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- PDB-2j2z: X-Ray Structure of the Chaperone PapD in complex with the Pilus t... -

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Basic information

Entry
Database: PDB / ID: 2j2z
TitleX-Ray Structure of the Chaperone PapD in complex with the Pilus terminator subunit PapH at 2.3 Angstrom resolution
Components
  • CHAPERONE PROTEIN PAPD
  • PAP FIMBRIAL MINOR PILIN PROTEIN
KeywordsCHAPERONE/SURFACE ACTIVE PROTEIN / PERIPLASMIC / PILUS TERMINATION / IMMUNOGLOBULIN DOMAIN / PAPH / PAPD / FIMBRIA / CHAPERONE / P5 POCKET / CHAPERONE- SURFACE ACTIVE PROTEIN COMPLEX / CHAPERONE-SURFACE ACTIVE PROTEIN complex
Function / homology
Function and homology information


cell adhesion involved in single-species biofilm formation / pilus / chaperone-mediated protein folding / cell wall organization / outer membrane-bounded periplasmic space / extracellular region
Similarity search - Function
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 ...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 / Immunoglobulins / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
: / PAP fimbrial minor pilin protein / Chaperone protein PapD / PapD
Similarity search - Component
Biological speciesESCHERICHIA COLI (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsVerger, D. / Miller, E. / Remaut, H. / Waksman, G. / Hultgren, S.
CitationJournal: Embo Rep. / Year: 2006
Title: Molecular Mechanism of P Pilus Termination in Uropathogenic Escherichia Coli.
Authors: Verger, D. / Miller, E. / Remaut, H. / Waksman, G. / Hultgren, S.
History
DepositionAug 17, 2006Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 8, 2006Provider: repository / Type: Initial release
Revision 1.1May 8, 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 / Derived calculations / 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 / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr1_symmetry / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry
Revision 1.4Nov 6, 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

Downloads & links

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Assembly

Deposited unit
A: CHAPERONE PROTEIN PAPD
B: PAP FIMBRIAL MINOR PILIN PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,00314
Polymers43,8882
Non-polymers1,11612
Water4,936274
1
A: CHAPERONE PROTEIN PAPD
B: PAP FIMBRIAL MINOR PILIN PROTEIN
hetero molecules

A: CHAPERONE PROTEIN PAPD
B: PAP FIMBRIAL MINOR PILIN PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)90,00628
Polymers87,7754
Non-polymers2,23124
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_555-x,y,-z+1/21
MethodPQS
Unit cell
Length a, b, c (Å)103.460, 149.300, 82.840
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11B-1174-

CO

21A-2018-

HOH

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Components

#1: Protein CHAPERONE PROTEIN PAPD / PERIPLASMIC CHAPERONE 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: UTI 89 / Plasmid: PTRC99A / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): C600 / References: UniProt: P15319, UniProt: Q7ATU9*PLUS
#2: Protein PAP FIMBRIAL MINOR PILIN PROTEIN / PAPH


Mass: 19297.713 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: RESIDUES 2 TO 22 DELETED (NON DONOR STRAND EXCHANGE REGION). N_TERMINAL EXTENSION 1 DELETED (NTD1).
Source: (gene. exp.) ESCHERICHIA COLI (E. coli) / Strain: J96 / Plasmid: PTRC99A / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): C600 / References: UniProt: P07111
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-CO / COBALT (II) ION


Mass: 58.933 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Co
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 274 / 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: 3.7 Å3/Da / Density % sol: 67 %
Crystal growpH: 6.5 / Details: 0.01M COCL2, 0.1 M MES PH 6.5, 1.8 M AS

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX14.2 / Wavelength: 0.9793
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Jun 6, 2004
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 2.3→20 Å / Num. obs: 28676 / % possible obs: 99.9 % / Observed criterion σ(I): 0 / Redundancy: 9 % / Biso Wilson estimate: 33.2 Å2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 8.7
Reflection shellResolution: 2.3→2.42 Å / Redundancy: 7.7 % / Rmerge(I) obs: 0.27 / Mean I/σ(I) obs: 2.3 / % possible all: 99.5

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Processing

Software
NameVersionClassification
CNS1.1refinement
MOSFLMdata reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1N0L

1n0l


Resolution: 2.3→20 Å / Rfactor Rfree error: 0.0002 / Data cutoff high absF: 10000 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: THE FINAL MODEL INCLUDES ALL PAPD MAIN CHAIN ATOMS EXCEPT THE LAST TWO RESIDUES AND ALL PAPHNTD1 MAIN CHAIN ATOMS EXCEPT THE FIRST 2 (RESIDUES 1 AND 23). THE FINAL MODEL ALSO MISSES ONE SIDE ...Details: THE FINAL MODEL INCLUDES ALL PAPD MAIN CHAIN ATOMS EXCEPT THE LAST TWO RESIDUES AND ALL PAPHNTD1 MAIN CHAIN ATOMS EXCEPT THE FIRST 2 (RESIDUES 1 AND 23). THE FINAL MODEL ALSO MISSES ONE SIDE CHAIN OF PAPD AND 13 SIDE CHAINS OF PAPHNTD1.THE ELECTRON DENSITY WAS ABSENT FOR THESE EXPOSED RESIDUES THUS THEY WERE MODELLED AS ALANINES
RfactorNum. reflection% reflectionSelection details
Rfree0.2404 1456 5.1 %RANDOM
Rwork0.2086 ---
obs0.2086 28668 99.5 %-
Solvent computationBsol: 40.5143 Å2 / ksol: 0.361159 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--15.226 Å20 Å20 Å2
2--7.144 Å20 Å2
3---8.083 Å2
Refinement stepCycle: LAST / Resolution: 2.3→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2804 0 56 274 3134
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.005607
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_deg1.25268
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_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
LS refinement shellResolution: 2.3→2.33 Å / Rfactor Rfree error: 0.005 / Total num. of bins used: 29
RfactorNum. reflection% reflection
Rfree0.293 54 3.7 %
Rwork0.281 924 -
obs--98.5 %
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1PROTEIN_REP.PARAM
X-RAY DIFFRACTION2WATER_REP.PARAM
X-RAY DIFFRACTION3ION.PARAM

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