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- PDB-2j7l: E. coli P Pilus chaperone PapD in complex with a pilus biogenesis... -

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Basic information

Entry
Database: PDB / ID: 2j7l
TitleE. coli P Pilus chaperone PapD in complex with a pilus biogenesis inhibitor, pilicide 2c
ComponentsCHAPERONE PROTEIN PAPD
KeywordsCHAPERONE/SURFACE ACTIVE PROTEIN / FIMBRIA / INHIBITOR / CHAPERONE / PERIPLASMIC / IMMUNOGLOBULIN DOMAIN / CHAPERONE-SURFACE ACTIVE PROTEIN complex
Function / homology
Function and homology information


chaperone-mediated protein folding / 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 / Immunoglobulins ...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 / Immunoglobulins / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Chem-XC2 / Chaperone protein PapD
Similarity search - Component
Biological speciesESCHERICHIA COLI (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsRemaut, H. / Pinkner, J.S. / Hultgren, S.J. / Almqvist, F. / Waksman, G.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2006
Title: Rationally Designed Small Compounds Inhibit Pilus Biogenesis in Uropathogenic Bacteria.
Authors: Pinkner, J.S. / Remaut, H. / Buelens, F. / Miller, E. / Aberg, V. / Pemberton, N. / Hedenstrom, M. / Larsson, A. / Seed, P. / Waksman, G. / Hultgren, S.J. / Almqvist, F.
History
DepositionOct 12, 2006Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 1, 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 / 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: CHAPERONE PROTEIN PAPD
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,0522
Polymers24,5761
Non-polymers4771
Water93752
1
A: CHAPERONE PROTEIN PAPD
hetero molecules

A: CHAPERONE PROTEIN PAPD
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,1054
Polymers49,1522
Non-polymers9532
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_556x-y,-y,-z+11
MethodPQS
Unit cell
Length a, b, c (Å)94.315, 94.315, 121.992
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number182
Space group name H-MP6322

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Components

#1: Protein CHAPERONE PROTEIN PAPD / PAPD


Mass: 24575.869 Da / Num. of mol.: 1 / Fragment: RESIDUES 22-239
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) ESCHERICHIA COLI (E. coli) / Strain: J96 / Plasmid: PMMB91 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): C600 / References: UniProt: P15319
#2: Chemical ChemComp-XC2 / (3R)-8-CYCLOPROPYL-6-(MORPHOLIN-4-YLMETHYL)-7-(1-NAPHTHYLMETHYL)-5-OXO-2,3-DIHYDRO-5H-[1,3]THIAZOLO[3,2-A]PYRIDINE-3-CARBOXYLIC ACID


Mass: 476.587 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C27H28N2O4S
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 52 / Source method: isolated from a natural source / Formula: H2O

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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: 3.19 Å3/Da / Density % sol: 61.2 %
Crystal growpH: 6
Details: 16 % PEG 4000, 100MM TRIS HCL PH 8.5 AND 200 MM LI2SO4

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.9756
DetectorType: ADSC CCD / Detector: CCD / Date: Feb 25, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9756 Å / Relative weight: 1
ReflectionResolution: 2.6→20 Å / Num. obs: 20651 / % possible obs: 99.9 % / Observed criterion σ(I): 0 / Redundancy: 13.7 % / Biso Wilson estimate: 50.9 Å2 / Rmerge(I) obs: 0.09 / Net I/σ(I): 23.4
Reflection shellResolution: 2.6→2.74 Å / Redundancy: 14.1 % / Rmerge(I) obs: 0.43 / Mean I/σ(I) obs: 7.1 / % 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 1QPP

1qpp


Resolution: 2.6→15 Å / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.2726 512 5 %RANDOM
Rwork0.2324 ---
obs0.2324 9815 95.1 %-
Solvent computationBsol: 45.463 Å2 / ksol: 0.343506 e/Å3
Displacement parametersBiso mean: 54.02 Å2
Baniso -1Baniso -2Baniso -3
1--14.926 Å2-7.157 Å20 Å2
2---14.926 Å20 Å2
3---29.852 Å2
Refinement stepCycle: LAST / Resolution: 2.6→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1664 0 34 52 1750
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.008812
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_deg1.25549
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_it1.441.5
X-RAY DIFFRACTIONc_mcangle_it2.4772
X-RAY DIFFRACTIONc_scbond_it2.0512
X-RAY DIFFRACTIONc_scangle_it3.2442.5
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2DNA-RNA_REP.PARAMDNA-RNA.TOP
X-RAY DIFFRACTION3WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION4ION.PARAMION.TOP
X-RAY DIFFRACTION5P-048.PARAMP-048.TOPOL

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