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- PDB-2j6r: FaeG from F4ac ETEC strain GIS26, produced in tobacco plant chlor... -

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Basic information

Entry
Database: PDB / ID: 2j6r
TitleFaeG from F4ac ETEC strain GIS26, produced in tobacco plant chloroplast
Components(K88 FIMBRIAL PROTEIN) x 2
KeywordsCELL ADHESION / PLASMID / FIMBRIA / IG-FOLD / F4 FIMBRIAE / CHAPERONE-USHER PATHWAY / STRAND SWAPPING / CHLOROPLAST TARGETING
Function / homologyFimbrial, major/minor subunit / Fimbrial, major and minor subunit / pilus / cell adhesion / PHOSPHATE ION / K88 fimbrial protein AC / K88 fimbrial protein AC
Function and homology information
Biological speciesESCHERICHIA COLI (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsVan Molle, I. / Joensuu, J.J. / Buts, L. / Panjikar, S. / Kotiaho, M. / Bouckaert, J. / Wyns, L. / Niklander-Teeri, V. / De Greve, H.
CitationJournal: J.Mol.Biol. / Year: 2007
Title: Chloroplasts Assemble the Major Subunit Faeg of Escherichia Coli F4 (K88) Fimbriae Into Strand-Swapped Dimers
Authors: Van Molle, I. / Joensuu, J.J. / Buts, L. / Panjikar, S. / Kotiaho, M. / Bouckaert, J. / Wyns, L. / Niklander-Teeri, V. / De Greve, H.
History
DepositionOct 3, 2006Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 10, 2007Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jul 24, 2019Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.4Dec 13, 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
Remark 650 HELIX DETERMINATION METHOD: AUTHOR PROVIDED.
Remark 700 SHEET DETERMINATION METHOD: AUTHOR PROVIDED.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: K88 FIMBRIAL PROTEIN
B: K88 FIMBRIAL PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,3667
Polymers55,8912
Non-polymers4755
Water6,125340
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)56.165, 91.232, 108.434
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein K88 FIMBRIAL PROTEIN / K88 PILIN / K88 ANTIGEN / FAEG


Mass: 27954.078 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) ESCHERICHIA COLI (E. coli) / Production host: NICOTIANA TABACUM (common tobacco) / References: UniProt: Q708I8, UniProt: P14190*PLUS
#2: Protein K88 FIMBRIAL PROTEIN / K88 PILIN / K88 ANTIGEN / FAEG


Mass: 27937.090 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) ESCHERICHIA COLI (E. coli) / Production host: NICOTIANA TABACUM (common tobacco) / References: UniProt: Q708I8, UniProt: P14190*PLUS
#3: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: PO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 340 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsEXTRA AMINO ACIDS (MDRS) AT N-TERMINUS DUE TO CLONING

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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: 2.5 Å3/Da / Density % sol: 50.9 %
Crystal growDetails: 30 % PEG8000, 0.1 M NA CACODYLATE, 0.2 M NH4H2PO4

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X13 / Wavelength: 0.8075
DetectorType: MARRESEARCH / Detector: CCD / Date: Oct 14, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8075 Å / Relative weight: 1
ReflectionResolution: 1.9→35 Å / Num. obs: 42391 / % possible obs: 99.9 % / Redundancy: 6.1 % / Rmerge(I) obs: 0.09 / Net I/σ(I): 14.25
Reflection shellResolution: 1.9→1.97 Å / Redundancy: 6.1 % / Rmerge(I) obs: 0.45 / Mean I/σ(I) obs: 3.77 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2J6G

2j6g


Resolution: 1.9→18.45 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.926 / SU B: 2.808 / SU ML: 0.084 / Cross valid method: THROUGHOUT / ESU R: 0.141 / ESU R Free: 0.136 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.226 2248 5 %RANDOM
Rwork0.183 ---
obs0.185 42391 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 17.42 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 1.9→18.45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3726 0 25 340 4091
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0223832
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.4261.9545211
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3155508
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.58724.795146
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.45315579
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.9531515
X-RAY DIFFRACTIONr_chiral_restr0.1020.2600
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.022876
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.1970.21631
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3050.22635
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1340.2330
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2050.234
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1490.222
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.8381.52562
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.40223975
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.12231473
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.1564.51235
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.9→1.95 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.297 169
Rwork0.212 3059

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