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- PDB-4b9i: Structure of CssA subunit complemented with donor strand from Css... -

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Basic information

Entry
Database: PDB / ID: 4b9i
TitleStructure of CssA subunit complemented with donor strand from CssB subunit of enterotoxigenic Escherichia coli colonization factor CS6
ComponentsCS6 FIMBRIAL SUBUNIT A, CS6 FIMBRIAL SUBUNIT B
KeywordsCELL ADHESION / DIARRHEAL DISEASE / FIMBRIAE / FUSION PROTEIN
Function / homology
Function and homology information


CS6 fimbrial subunit A/B / CS6 fimbrial subunits A and B, Coli surface antigen 6 / Immunoglobulin-like - #3480 / : / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
CS6 fimbrial subunit A / CS6 fimbrial subunit B
Similarity search - Component
Biological speciesESCHERICHIA COLI (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.5 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 1.2May 8, 2024Group: Data collection / Database references / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status
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, CS6 FIMBRIAL SUBUNIT B


Theoretical massNumber of molelcules
Total (without water)16,6561
Polymers16,6561
Non-polymers00
Water2,504139
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)44.455, 49.150, 56.730
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-2092-

HOH

21A-2104-

HOH

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Components

#1: Protein CS6 FIMBRIAL SUBUNIT A, CS6 FIMBRIAL SUBUNIT B / CS6 PILIN / CSSADSB


Mass: 16656.416 Da / Num. of mol.: 1 / Fragment: RESIDUES 28-154 OF CSSA AND 22-36 OF CSSB
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, UniProt: P53510
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 139 / 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: 1.85 Å3/Da / Density % sol: 33.49 % / 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: 0.8726
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: 0.8726 Å / Relative weight: 1
ReflectionResolution: 1.5→44.43 Å / Num. obs: 20523 / % possible obs: 100 % / Observed criterion σ(I): 2 / Redundancy: 4.5 % / Biso Wilson estimate: 16.163 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 13.5
Reflection shellResolution: 1.5→1.58 Å / Redundancy: 4 % / Rmerge(I) obs: 0.43 / Mean I/σ(I) obs: 3.2 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
MOSFLMdata reduction
SCALAdata scaling
PHENIXphasing
RefinementMethod to determine structure: SAD
Starting model: NONE

Resolution: 1.5→34.991 Å / SU ML: 0.18 / σ(F): 0 / Phase error: 20.52 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2291 1035 5.2 %
Rwork0.2089 --
obs0.21 19987 97.39 %
Solvent computationShrinkage radii: 0.72 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 38.893 Å2 / ksol: 0.359 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--1.1783 Å20 Å20 Å2
2--0.1985 Å20 Å2
3---0.9798 Å2
Refinement stepCycle: LAST / Resolution: 1.5→34.991 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms986 0 0 139 1125
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0071007
X-RAY DIFFRACTIONf_angle_d1.0731371
X-RAY DIFFRACTIONf_dihedral_angle_d13.857363
X-RAY DIFFRACTIONf_chiral_restr0.072152
X-RAY DIFFRACTIONf_plane_restr0.005180
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5002-1.57930.28281580.25312497X-RAY DIFFRACTION92
1.5793-1.67830.30681430.23672584X-RAY DIFFRACTION95
1.6783-1.80780.25511390.21782646X-RAY DIFFRACTION97
1.8078-1.98980.22371440.20442723X-RAY DIFFRACTION99
1.9898-2.27760.21871560.19922760X-RAY DIFFRACTION100
2.2776-2.86940.23851580.21112789X-RAY DIFFRACTION100
2.8694-35.00080.20561370.2022953X-RAY DIFFRACTION100

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