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- PDB-1n12: Crystal structure of the PapE (N-terminal-deleted) pilus subunit ... -

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Basic information

Entry
Database: PDB / ID: 1n12
TitleCrystal structure of the PapE (N-terminal-deleted) pilus subunit bound to a peptide corresponding to the N-terminal extension of the PapK pilus subunit (residues 1-11) from uropathogenic E. coli
Components
  • Peptide corresponding to the N-terminal extension of protein PapK
  • mature Fimbrial protein PapE
KeywordsCHAPERONE / Immunoglobulin-like fold / donor strand complementation / donor strand exchange / chaperone priming / pilus fiber assembly / organelle biogenesis
Function / homology
Function and homology information


cell adhesion involved in single-species biofilm formation / pilus / cell adhesion / extracellular region
Similarity search - Function
P pili tip fibrillum PapE protein, Enterobacteriaceae / Fimbrial-type adhesion domain / Fimbrial-type adhesion domain / Fimbrial protein / : / Fimbrial-type adhesion domain superfamily / Adhesion domain superfamily / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Fimbrial protein PapE / Fimbrial adapter PapK / Protein PrsK
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.87 Å
AuthorsSauer, F.G. / Pinkner, J.S. / Waksman, G. / Hultgren, S.J.
CitationJournal: Cell(Cambridge,Mass.) / Year: 2002
Title: Chaperone priming of pilus subunits facilitates a topological transition that drives fiber formation
Authors: Sauer, F.G. / Pinkner, J.S. / Waksman, G. / Hultgren, S.J.
History
DepositionOct 16, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 11, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 9, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: mature Fimbrial protein PapE
B: Peptide corresponding to the N-terminal extension of protein PapK
C: mature Fimbrial protein PapE
D: Peptide corresponding to the N-terminal extension of protein PapK


Theoretical massNumber of molelcules
Total (without water)32,0794
Polymers32,0794
Non-polymers00
Water2,522140
1
A: mature Fimbrial protein PapE
B: Peptide corresponding to the N-terminal extension of protein PapK


Theoretical massNumber of molelcules
Total (without water)16,0392
Polymers16,0392
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2010 Å2
ΔGint-9 kcal/mol
Surface area7410 Å2
MethodPISA
2
C: mature Fimbrial protein PapE
D: Peptide corresponding to the N-terminal extension of protein PapK


Theoretical massNumber of molelcules
Total (without water)16,0392
Polymers16,0392
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1960 Å2
ΔGint-9 kcal/mol
Surface area7510 Å2
MethodPISA
Unit cell
Length a, b, c (Å)25.254, 91.922, 51.244
Angle α, β, γ (deg.)90.00, 99.26, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein mature Fimbrial protein PapE


Mass: 14832.035 Da / Num. of mol.: 2 / Fragment: residue 25-173, residue 26-36 deleted
Mutation: N-terminal residue 26-36 deleted, contains selenomethionine at methionine positions
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Production host: Escherichia coli (E. coli) / References: UniProt: P08407
#2: Protein/peptide Peptide corresponding to the N-terminal extension of protein PapK


Mass: 1207.315 Da / Num. of mol.: 2 / Fragment: residue 22-32 / Source method: obtained synthetically / Details: synthesized peptide / References: UniProt: P42190, UniProt: P42191*PLUS
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 140 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 1.75 Å3/Da / Density % sol: 29.19 %
Crystal growTemperature: 294 K / Method: vapor diffusion / pH: 8.5
Details: 100 mM Tris pH 8.5, 200 mM NaCl, 27-32% PEG 4000, 1 mM beta-mercaptoethanol, VAPOR DIFFUSION, temperature 294K

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Data collection

DiffractionMean temperature: 98 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9667
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9667 Å / Relative weight: 1
ReflectionBiso Wilson estimate: 8 Å2
Reflection
*PLUS
Highest resolution: 1.87 Å / Lowest resolution: 30 Å / Num. obs: 18969 / % possible obs: 99.2 % / Num. measured all: 232749 / Rmerge(I) obs: 0.05
Reflection shell
*PLUS
% possible obs: 96.8 % / Rmerge(I) obs: 0.149 / Mean I/σ(I) obs: 8.4

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Processing

Software
NameClassification
HKL-2000data collection
SCALEPACKdata scaling
CNSrefinement
HKL-2000data reduction
CNSphasing
RefinementMethod to determine structure: SAD / Resolution: 1.87→26.21 Å / Rfactor Rfree error: 0.007 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.249 1109 5.9 %RANDOM
Rwork0.208 ---
all0.211 ---
obs0.208 18937 99 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 32.9399 Å2 / ksol: 0.348785 e/Å3
Displacement parametersBiso mean: 19.9 Å2
Baniso -1Baniso -2Baniso -3
1-3.26 Å20 Å2-1.47 Å2
2---4.5 Å20 Å2
3---1.24 Å2
Refine analyzeLuzzati coordinate error free: 0.28 Å / Luzzati sigma a free: 0.21 Å
Refinement stepCycle: LAST / Resolution: 1.87→26.21 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2255 0 0 140 2395
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d26.9
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.66
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.571.5
X-RAY DIFFRACTIONc_mcangle_it2.442
X-RAY DIFFRACTIONc_scbond_it2.572
X-RAY DIFFRACTIONc_scangle_it3.842.5
LS refinement shellResolution: 1.87→1.99 Å / Rfactor Rfree error: 0.021 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.292 189 6.1 %
Rwork0.228 2916 -
obs--97.2 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER_REP.TOP
Refinement
*PLUS
Lowest resolution: 30 Å
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.0054
X-RAY DIFFRACTIONc_angle_deg1.22
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg26.9
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.66

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