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- PDB-2wmp: Structure of the E. coli chaperone PapD in complex with the pilin... -

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Basic information

Entry
Database: PDB / ID: 2wmp
TitleStructure of the E. coli chaperone PapD in complex with the pilin domain of the PapGII adhesin
Components
  • CHAPERONE PROTEIN PAPD
  • PAPG PROTEIN
KeywordsCHAPERONE / CELL ADHESION / DONOR STRAND COMPLEMENTATION / PILIN DOMAIN / IMMUNOGLOBULIN DOMAIN / BACTERIAL ATTACHMENT AND INVASION / DONOR STRAND EXCHANGE / CHAPERONE USHER PATHWAY
Function / homology
Function and homology information


pilus / : / cell wall organization / outer membrane-bounded periplasmic space / carbohydrate binding / cell adhesion
Similarity search - Function
PapG, chaperone-binding / PapG chaperone-binding domain / PapG, carbohydrate-binding domain / PapG, carbohydrate-binding domain superfamily / PapG carbohydrate binding domain / 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 ...PapG, chaperone-binding / PapG chaperone-binding domain / PapG, carbohydrate-binding domain / PapG, carbohydrate-binding domain superfamily / PapG carbohydrate binding domain / 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 superfamily / Adhesion domain superfamily / Immunoglobulin-like fold / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Chaperone protein PapD / Periplasmid chaperone PapD protein / Fimbrial protein
Similarity search - Component
Biological speciesESCHERICHIA COLI (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsFord, B.A. / Verger, D. / Elam, J.S. / Dodson, K.W. / Pinkner, J.S. / Hultgren, S.J.
Citation
Journal: J.Bacteriol. / Year: 2012
Title: Structure of the Papd-Papgii Pilin Complex Reveals an Open and Flexible P5 Pocket.
Authors: Ford, B.A. / Verger, D. / Dodson, K.W. / Volkan, E. / Kostakioti, M. / Elam, J.S. / Pinkner, J.S. / Waksman, G. / Hultgren, S.J.
#1: Journal: Cell(Cambridge,Mass.) / Year: 2001
Title: Structural Basis of the Interaction of the Pyelonephritic E. Coli Adhesin to its Human Kidney Receptor
Authors: Dodson, K.W. / Pinkner, J.S. / Rose, T. / Magnusson, G. / Hultgren, S.J. / Waksman, G.
History
DepositionJul 2, 2009Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 25, 2010Provider: repository / Type: Initial release
Revision 1.1Oct 3, 2012Group: Database references / Other ...Database references / Other / Refinement description / Version format compliance
Revision 1.2Dec 26, 2012Group: Database references
Revision 1.3Dec 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
Revision 1.4Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature
Remark 700 SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: CHAPERONE PROTEIN PAPD
B: PAPG PROTEIN


Theoretical massNumber of molelcules
Total (without water)38,5562
Polymers38,5562
Non-polymers00
Water3,459192
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2880 Å2
ΔGint-13.1 kcal/mol
Surface area15550 Å2
MethodPISA
Unit cell
Length a, b, c (Å)66.560, 90.470, 64.490
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein CHAPERONE PROTEIN PAPD / PAPD


Mass: 25418.777 Da / Num. of mol.: 1 / Fragment: RESIDUES 22-239
Source method: isolated from a genetically manipulated source
Details: C TERMINUS 6-HISTIDINE TAG / Source: (gene. exp.) ESCHERICHIA COLI (E. coli) / Strain: UTI89 / Description: GENOMIC DNA / Plasmid: PTRC99A / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): C600 / References: UniProt: P15319, UniProt: Q1R2W9*PLUS
#2: Protein PAPG PROTEIN / PAPGII


Mass: 13136.854 Da / Num. of mol.: 1 / Fragment: PILIN DOMAIN, RESIDUES 214-336
Source method: isolated from a genetically manipulated source
Details: ADHESIN DOMAIN DELETED (RESIDUES 1 TO 193) / Source: (gene. exp.) ESCHERICHIA COLI (E. coli) / Strain: AD110 / Description: GENOMIC DNA / Plasmid: PTRC99A / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): C600 / References: UniProt: Q47445
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 192 / 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: 2.52 Å3/Da / Density % sol: 51 % / Description: NONE
Crystal growpH: 8.5
Details: PROTEIN (COMPLEX) AT 9.9 MG/ML 10-12% PEG 4K 0.1M TRIS-HCL PH 8.5 5% ISOPROPANOL

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.8726
DetectorType: ADSC CCD / Detector: CCD / Date: Apr 24, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8726 Å / Relative weight: 1
ReflectionResolution: 2.3→66.56 Å / Num. obs: 17935 / % possible obs: 100 % / Observed criterion σ(I): 1 / Redundancy: 6.6 % / Biso Wilson estimate: 32.2 Å2 / Rmerge(I) obs: 0.13 / Net I/σ(I): 4.6
Reflection shellResolution: 2.3→2.42 Å / Redundancy: 6.7 % / Rmerge(I) obs: 0.5 / Mean I/σ(I) obs: 1.4 / % possible all: 100

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Processing

Software
NameVersionClassification
CNS1.2refinement
MOSFLMdata reduction
SCALAdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1PDK

1pdk


Resolution: 2.3→200 Å / Rfactor Rfree error: 0.01 / Data cutoff high absF: 10000 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: THIS PDB FILE IS LINKED TO ENTRY 3ME0 AS BOTH FILES WILL APPEAR IN THE SAME PUBLICATION.
RfactorNum. reflection% reflectionSelection details
Rfree0.2893 914 5.1 %RANDOM
Rwork0.2272 ---
obs0.2272 17899 100 %-
Solvent computationSolvent model: DENSITY MODIFICATION / Bsol: 25.1473 Å2 / ksol: 0.3 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-0.393 Å20 Å20 Å2
2---5.668 Å20 Å2
3---5.275 Å2
Refinement stepCycle: LAST / Resolution: 2.3→200 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2543 0 0 192 2735
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.005767
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_deg1.31787
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.70.2
X-RAY DIFFRACTIONc_mcangle_it2.920.9
X-RAY DIFFRACTIONc_scbond_it2.220.2
X-RAY DIFFRACTIONc_scangle_it3.10.6
LS refinement shellResolution: 2.3→2.34 Å / Rfactor Rfree error: 0.054 / Total num. of bins used: 18
RfactorNum. reflection% reflection
Rfree0.3858 52 5.1 %
Rwork0.2781 915 -
obs--100 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN_REP.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER_REP.TOP

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