O. / Pinkner, J.S. / Hultgren, S.J.
Funding support United States, 3items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R37AI048689 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01AI029549 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)T32 AI007172-40 United States
CitationJournal: To Be Published
Title: The Yeh pilus, tipped by an adhesin equipped with a mobile alpha-helical flap motif, mediates GI colonization via pectin adherence.
Authors: Tamadonfar, K.O. / Klein, R.D. / Lopatto, E. / Zimmerman, M.I. / Azimzadeh, P. / Porter, J. / Bazan Villicana, J. / Pinkner, J.S. / Birchenough, G. / Dodson, K.W. / Bowman, G.R. / Hultgren, S.J.
History
DepositionFeb 2, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 26, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: YehD protein
B: YehD protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,1064
Polymers36,9222
Non-polymers1842
Water97354
1
A: YehD protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,5532
Polymers18,4611
Non-polymers921
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: YehD protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,5532
Polymers18,4611
Non-polymers921
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)102.787, 50.486, 71.877
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein YehD protein


Mass: 18460.916 Da / Num. of mol.: 2 / Fragment: Receptor Binding Domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Production host: Escherichia coli (E. coli) / References: UniProt: P33340
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 54 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationY

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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: 2.53 Å3/Da / Density % sol: 51.43 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / Details: 0.2 M AmH2PO4, 20% w/v PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 4.2.2 / Wavelength: 0.97625 Å
DetectorType: NOIR-1 / Detector: CMOS / Date: Aug 6, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97625 Å / Relative weight: 1
ReflectionResolution: 1.7→45.31 Å / Num. obs: 41949 / % possible obs: 98.83 % / Redundancy: 6.9 % / CC1/2: 0.999 / Rmerge(I) obs: 0.1019 / Rrim(I) all: 0.1102 / Net I/σ(I): 15.66
Reflection shellResolution: 1.7→1.761 Å / Redundancy: 6.3 % / Rmerge(I) obs: 2.169 / Mean I/σ(I) obs: 0.75 / Num. unique obs: 4127 / CC1/2: 0.388 / Rrim(I) all: 2.367 / % possible all: 99.78

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Processing

Software
NameVersionClassification
PHENIX(1.13_2998: ???)refinement
XDSdata scaling
AutoSolphasing
XDSdata reduction
RefinementMethod to determine structure: SAD / Resolution: 1.7→45.31 Å / SU ML: 0.25 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 28.18 / Stereochemistry target values: MLHL
RfactorNum. reflection% reflection
Rfree0.2561 2029 4.89 %
Rwork0.2346 --
obs0.2357 41491 98.9 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.7→45.31 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2561 0 12 54 2627
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0042642
X-RAY DIFFRACTIONf_angle_d0.6813609
X-RAY DIFFRACTIONf_dihedral_angle_d9.641557
X-RAY DIFFRACTIONf_chiral_restr0.046428
X-RAY DIFFRACTIONf_plane_restr0.003465
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7-1.74250.31481370.31292823X-RAY DIFFRACTION100
1.7425-1.78960.35921500.30082806X-RAY DIFFRACTION100
1.7896-1.84230.3121420.29262799X-RAY DIFFRACTION100
1.8423-1.90180.35761390.30812746X-RAY DIFFRACTION98
1.9018-1.96970.3941250.37412685X-RAY DIFFRACTION95
1.9697-2.04860.26541280.24262859X-RAY DIFFRACTION100
2.0486-2.14180.27091540.24772808X-RAY DIFFRACTION100
2.1418-2.25480.31671570.30312691X-RAY DIFFRACTION96
2.2548-2.3960.28771600.27132701X-RAY DIFFRACTION96
2.396-2.5810.26051290.24152871X-RAY DIFFRACTION100
2.581-2.84070.2551420.24472842X-RAY DIFFRACTION100
2.8407-3.25170.25951510.23742878X-RAY DIFFRACTION100
3.2517-4.09630.25141540.19252903X-RAY DIFFRACTION100
4.0963-45.310.17181610.17213050X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: 36.4919 Å / Origin y: 33.4807 Å / Origin z: 49.3841 Å
111213212223313233
T0.175 Å20.0222 Å20.0246 Å2-0.2067 Å20.0184 Å2--0.2033 Å2
L0.3861 °20.174 °20.3717 °2-0.7305 °20.3328 °2--0.8172 °2
S-0.0008 Å °-0.0457 Å °-0.0387 Å °0.0719 Å °-0.0014 Å °-0.0106 Å °0.0282 Å °0.0184 Å °-0.0052 Å °
Refinement TLS groupSelection details: all

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