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- PDB-3hlr: Donor strand complemented FaeG of F4ad fimbriae -

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Basic information

Entry
Database: PDB / ID: 3hlr
TitleDonor strand complemented FaeG of F4ad fimbriae
ComponentsK88 fimbrial protein AD
KeywordsCELL ADHESION / immunoglobuline like fold / Fimbrium
Function / homologypilus / K88 fimbrial protein AD
Function and homology information
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsVan Molle, I. / Moonens, K. / Garcia-Pino, A. / Buts, L. / Bouckaert, J. / De Greve, H.
CitationJournal: J.Mol.Biol. / Year: 2009
Title: Structural and thermodynamic characterization of pre- and postpolymerization states in the F4 fimbrial subunit FaeG
Authors: Van Molle, I. / Moonens, K. / Garcia-Pino, A. / Buts, L. / De Kerpel, M. / Wyns, L. / Bouckaert, J. / De Greve, H.
History
DepositionMay 28, 2009Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Oct 20, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 5, 2014Group: Database references
Revision 1.3Aug 9, 2017Group: Refinement description / Source and taxonomy / Category: entity_src_gen / software
Revision 1.4Oct 4, 2017Group: Data collection / Experimental preparation / Category: diffrn_detector / exptl_crystal_grow
Item: _diffrn_detector.detector / _exptl_crystal_grow.pdbx_details
Revision 1.5Nov 1, 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
Revision 1.6Mar 20, 2024Group: Source and taxonomy / Category: entity_src_gen

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: K88 fimbrial protein AD


Theoretical massNumber of molelcules
Total (without water)28,3441
Polymers28,3441
Non-polymers00
Water3,495194
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)37.290, 39.730, 76.370
Angle α, β, γ (deg.)90.00, 101.24, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein K88 fimbrial protein AD / FaeG / K88 pilin / K88 antigen


Mass: 28344.375 Da / Num. of mol.: 1 / Fragment: FaeGntd/dsc2
Source method: isolated from a genetically manipulated source
Details: The sequence consists of MG, UNP residues 43-285 (Uniprot 14191), a linker of 10 GLYs, and UNP residues 22-42 (Uniprot P14191).
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: faeG / Plasmid: pEXP215 / Production host: Escherichia coli (E. coli) / Strain (production host): C43(DE3) / References: UniProt: P14191
#2: Water ChemComp-HOH / water / K88 pilin / K88 antigen


Mass: 18.015 Da / Num. of mol.: 194 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE CONFLICT BASED ON REFERENCE 2 OF DATABASE FAEG3_ECOLX (UNIPROTKB/SWISS-PROT P14191). N19S (UNP ...THE CONFLICT BASED ON REFERENCE 2 OF DATABASE FAEG3_ECOLX (UNIPROTKB/SWISS-PROT P14191). N19S (UNP RESIDUE 59) IS CONFLICT OF FAEG3_ECOLX.

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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: 1.96 Å3/Da / Density % sol: 37.17 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.1M Na cacodylate pH 6.5, 0.2M ammonium acetate, 20% PEG, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.9801 Å
DetectorType: MAR555 FLAT PANEL / Detector: IMAGE PLATE / Date: Jan 31, 2009
RadiationMonochromator: Graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9801 Å / Relative weight: 1
ReflectionResolution: 2.3→35 Å / Num. all: 64572 / Num. obs: 64572 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 22.28 Å2 / Rmerge(I) obs: 0.1572 / Net I/σ(I): 2.97
Reflection shellResolution: 2.3→2.32 Å / Rmerge(I) obs: 0.32 / Mean I/σ(I) obs: 1.97 / % possible all: 97

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
PHASERphasing
PHENIX(phenix.refine)refinement
XDSdata reduction
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3GEA

3gea


Resolution: 2.3→29.162 Å / SU ML: 0.4 / Cross valid method: THROUGHOUT / σ(F): 2 / σ(I): 0 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2937 479 5.01 %random
Rwork0.2347 ---
all0.24 9560 --
obs0.2377 9560 95.88 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 35.961 Å2 / ksol: 0.33 e/Å3
Displacement parametersBiso mean: 24.204 Å2
Baniso -1Baniso -2Baniso -3
1-1.686 Å20 Å20.786 Å2
2---1.438 Å2-0 Å2
3----0.247 Å2
Refinement stepCycle: LAST / Resolution: 2.3→29.162 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1883 0 0 194 2077
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0041916
X-RAY DIFFRACTIONf_angle_d0.9042602
X-RAY DIFFRACTIONf_chiral_restr0.066299
X-RAY DIFFRACTIONf_plane_restr0.003338
X-RAY DIFFRACTIONf_dihedral_angle_d17.355650
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3001-2.63270.33141580.26612990X-RAY DIFFRACTION95
2.6327-3.31620.34111580.24532999X-RAY DIFFRACTION96
3.3162-29.16460.25131630.21633092X-RAY DIFFRACTION96

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