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- PDB-3dpa: CRYSTAL STRUCTURE OF CHAPERONE PROTEIN PAPD REVEALS AN IMMUNOGLOB... -

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Basic information

Entry
Database: PDB / ID: 3dpa
TitleCRYSTAL STRUCTURE OF CHAPERONE PROTEIN PAPD REVEALS AN IMMUNOGLOBULIN FOLD
ComponentsCHAPERONE PROTEIN PAPD
KeywordsCHAPERONE PROTEIN
Function / homology
Function and homology information


: / cell wall organization / outer membrane-bounded periplasmic space
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 / Immunoglobulin-like fold
Similarity search - Domain/homology
Chaperone protein PapD
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / Resolution: 2.5 Å
AuthorsHolmgren, A. / Branden, C.-I.
Citation
Journal: Nature / Year: 1989
Title: Crystal structure of chaperone protein PapD reveals an immunoglobulin fold.
Authors: Holmgren, A. / Branden, C.I.
#1: Journal: J.Mol.Biol. / Year: 1988
Title: Preliminary X-Ray Study of Papd Crystals from Uropathogenic Escherichia Coli
Authors: Holmgren, A. / Branden, C.-I. / Lindberg, F. / Tennant, J.M.
History
DepositionOct 9, 1991Processing site: BNL
Revision 1.0Oct 15, 1991Provider: repository / Type: Initial release
Revision 1.1Mar 25, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 20, 2017Group: Advisory / Other / Category: pdbx_database_status / pdbx_validate_symm_contact / Item: _pdbx_database_status.process_site
Revision 1.4Feb 21, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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


Theoretical massNumber of molelcules
Total (without water)24,5761
Polymers24,5761
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)58.200, 64.000, 67.000
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein CHAPERONE PROTEIN PAPD / Coordinate model: Cα atoms only


Mass: 24575.869 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / References: UniProt: P15319

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.54 Å3/Da / Density % sol: 51.52 %
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
112 mg/mlprotein1drop
215 %PEG80001reservoir

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Data collection

Reflection
*PLUS
Highest resolution: 2.5 Å / Num. obs: 6353 / % possible obs: 69.2 % / Num. measured all: 20920 / Rmerge(I) obs: 0.053

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Processing

SoftwareName: X-PLOR / Classification: refinement
RefinementRfactor Rwork: 0.184 / Highest resolution: 2.5 Å
Refinement stepCycle: LAST / Highest resolution: 2.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms218 0 0 0 218
Refinement
*PLUS
Highest resolution: 2.5 Å / Rfactor obs: 0.184
Solvent computation
*PLUS
Displacement parameters
*PLUS

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