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- PDB-4b9g: Structure of CssB subunit complemented with donor strand from Css... -

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Basic information

Entry
Database: PDB / ID: 4b9g
TitleStructure of CssB subunit complemented with donor strand from CssA subunit of enterotoxigenic Escherichia coli colonization factor CS6
ComponentsCS6 FIMBRIAL SUBUNIT B, CS6 FIMBRIAL SUBUNIT A
KeywordsCELL ADHESION / DIARRHEAL DISEASE / FIMBRIAE / FUSION PROTEIN
Function / homologyCS6 fimbrial subunit A/B / CS6 fimbrial subunits A and B, Coli surface antigen 6 / Immunoglobulin-like - #3480 / pilus / Immunoglobulin-like / Sandwich / Mainly Beta / CS6 fimbrial subunit A / CS6 fimbrial subunit B
Function and homology information
Biological speciesESCHERICHIA COLI (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.04 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 5, 2012Group: Atomic model
Revision 1.2Dec 12, 2012Group: Database references
Revision 1.3May 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 B, CS6 FIMBRIAL SUBUNIT A
B: CS6 FIMBRIAL SUBUNIT B, CS6 FIMBRIAL SUBUNIT A


Theoretical massNumber of molelcules
Total (without water)35,1152
Polymers35,1152
Non-polymers00
Water8,395466
1
A: CS6 FIMBRIAL SUBUNIT B, CS6 FIMBRIAL SUBUNIT A


Theoretical massNumber of molelcules
Total (without water)17,5571
Polymers17,5571
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: CS6 FIMBRIAL SUBUNIT B, CS6 FIMBRIAL SUBUNIT A


Theoretical massNumber of molelcules
Total (without water)17,5571
Polymers17,5571
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)51.956, 69.225, 72.359
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection details
111CHAIN A AND (RESSEQ 16:141 OR RESSEQ 144:161 ) AND (NOT ELEMENT H)
211CHAIN B AND (RESSEQ 16:141 OR RESSEQ 144:161 ) AND (NOT ELEMENT H)

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Components

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


Mass: 17557.283 Da / Num. of mol.: 2 / Fragment: RESIDUES 30-167 OF CSSB1 AND 19-34 OF CSSA1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) ESCHERICHIA COLI (E. coli) / Strain: O167\:H5 / E10703 / EIEC / Plasmid: PET-CSSBDSA / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P53510, UniProt: P53508
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 466 / 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: 33.7 % / Description: NONE
Crystal growpH: 8.5
Details: 30% PEG4000 IN 0.2 M NA ACETATE, 0.1 M TRIS-HCL, PH 8.5

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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: 1.04→27.28 Å / Num. obs: 124292 / % possible obs: 99.1 % / Observed criterion σ(I): 3 / Redundancy: 4.6 % / Biso Wilson estimate: 5.833 Å2 / Rmerge(I) obs: 0.065 / Net I/σ(I): 12
Reflection shellResolution: 1.04→1.1 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.48 / Mean I/σ(I) obs: 2.7 / % possible all: 95.4

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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: 1.04→27.286 Å / SU ML: 0.12 / σ(F): 1.35 / Phase error: 13.79 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1665 6238 5 %
Rwork0.155 --
obs0.1556 124197 98.88 %
Solvent computationShrinkage radii: 0.65 Å / VDW probe radii: 0.8 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 40.822 Å2 / ksol: 0.435 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-0.2756 Å20 Å20 Å2
2--0.2925 Å20 Å2
3----0.5682 Å2
Refinement stepCycle: LAST / Resolution: 1.04→27.286 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2226 0 0 466 2692
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.022270
X-RAY DIFFRACTIONf_angle_d1.7223084
X-RAY DIFFRACTIONf_dihedral_angle_d12.79824
X-RAY DIFFRACTIONf_chiral_restr0.474346
X-RAY DIFFRACTIONf_plane_restr0.007404
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11A1097X-RAY DIFFRACTIONPOSITIONAL
12B1097X-RAY DIFFRACTIONPOSITIONAL1.012
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.0399-1.05170.29662110.30083717X-RAY DIFFRACTION95
1.0517-1.06410.29781910.25793868X-RAY DIFFRACTION97
1.0641-1.07710.2491960.23173829X-RAY DIFFRACTION98
1.0771-1.09070.23782020.20843824X-RAY DIFFRACTION98
1.0907-1.10510.21442130.1793846X-RAY DIFFRACTION98
1.1051-1.12020.19621980.15663838X-RAY DIFFRACTION98
1.1202-1.13620.15072120.14363883X-RAY DIFFRACTION98
1.1362-1.15320.14711920.13283883X-RAY DIFFRACTION98
1.1532-1.17120.15382030.13413868X-RAY DIFFRACTION98
1.1712-1.19040.17831950.1383868X-RAY DIFFRACTION98
1.1904-1.21090.16092190.13213888X-RAY DIFFRACTION98
1.2109-1.2330.16532200.13213866X-RAY DIFFRACTION99
1.233-1.25670.16322050.13523907X-RAY DIFFRACTION99
1.2567-1.28230.13882060.13413905X-RAY DIFFRACTION99
1.2823-1.31020.15472170.13543935X-RAY DIFFRACTION99
1.3102-1.34070.15922010.13583910X-RAY DIFFRACTION99
1.3407-1.37420.14682270.1373963X-RAY DIFFRACTION100
1.3742-1.41140.15152150.13523914X-RAY DIFFRACTION100
1.4114-1.45290.14672150.13443930X-RAY DIFFRACTION100
1.4529-1.49980.14862060.13773969X-RAY DIFFRACTION100
1.4998-1.55340.14442040.13233971X-RAY DIFFRACTION100
1.5534-1.61560.15712080.13744021X-RAY DIFFRACTION100
1.6156-1.68910.14872230.13683953X-RAY DIFFRACTION100
1.6891-1.77810.13932150.14483975X-RAY DIFFRACTION100
1.7781-1.88950.16781900.14794039X-RAY DIFFRACTION100
1.8895-2.03530.13442110.14024012X-RAY DIFFRACTION100
2.0353-2.24010.18322080.14154020X-RAY DIFFRACTION100
2.2401-2.5640.18372210.17084065X-RAY DIFFRACTION100
2.564-3.22960.17072000.17664096X-RAY DIFFRACTION100
3.2296-27.29580.16712140.16884196X-RAY DIFFRACTION98

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