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- PDB-4e9l: FdeC, a Novel Broadly Conserved Escherichia coli Adhesin Elicitin... -

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Basic information

Entry
Database: PDB / ID: 4e9l
TitleFdeC, a Novel Broadly Conserved Escherichia coli Adhesin Eliciting Protection against Urinary Tract Infections
ComponentsAttaching and effacing protein, pathogenesis factor
KeywordsCELL ADHESION / invasin-like / bacterial immunoglobulin / pathogenic / vaccine
Function / homology
Function and homology information


membrane => GO:0016020 / cell adhesion
Similarity search - Function
Invasin, domain 3 / Invasin, domain 3 / Intimin/invasin bacterial adhesion mediator protein / Inverse autotransporter, beta-domain / Inverse autotransporter, beta-domain superfamily / Bacterial Ig-like domain (group 1) / Inverse autotransporter, beta-domain / Bacterial Ig-like domain (group 1) / Big-1 (bacterial Ig-like domain 1) domain / Big-1 (bacterial Ig-like domain 1) domain profile. ...Invasin, domain 3 / Invasin, domain 3 / Intimin/invasin bacterial adhesion mediator protein / Inverse autotransporter, beta-domain / Inverse autotransporter, beta-domain superfamily / Bacterial Ig-like domain (group 1) / Inverse autotransporter, beta-domain / Bacterial Ig-like domain (group 1) / Big-1 (bacterial Ig-like domain 1) domain / Big-1 (bacterial Ig-like domain 1) domain profile. / Invasin/intimin cell-adhesion fragments / Immunoglobulins / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Attaching and effacing protein, pathogenesis factor EaeH / Attaching and effacing protein, pathogenesis factor
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsSpraggon, G. / Nesta, B. / Alteri, C. / Gomes Moriel, D. / Rosini, R. / Veggi, D. / Smith, S. / Bertoldi, I. / Pastorello, I. / Ferlenghi, I. ...Spraggon, G. / Nesta, B. / Alteri, C. / Gomes Moriel, D. / Rosini, R. / Veggi, D. / Smith, S. / Bertoldi, I. / Pastorello, I. / Ferlenghi, I. / Fontana, M.R. / Frankel, G. / Mobley, H.L.T. / Rappuoli, R. / Pizza, M. / Serino, L. / Soriana, M.
CitationJournal: MBio / Year: 2012
Title: FdeC, a novel broadly conserved Escherichia coli adhesin eliciting protection against urinary tract infections.
Authors: Nesta, B. / Spraggon, G. / Alteri, C. / Moriel, D.G. / Rosini, R. / Veggi, D. / Smith, S. / Bertoldi, I. / Pastorello, I. / Ferlenghi, I. / Fontana, M.R. / Frankel, G. / Mobley, H.L. / ...Authors: Nesta, B. / Spraggon, G. / Alteri, C. / Moriel, D.G. / Rosini, R. / Veggi, D. / Smith, S. / Bertoldi, I. / Pastorello, I. / Ferlenghi, I. / Fontana, M.R. / Frankel, G. / Mobley, H.L. / Rappuoli, R. / Pizza, M. / Serino, L. / Soriani, M.
History
DepositionMar 21, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 25, 2012Provider: repository / Type: Initial release
SupersessionAug 8, 2012ID: 3TKV
Revision 1.1Aug 8, 2012Group: Database references
Revision 1.2Jan 16, 2013Group: Database references
Revision 1.3Jul 10, 2013Group: Database references
Revision 1.4Sep 13, 2023Group: 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 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Attaching and effacing protein, pathogenesis factor


Theoretical massNumber of molelcules
Total (without water)42,6241
Polymers42,6241
Non-polymers00
Water5,747319
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Attaching and effacing protein, pathogenesis factor

A: Attaching and effacing protein, pathogenesis factor


Theoretical massNumber of molelcules
Total (without water)85,2482
Polymers85,2482
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_855-x+3,-y,z1
Buried area1700 Å2
ΔGint-3 kcal/mol
Surface area28700 Å2
MethodPISA
Unit cell
Length a, b, c (Å)44.630, 150.930, 47.380
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 Attaching and effacing protein, pathogenesis factor


Mass: 42623.848 Da / Num. of mol.: 1 / Fragment: unp residues 595-1008
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: UTI89 / UPEC / Gene: eaeH, UTI89_C0321 / Plasmid: SpeedET / Production host: Escherichia coli (E. coli) / References: UniProt: Q1RFP2, UniProt: A0A0H2YWG9*PLUS
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 319 / 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: 1.87 Å3/Da / Density % sol: 34.29 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 9
Details: 20% PEG-6000, 0.1M Bicine, pH 9.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 0.92 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 6, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92 Å / Relative weight: 1
ReflectionResolution: 1.9→50 Å / Num. all: 24734 / Num. obs: 24734 / % possible obs: 95.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 10.2 % / Biso Wilson estimate: 23.28 Å2 / Rmerge(I) obs: 0.084 / Rsym value: 0.084 / Net I/σ(I): 23.9

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Processing

Software
NameVersionClassification
PHASERphasing
BUSTER2.11.2refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entries 1CWV, 1F00

1cwv

1f00


Resolution: 1.9→47.38 Å / Cor.coef. Fo:Fc: 0.9489 / Cor.coef. Fo:Fc free: 0.9472 / SU R Cruickshank DPI: 0.143 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.2 1265 5.13 %RANDOM
Rwork0.1782 ---
obs0.1794 24678 94.61 %-
Displacement parametersBiso mean: 25.91 Å2
Baniso -1Baniso -2Baniso -3
1--0.599 Å20 Å20 Å2
2---0.5994 Å20 Å2
3---1.1984 Å2
Refine analyzeLuzzati coordinate error obs: 0.199 Å
Refinement stepCycle: LAST / Resolution: 1.9→47.38 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2190 0 0 319 2509
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.012246HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.173082HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d725SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes53HARMONIC2
X-RAY DIFFRACTIONt_gen_planes340HARMONIC5
X-RAY DIFFRACTIONt_it2246HARMONIC20
X-RAY DIFFRACTIONt_omega_torsion3.53
X-RAY DIFFRACTIONt_other_torsion15.1
X-RAY DIFFRACTIONt_chiral_improper_torsion326SEMIHARMONIC5
X-RAY DIFFRACTIONt_ideal_dist_contact2661SEMIHARMONIC4
LS refinement shellResolution: 1.9→1.98 Å / Total num. of bins used: 12
RfactorNum. reflection% reflection
Rfree0.2598 100 5.1 %
Rwork0.248 1860 -
all0.2486 1960 -
obs--94.61 %
Refinement TLS params.Method: refined / Origin x: 61.6151 Å / Origin y: 23.4539 Å / Origin z: 36.0183 Å
111213212223313233
T0.0176 Å20.013 Å2-0.0043 Å2--0.0398 Å20.0049 Å2--0.0161 Å2
L0.3258 °2-0.5732 °20.2492 °2-0.8076 °2-0.3265 °2--0.101 °2
S-0.0438 Å °-0.024 Å °0.0276 Å °0.0583 Å °0.0134 Å °-0.0516 Å °-0.0002 Å °-0.0328 Å °0.0304 Å °
Refinement TLS groupSelection details: { A|678 - A|991 }

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