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- PDB-9n4h: YehD receptor binding domain S49A -

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Basic information

Entry
Database: PDB / ID: 9n4h
TitleYehD receptor binding domain S49A
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 / FORMIC ACID / Uncharacterized fimbrial-like protein YehA
Function and homology information
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.65 Å
AuthorsTamadonfar, K.O. / Klein, R.D. / 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)36,6198
Polymers36,1802
Non-polymers4396
Water1,33374
1
A: YehD protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,2524
Polymers18,0901
Non-polymers1623
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: YehD protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,3664
Polymers18,0901
Non-polymers2763
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)34.852, 92.296, 44.939
Angle α, β, γ (deg.)90.00, 91.69, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein YehD protein


Mass: 18089.969 Da / Num. of mol.: 2 / Fragment: Receptor Binding Domain / Mutation: S49A
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.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CH2O2
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 74 / 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 Å3/Da / Density % sol: 38.4 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / Details: 0.2 M MgFormate, 15% 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: 1.072157 Å
DetectorType: NOIR-1 / Detector: CMOS / Date: Nov 6, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.072157 Å / Relative weight: 1
ReflectionResolution: 1.65→46.15 Å / Num. obs: 33872 / % possible obs: 98.04 % / Redundancy: 3.7 % / CC1/2: 0.994 / Rmerge(I) obs: 0.1679 / Rrim(I) all: 0.1967 / Net I/σ(I): 8.02
Reflection shellResolution: 1.65→1.709 Å / Redundancy: 3.7 % / Rmerge(I) obs: 2.143 / Num. unique obs: 3066 / CC1/2: 0.297 / Rrim(I) all: 2.511 / % possible all: 90.71

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Processing

Software
NameVersionClassification
PHENIX(1.13_2998: ???)refinement
XDSdata reduction
XDSdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.65→46.148 Å / SU ML: 0.23 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 26.49 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.238 1598 4.78 %
Rwork0.2022 --
obs0.2039 33451 98.04 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.65→46.148 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2536 0 28 74 2638
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0142608
X-RAY DIFFRACTIONf_angle_d1.0283555
X-RAY DIFFRACTIONf_dihedral_angle_d10.2011530
X-RAY DIFFRACTIONf_chiral_restr0.069420
X-RAY DIFFRACTIONf_plane_restr0.008456
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.65-1.70330.36971210.32292631X-RAY DIFFRACTION90
1.7033-1.76420.331260.29882873X-RAY DIFFRACTION97
1.7642-1.83480.33231520.27712941X-RAY DIFFRACTION100
1.8348-1.91830.27791520.24242940X-RAY DIFFRACTION100
1.9183-2.01940.25781480.20482939X-RAY DIFFRACTION100
2.0194-2.1460.22781600.20022940X-RAY DIFFRACTION100
2.146-2.31160.22421340.19922949X-RAY DIFFRACTION100
2.3116-2.54430.24151370.20982940X-RAY DIFFRACTION100
2.5443-2.91240.25921530.20072934X-RAY DIFFRACTION99
2.9124-3.66910.23751390.18062890X-RAY DIFFRACTION98
3.6691-46.1480.17671760.15672876X-RAY DIFFRACTION97
Refinement TLS params.Method: refined / Origin x: 17.8533 Å / Origin y: -19.776 Å / Origin z: 11.2197 Å
111213212223313233
T0.1026 Å20.0026 Å20.0209 Å2-0.1098 Å2-0.0039 Å2--0.0729 Å2
L1.0088 °20.0246 °20.5687 °2-0.3827 °20.0837 °2--0.723 °2
S-0.0434 Å °0.004 Å °0.0741 Å °-0.0281 Å °0.0067 Å °-0.0205 Å °-0.0999 Å °-0.0036 Å °0.0348 Å °
Refinement TLS groupSelection details: all

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