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- PDB-4b9j: Structure of self-complemented CssA subunit of enterotoxigenic Es... -

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Basic information

Entry
Database: PDB / ID: 4b9j
TitleStructure of self-complemented CssA subunit of enterotoxigenic Escherichia coli colonization factor CS6
ComponentsCS6 FIMBRIAL SUBUNIT A
KeywordsCELL ADHESION / DIARRHEAL DISEASE / FIMBRIAE / FUSION PROTEIN
Function / homologyImmunoglobulin-like - #3480 / : / pilus / Immunoglobulin-like / Sandwich / Mainly Beta / CS6 fimbrial subunit A
Function and homology information
Biological speciesESCHERICHIA COLI (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.542 Å
AuthorsRoy, S.P. / Rahman, M.M. / Yu, X.D. / Tuittila, M. / Knight, S.D. / Zavialov, A.V.
CitationJournal: Mol.Microbiol. / Year: 2012
Title: Crystal Structure of Enterotoxigenic Escherichia Coli Colonization Factor Cs6 Reveals a Novel Type of Functional Assembly.
Authors: Roy, S.P. / Rahman, M.M. / Yu, X.D. / Tuittila, M. / Knight, S.D. / Zavialov, A.V.
History
DepositionSep 4, 2012Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 7, 2012Provider: repository / Type: Initial release
Revision 1.1Dec 12, 2012Group: Database references
Revision 1.2Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: CS6 FIMBRIAL SUBUNIT A


Theoretical massNumber of molelcules
Total (without water)16,6431
Polymers16,6431
Non-polymers00
Water50428
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)42.998, 48.954, 56.955
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11A-2013-

HOH

21A-2025-

HOH

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Components

#1: Protein CS6 FIMBRIAL SUBUNIT A / CS6 PILIN / CSSADSA


Mass: 16643.484 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: LINKER SEQUENCE DNKQ / Source: (gene. exp.) ESCHERICHIA COLI (E. coli) / Strain: O167\:H5 / E10703 / EIEC / Plasmid: PET-CSSADSB / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P53508
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 28 / 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: 1.78 Å3/Da / Density % sol: 31 % / Description: NONE
Crystal growpH: 4.6
Details: 24-30 % PEG4000 IN 0.2 M AMMONIUM ACETATE, 0.1 M NA ACETATE, PH 4.6

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Data collection

DiffractionMean temperature: 287 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.9334
DetectorType: MARRESEARCH / Detector: CCD / Date: Feb 24, 2011 / Details: BAND PASS 1.9X10-4 FOR A SI(111) MONOCHROMATOR
RadiationMonochromator: SI(111) MONOCHROMATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9334 Å / Relative weight: 1
ReflectionResolution: 2.54→43 Å / Num. obs: 4190 / % possible obs: 98.8 % / Observed criterion σ(I): 2 / Redundancy: 3.2 % / Biso Wilson estimate: 37.719 Å2 / Rmerge(I) obs: 0.03 / Net I/σ(I): 33.9
Reflection shellResolution: 2.54→2.68 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.07 / Mean I/σ(I) obs: 16.8 / % possible all: 98.3

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4B9I

4b9i


Resolution: 2.542→37.125 Å / SU ML: 0.27 / σ(F): 0 / Phase error: 27.1 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2771 191 4.6 %
Rwork0.2046 --
obs0.2078 4124 96.92 %
Solvent computationShrinkage radii: 0.95 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 32.603 Å2 / ksol: 0.355 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-0.7955 Å20 Å20 Å2
2---5.3967 Å20 Å2
3---4.6012 Å2
Refinement stepCycle: LAST / Resolution: 2.542→37.125 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms949 0 0 28 977
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.005967
X-RAY DIFFRACTIONf_angle_d0.8341316
X-RAY DIFFRACTIONf_dihedral_angle_d14.625352
X-RAY DIFFRACTIONf_chiral_restr0.052152
X-RAY DIFFRACTIONf_plane_restr0.003171
LS refinement shellResolution: 2.5423→37.1289 Å
RfactorNum. reflection% reflection
Rfree0.2771 191 -
Rwork0.2046 3933 -
obs--97 %

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