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- PDB-2w07: Structural determinants of polymerization reactivity of the P pil... -

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Basic information

Entry
Database: PDB / ID: 2w07
TitleStructural determinants of polymerization reactivity of the P pilus adaptor subunit PapF
Components
  • CHAPERONE PROTEIN PAPD
  • MINOR PILIN SUBUNIT PAPF
KeywordsCELL ADHESION / DONOR STRAND COMPLEMENTATION / NTE / PAPD / PAPF / PILI / PILIN / GROOVE / SUBUNIT / IMMUNOGLOBULIN DOMAIN / DONOR-STRAND EXCHANGE / SECRETED / FIMBRIUM / PERIPLASM / P5 POCKET / CHAPERONE / CELL PROJECTION / PILUS BIOGENESIS / ORDER OF ASSEMBLY / N-TERMINAL EXTENSION
Function / homology
Function and homology information


pilus / : / chaperone-mediated protein folding / cell wall organization / outer membrane-bounded periplasmic space / cell adhesion
Similarity search - Function
P pili tip fibrillum PapF protein / 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 ...P pili tip fibrillum PapF protein / 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 / Immunoglobulins / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Periplasmid chaperone PapD protein / Minor pilin subunit PapF
Similarity search - Component
Biological speciesESCHERICHIA COLI (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsVerger, D. / Rose, R.J. / Paci, E. / Costakes, G. / Daviter, T. / Hultgren, S. / Remaut, H. / Ashcroft, A.E. / Radford, S.E. / Waksman, G.
CitationJournal: Structure / Year: 2008
Title: Structural Determinants of Polymerization Reactivity of the P Pilus Adaptor Subunit Papf.
Authors: Verger, D. / Rose, R.J. / Paci, E. / Costakes, G. / Daviter, T. / Hultgren, S. / Remaut, H. / Ashcroft, A.E. / Radford, S.E. / Waksman, G.
History
DepositionAug 12, 2008Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 25, 2008Provider: repository / Type: Initial release
Revision 1.1May 7, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
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
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

Downloads & links

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Assembly

Deposited unit
A: CHAPERONE PROTEIN PAPD
B: MINOR PILIN SUBUNIT PAPF
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,5494
Polymers40,3562
Non-polymers1922
Water1,53185
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3830 Å2
ΔGint-24.4 kcal/mol
Surface area18830 Å2
MethodPQS
Unit cell
Length a, b, c (Å)65.420, 65.420, 166.110
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein CHAPERONE PROTEIN PAPD / PAPD


Mass: 24589.895 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) ESCHERICHIA COLI (E. coli) / Strain: UTI89 / Plasmid: PTRC99A / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): C600 / References: UniProt: Q1R2W9
#2: Protein MINOR PILIN SUBUNIT PAPF / PAPF


Mass: 15766.592 Da / Num. of mol.: 1 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) ESCHERICHIA COLI (E. coli) / Strain: UTI89 / Plasmid: PTRC99A / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): C600 / References: UniProt: Q1R2X3
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 85 / Source method: isolated from a natural source / Formula: H2O
Compound detailsENGINEERED RESIDUE IN CHAIN B, GLY 27 TO ASN
Sequence detailsCHAIN A: FIRST 21 AMINO ACIDS ARE THE SIGNAL PEPTIDE, NOT PART OF THE MATURE PROTEIN SEQUENCE CHAIN ...CHAIN A: FIRST 21 AMINO ACIDS ARE THE SIGNAL PEPTIDE, NOT PART OF THE MATURE PROTEIN SEQUENCE CHAIN B: FIRST 19 AMINO ACIDS ARE THE SIGNAL PEPTIDE, NOT PART OF THE MATURE PROTEIN SEQUENCE

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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: 2.2 Å3/Da / Density % sol: 44 % / Description: NONE
Crystal growDetails: 2.2 M AMMONIUM SULFATE 20% GLYCEROL

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.931
DetectorType: ADSC CCD / Detector: CCD / Date: Feb 19, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.931 Å / Relative weight: 1
ReflectionResolution: 2.2→20 Å / Num. obs: 19065 / % possible obs: 100 % / Observed criterion σ(I): 0 / Redundancy: 7.2 % / Rmerge(I) obs: 0.05 / Net I/σ(I): 9.4
Reflection shellResolution: 2→2.32 Å / Redundancy: 6.4 % / Rmerge(I) obs: 0.29 / Mean I/σ(I) obs: 2.6 / % possible all: 100

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Processing

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

1pdk


Resolution: 2.2→20 Å / Rfactor Rfree error: 0.009 / Data cutoff high absF: 10000 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.2773 980 5.1 %RANDOM
Rwork0.2355 ---
obs0.2355 19065 100 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 35.5584 Å2 / ksol: 0.359103 e/Å3
Displacement parametersBiso mean: 41.7 Å2
Baniso -1Baniso -2Baniso -3
1--1.463 Å20 Å20 Å2
2---1.463 Å20 Å2
3---2.926 Å2
Refine analyzeLuzzati d res low obs: 20 Å
Refinement stepCycle: LAST / Resolution: 2.2→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2531 0 10 85 2626
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.005819
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_deg1.26447
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_it1.51.5
X-RAY DIFFRACTIONc_mcangle_it2.422
X-RAY DIFFRACTIONc_scbond_it2.192
X-RAY DIFFRACTIONc_scangle_it3.042.5
LS refinement shellResolution: 2.2→2.24 Å / Rfactor Rfree error: 0.009 / Total num. of bins used: 19
RfactorNum. reflection% reflection
Rfree0.2826 52 5.3 %
Rwork0.2512 915 -
obs--100 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION3ION.PARAMION.TOP

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