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- PDB-8bje: A structure of the truncated LpMIP with bound inhibitor JK236. -

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Basic information

Entry
Database: PDB / ID: 8bje
TitleA structure of the truncated LpMIP with bound inhibitor JK236.
ComponentsPeptidyl-prolyl cis-trans isomerase
KeywordsSTRUCTURAL PROTEIN / Macrophage / potentiator / soluble / protein.
Function / homology
Function and homology information


peptidylprolyl isomerase / peptidyl-prolyl cis-trans isomerase activity / cell outer membrane / protein folding
Similarity search - Function
Macrophage infectivity potentiator / Peptidyl-prolyl cis-trans isomerase, FKBP-type, N-terminal / Peptidyl-prolyl cis-trans isomerase, FKBP-type, N-terminal domain superfamily / Domain amino terminal to FKBP-type peptidyl-prolyl isomerase / FKBP-type peptidyl-prolyl cis-trans isomerase / FKBP-type peptidyl-prolyl cis-trans isomerase domain / FKBP-type peptidyl-prolyl cis-trans isomerase domain profile. / Peptidyl-prolyl cis-trans isomerase domain superfamily
Similarity search - Domain/homology
Chem-WRL / Peptidyl-prolyl cis-trans isomerase
Similarity search - Component
Biological speciesLegionella pneumophila (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.49 Å
AuthorsWhittaker, J.J. / Guskov, A. / Goretzki, B. / Hellmich, U.A.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research Foundation (DFG)390713860 Germany
CitationJournal: Int.J.Biol.Macromol. / Year: 2023
Title: Legionella pneumophila macrophage infectivity potentiator protein appendage domains modulate protein dynamics and inhibitor binding.
Authors: Wiedemann, C. / Whittaker, J.J. / Perez Carrillo, V.H. / Goretzki, B. / Dajka, M. / Tebbe, F. / Harder, J.M. / Krajczy, P.R. / Joseph, B. / Hausch, F. / Guskov, A. / Hellmich, U.A.
History
DepositionNov 4, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 6, 2023Provider: repository / Type: Initial release
Revision 1.1Sep 13, 2023Group: Database references / Category: citation / citation_author / Item: _citation.journal_volume / _citation_author.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Peptidyl-prolyl cis-trans isomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,9154
Polymers14,2321
Non-polymers6833
Water93752
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: NMR relaxation study
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area330 Å2
ΔGint-1 kcal/mol
Surface area7170 Å2
MethodPISA
Unit cell
Length a, b, c (Å)52.951, 52.951, 73.146
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

#1: Protein Peptidyl-prolyl cis-trans isomerase


Mass: 14232.267 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Legionella pneumophila (bacteria) / Gene: C3927_03235 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A2S6FAG4, peptidylprolyl isomerase
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-WRL / (1~{S},5~{S},6~{R})-10-[3,5-bis(chloranyl)phenyl]sulfonyl-5-(hydroxymethyl)-3-[(1~{S})-1-pyridin-2-ylethyl]-3,10-diazabicyclo[4.3.1]decan-2-one


Mass: 498.423 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C22H25Cl2N3O4S
#4: Water ChemComp-HOH / water


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

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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: 2.08 Å3/Da / Density % sol: 40.86 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 18 %(w/v) PEG 8000, 0.2 M zinc acetate, 0.1 M sodium cacodylate, pH 6.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.9763 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 15, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 1.44→45.86 Å / Num. obs: 23619 / % possible obs: 99.21 % / Redundancy: 10.5 % / Rrim(I) all: 0.07 / Net I/σ(I): 9.92
Reflection shellResolution: 1.44→1.49 Å / Num. unique obs: 2330 / Rrim(I) all: 0.1

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Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
Aimlessdata scaling
PDB_EXTRACT3.27data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1FD9

1fd9


Resolution: 1.49→45.86 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 36.27 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2328 745 4.88 %RANDOM
Rwork0.1975 ---
obs0.1993 15277 76.09 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.49→45.86 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1003 0 44 52 1099
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0171089
X-RAY DIFFRACTIONf_angle_d1.6911481
X-RAY DIFFRACTIONf_dihedral_angle_d10.931175
X-RAY DIFFRACTIONf_chiral_restr0.11168
X-RAY DIFFRACTIONf_plane_restr0.029186
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.49-1.60.3367520.215906X-RAY DIFFRACTION24
1.6-1.760.29771180.22562261X-RAY DIFFRACTION60
1.76-2.020.30521870.23783550X-RAY DIFFRACTION94
2.02-2.540.21331870.21323834X-RAY DIFFRACTION100
2.54-60.21832010.17763981X-RAY DIFFRACTION100

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