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- PDB-5nkt: FimA wt from E. coli -

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Basic information

Entry
Database: PDB / ID: 5nkt
TitleFimA wt from E. coli
ComponentsType-1 fimbrial protein, A chain
KeywordsSTRUCTURAL PROTEIN / FimA / pilus / monomer / subunit / pili / Escherichia / coli / pathogenic / main structural subunit / high resolution
Function / homologyFimbrial-type adhesion domain / Fimbrial protein / cell adhesion involved in single-species biofilm formation / Fimbrial-type adhesion domain superfamily / Adhesion domain superfamily / pilus / cell adhesion / identical protein binding / Type-1 fimbrial protein, A chain
Function and homology information
Biological speciesEscherichia coli K-12 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.5 Å
AuthorsZyla, D. / Capitani, G. / Prota, A. / Glockshuber, R.
Funding support Switzerland, 1items
OrganizationGrant numberCountry
Swiss National Science Foundation156304 Switzerland
CitationJournal: J.Biol.Chem. / Year: 2019
Title: Alternative folding to a monomer or homopolymer is a common feature of the type 1 pilus subunit FimA from enteroinvasive bacteria.
Authors: Zyla, D.S. / Prota, A.E. / Capitani, G. / Glockshuber, R.
History
DepositionApr 3, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 16, 2018Provider: repository / Type: Initial release
Revision 1.1Jun 26, 2019Group: Data collection / Database references / Derived calculations
Category: citation / citation_author ...citation / citation_author / database_PDB_rev / database_PDB_rev_record / pdbx_database_proc / pdbx_struct_special_symmetry
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Apr 22, 2020Group: Database references / Category: pdbx_related_exp_data_set
Revision 1.3Jan 17, 2024Group: 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: Type-1 fimbrial protein, A chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,2195
Polymers15,8351
Non-polymers3844
Water2,756153
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, Self-complemented FimA eluted from Superdex 75 10/300 as a monomer
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area420 Å2
ΔGint-27 kcal/mol
Surface area7440 Å2
MethodPISA
Unit cell
Length a, b, c (Å)86.990, 86.990, 162.710
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number155
Space group name H-MH32
Components on special symmetry positions
IDModelComponents
11A-204-

SO4

21A-332-

HOH

31A-373-

HOH

41A-450-

HOH

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Components

#1: Protein Type-1 fimbrial protein, A chain / Type-1A pilin


Mass: 15835.243 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli K-12 (bacteria) / Gene: fimA, pilA, b4314, JW4277 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P04128
#2: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 153 / 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

Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 2.6
Details: 0.1 M Sodium Malonate, pH 2.6, 45% ammonium sulphate, 23 mg/ml of protein 1:1 mixture with reservoir
PH range: 2.0 - 3.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X6A / Wavelength: 1.00002 Å
DetectorType: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Aug 21, 2015
RadiationMonochromator: SI(111) MONOCHROMATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.00002 Å / Relative weight: 1
ReflectionResolution: 1.5→29.874 Å / Num. obs: 37772 / % possible obs: 98.9 % / Observed criterion σ(I): -3 / Redundancy: 9.381 % / Biso Wilson estimate: 26.19 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.052 / Rrim(I) all: 0.055 / Χ2: 0.986 / Net I/σ(I): 20.1 / Num. measured all: 354327 / Scaling rejects: 8
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
1.5-1.66.5711.2521.5862260.6681.36193.8
1.6-1.89.8930.6134.8192740.9650.64699.9
1.8-210.0280.20312.5559690.9950.214100
2-2.510.0350.07926.2778360.9990.083100
2.5-39.8580.04441.5135180.9990.04799.9
3-59.9410.03655.6538310.9990.038100
5-69.8630.03358.784610.9990.035100
6-88.8560.03356.463690.9990.03599.2
8-109.0220.03558.0813610.037100
10-209.2070.03558.841350.9990.038100
20-258.6360.03458.25110.9980.037100
25-29.8745.6670.02845.06610.0342.9

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
PHENIX1.11.1-2575refinement
XSCALEOct 15, 2015 BUILT=20151231data scaling
PHASERphasing
PDB_EXTRACT3.2data extraction
Coot0.8.6.1model building
XDSOct 15, 2015 BUILT=20151231data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5LP9

5lp9


Resolution: 1.5→29.874 Å / SU ML: 0.17 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 21.93
RfactorNum. reflection% reflectionSelection details
Rfree0.1881 1133 3 %Random
Rwork0.1579 ---
obs0.1588 37740 98.82 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 128.55 Å2 / Biso mean: 48.3173 Å2 / Biso min: 19.53 Å2
Refinement stepCycle: final / Resolution: 1.5→29.874 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1059 0 25 153 1237
Biso mean--73.98 48.51 -
Num. residues----151
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0041091
X-RAY DIFFRACTIONf_angle_d0.6551492
X-RAY DIFFRACTIONf_chiral_restr0.05181
X-RAY DIFFRACTIONf_plane_restr0.004196
X-RAY DIFFRACTIONf_dihedral_angle_d8.61623
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 8

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.5001-1.56840.34011290.33784149427891
1.5684-1.65110.21261420.215545834725100
1.6511-1.75450.19021420.17345894731100
1.7545-1.88990.17341410.139146004741100
1.8899-2.08010.15351420.124845894731100
2.0801-2.3810.15921440.1446294773100
2.381-2.99930.18551440.169946684812100
2.9993-29.87990.19881490.156148004949100

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