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- PDB-1n0l: Crystal structure of the PapD chaperone (C-terminally 6x histidin... -

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Basic information

Entry
Database: PDB / ID: 1n0l
TitleCrystal structure of the PapD chaperone (C-terminally 6x histidine-tagged) bound to the PapE pilus subunit (N-terminal-deleted) from uropathogenic E. coli
Components
  • Chaperone protein PapD
  • mature Fimbrial protein PapE
KeywordsCHAPERONE / Immunoglobulin-like fold / donor strand complemenation / donor strand exchange / chaperone priming / pilus fiber assembly
Function / homology
Function and homology information


cell adhesion involved in single-species biofilm formation / pilus / : / cell wall organization / outer membrane-bounded periplasmic space / extracellular region
Similarity search - Function
P pili tip fibrillum PapE protein, Enterobacteriaceae / Pili assembly chaperone, C-terminal / Pili assembly chaperone PapD, C-terminal domain / Pili assembly chaperone, bacterial / Pili assembly chaperone, conserved site / Pili assembly chaperone, C-terminal domain superfamily / Gram-negative pili assembly chaperone signature. / Pili assembly chaperone, N-terminal / : / Pili and flagellar-assembly chaperone, PapD N-terminal domain ...P pili tip fibrillum PapE protein, Enterobacteriaceae / Pili assembly chaperone, C-terminal / Pili assembly chaperone PapD, C-terminal domain / Pili assembly chaperone, bacterial / Pili assembly chaperone, conserved site / Pili assembly chaperone, C-terminal domain superfamily / Gram-negative pili assembly chaperone signature. / Pili assembly chaperone, N-terminal / : / Pili and flagellar-assembly chaperone, PapD N-terminal domain / PapD-like superfamily / Fimbrial-type adhesion domain / Fimbrial-type adhesion domain / Fimbrial protein / : / Fimbrial-type adhesion domain superfamily / Adhesion domain superfamily / Immunoglobulin-like fold / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Fimbrial protein PapE / Chaperone protein PapD
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / MAD / Resolution: 2.3 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 14, 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 1.3Nov 20, 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

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Assembly

Deposited unit
A: Chaperone protein PapD
B: mature Fimbrial protein PapE
C: Chaperone protein PapD
D: mature Fimbrial protein PapE


Theoretical massNumber of molelcules
Total (without water)80,7834
Polymers80,7834
Non-polymers00
Water2,954164
1
A: Chaperone protein PapD
B: mature Fimbrial protein PapE


Theoretical massNumber of molelcules
Total (without water)40,3912
Polymers40,3912
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3110 Å2
ΔGint-10 kcal/mol
Surface area16100 Å2
MethodPISA
2
C: Chaperone protein PapD
D: mature Fimbrial protein PapE


Theoretical massNumber of molelcules
Total (without water)40,3912
Polymers40,3912
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3150 Å2
ΔGint-8 kcal/mol
Surface area15160 Å2
MethodPISA
Unit cell
Length a, b, c (Å)56.070, 56.863, 60.931
Angle α, β, γ (deg.)108.57, 89.26, 104.14
Int Tables number1
Space group name H-MP1

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Components

#1: Protein Chaperone protein PapD


Mass: 25559.463 Da / Num. of mol.: 2 / Fragment: residues 22-239
Mutation: 6x histidine tag at C-terminus, selenomethionine at methionine positions
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: papD / Production host: Escherichia coli (E. coli) / References: UniProt: P15319
#2: Protein mature Fimbrial protein PapE


Mass: 14832.035 Da / Num. of mol.: 2 / Fragment: residues 25-173, residues 26-36 deleted
Mutation: N-terminal residues 26-36 deleted , selenomethionine at methionine positions
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: papE / Production host: Escherichia coli (E. coli) / References: UniProt: P08407
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 164 / 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: 2.43 Å3/Da / Density % sol: 49.08 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 100 mM Tris pH 8.5, 250 mM MgCl2, 17-18% PEG 4000, 4-7% glycerol, VAPOR DIFFUSION, SITTING DROP, temperature 294K
Crystal grow
*PLUS
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
1100 mMTris1reservoirpH8.5
2250 mM1reservoirMgCl2
317-18 %PEG40001reservoir
44-7 %glycerol1reservoir

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Data collection

DiffractionMean temperature: 98 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.3→30 Å / Num. obs: 27884 / % possible obs: 91 % / Observed criterion σ(I): 0 / Biso Wilson estimate: 32.9 Å2 / Rsym value: 0.041 / Net I/σ(I): 28.7
Reflection
*PLUS
Lowest resolution: 30 Å / Num. measured all: 162110 / Rmerge(I) obs: 0.041
Reflection shell
*PLUS
% possible obs: 91.5 % / Rmerge(I) obs: 0.175 / Mean I/σ(I) obs: 6.5

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
CNSphasing
RefinementMethod to determine structure: MAD / Resolution: 2.3→24.73 Å / Rfactor Rfree error: 0.006 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.279 2020 7.2 %RANDOM
Rwork0.226 ---
all0.23 ---
obs0.226 27882 90.9 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 35.3694 Å2 / ksol: 0.309847 e/Å3
Displacement parametersBiso mean: 39.7 Å2
Baniso -1Baniso -2Baniso -3
1-1.64 Å2-2.59 Å20.34 Å2
2---0.27 Å2-0.81 Å2
3----1.37 Å2
Refine analyzeLuzzati coordinate error free: 0.39 Å / Luzzati sigma a free: 0.34 Å
Refinement stepCycle: LAST / Resolution: 2.3→24.73 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5064 0 0 164 5228
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.006
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_deg1.3
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d26.6
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.81
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.651.5
X-RAY DIFFRACTIONc_mcangle_it2.662
X-RAY DIFFRACTIONc_scbond_it2.322
X-RAY DIFFRACTIONc_scangle_it3.182.5
LS refinement shellResolution: 2.3→2.44 Å / Rfactor Rfree error: 0.017 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.325 346 7.3 %
Rwork0.273 4374 -
obs--92.3 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
Refinement
*PLUS
Highest resolution: 2.3 Å / Lowest resolution: 30 Å
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.0061
X-RAY DIFFRACTIONc_angle_deg1.29
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg26.6
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.81

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