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- PDB-5ypz: Crystal structure of minor pilin CofB from CFA/III complexed with... -

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Basic information

Entry
Database: PDB / ID: 5ypz
TitleCrystal structure of minor pilin CofB from CFA/III complexed with N-terminal peptide fragment of CofJ
Components
  • CofB
  • CofJ
KeywordsCELL ADHESION / Colonization factor / Type IVb pili / minor pilin / CFA/III
Function / homology: / CofB, pilin domain / Prokaryotic N-terminal methylation site. / Prokaryotic N-terminal methylation motif / Prokaryotic N-terminal methylation site / membrane / metal ion binding / CofJ / CofB
Function and homology information
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.521 Å
AuthorsOki, H. / Kawahara, K. / Maruno, T. / Imai, T. / Muroga, Y. / Fukakusa, S. / Iwashita, T. / Kobayashi, Y. / Matsuda, S. / Kodama, T. ...Oki, H. / Kawahara, K. / Maruno, T. / Imai, T. / Muroga, Y. / Fukakusa, S. / Iwashita, T. / Kobayashi, Y. / Matsuda, S. / Kodama, T. / Iida, T. / Yoshida, T. / Ohkubo, T. / Nakamura, S.
CitationJournal: Proc. Natl. Acad. Sci. U.S.A. / Year: 2018
Title: Interplay of a secreted protein with type IVb pilus for efficient enterotoxigenicEscherichia colicolonization.
Authors: Oki, H. / Kawahara, K. / Maruno, T. / Imai, T. / Muroga, Y. / Fukakusa, S. / Iwashita, T. / Kobayashi, Y. / Matsuda, S. / Kodama, T. / Iida, T. / Yoshida, T. / Ohkubo, T. / Nakamura, S.
History
DepositionNov 4, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 27, 2018Provider: repository / Type: Initial release
Revision 1.1Jul 18, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_abbrev / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Jul 25, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title
Revision 1.3Nov 22, 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: CofB
B: CofB
C: CofB
D: CofJ
E: CofJ
F: CofJ


Theoretical massNumber of molelcules
Total (without water)168,2376
Polymers168,2376
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: isothermal titration calorimetry, CofB, chain A and B and C, forms homo-trimer. The complex was confirmed AUC. N-terminal fragments of CofJ, chain D and E and F, bind to the homotrimer of CofB.
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area29770 Å2
ΔGint-145 kcal/mol
Surface area60120 Å2
MethodPISA
Unit cell
Length a, b, c (Å)157.216, 157.216, 118.132
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number170
Space group name H-MP65

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Components

#1: Protein CofB


Mass: 53593.441 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: cofB / Plasmid: pET-48b / Cell line (production host): T7 Express LysY cells / Production host: Escherichia coli (E. coli) / Strain (production host): SHuffle / References: UniProt: Q93I73
#2: Protein/peptide CofJ


Mass: 2485.682 Da / Num. of mol.: 3 / Source method: obtained synthetically / Source: (synth.) Escherichia coli (E. coli) / References: UniProt: Q93I65

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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: 2.63 Å3/Da / Density % sol: 53.24 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 100mM CAPS pH 10.5, 20% PEG8000, 200mM NaCl

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL26B1 / Wavelength: 1 Å
DetectorType: RIGAKU SATURN A200 / Detector: CCD / Date: Oct 29, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.52→60 Å / Num. obs: 20699 / % possible obs: 100 % / Redundancy: 11.1 % / Biso Wilson estimate: 90.75 Å2 / Rmerge(I) obs: 0.29 / Rpim(I) all: 0.091 / Rrim(I) all: 0.304 / Χ2: 1.928 / Net I/σ(I): 4.7 / Num. measured all: 229612
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
3.52-3.5810.61.86310350.50.6011.9581.627100
3.58-3.6510.71.65810210.5110.5311.7421.647100
3.65-3.7210.81.25710400.6290.4011.321.625100
3.72-3.7910.81.00210240.7580.3191.0521.659100
3.79-3.8710.91.04710000.7690.3321.0991.671100
3.87-3.96110.86310550.8930.2730.9051.692100
3.96-4.0611.10.73310190.8930.2310.7691.738100
4.06-4.1711.20.60910250.9020.1910.6381.74100
4.17-4.311.20.50210350.9440.1570.5261.8100
4.3-4.4311.30.41610320.950.130.4361.868100
4.43-4.5911.30.33110310.9690.1030.3471.866100
4.59-4.7811.30.30610330.9740.0950.3211.949100
4.78-4.9911.40.27610220.9760.0860.2891.911100
4.99-5.2611.30.26710480.9780.0830.2791.944100
5.26-5.5911.40.27710310.9780.0860.291.915100
5.59-6.0211.30.26110400.9820.0810.2731.955100
6.02-6.6211.30.22610330.9860.070.2372.001100
6.62-7.5811.30.1510500.9920.0470.1582.118100
7.58-9.5411.20.09310480.9970.0290.0972.418100
9.54-6010.60.06410770.9980.0210.0673.35199.7

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Processing

Software
NameVersionClassification
PHENIX1.11.1_2575refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5AX6

5ax6


Resolution: 3.521→54.187 Å / SU ML: 0.41 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 23.56 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2316 1985 9.6 %
Rwork0.1921 18683 -
obs0.1958 20668 99.97 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 222.38 Å2 / Biso mean: 106.5354 Å2 / Biso min: 25.02 Å2
Refinement stepCycle: final / Resolution: 3.521→54.187 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11241 0 0 0 11241
Num. residues----1473
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00411436
X-RAY DIFFRACTIONf_angle_d0.77715507
X-RAY DIFFRACTIONf_chiral_restr0.0521773
X-RAY DIFFRACTIONf_plane_restr0.0052022
X-RAY DIFFRACTIONf_dihedral_angle_d15.9034218
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
3.5209-3.6090.36521410.301713181459
3.609-3.70650.34371420.291913351477
3.7065-3.81550.28891410.260213151456
3.8155-3.93870.2971390.244113451484
3.9387-4.07940.26251460.217113221468
4.0794-4.24270.24671400.195113301470
4.2427-4.43570.22421340.168513291463
4.4357-4.66940.21071470.156813261473
4.6694-4.96180.20291440.157513261470
4.9618-5.34460.20191430.157113321475
5.3446-5.88180.20351410.170913381479
5.8818-6.73160.23591420.189113351477
6.7316-8.47590.18541390.18313631502
8.4759-54.19310.20511460.176713691515

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