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- PDB-8bk6: A truncated structure of LpMIP with bound inhibitor JK095. -

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Basic information

Entry
Database: PDB / ID: 8bk6
TitleA truncated structure of LpMIP with bound inhibitor JK095.
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 domain profile. / FKBP-type peptidyl-prolyl cis-trans isomerase domain / FKBP-type peptidyl-prolyl cis-trans isomerase / Peptidyl-prolyl cis-trans isomerase domain superfamily
Similarity search - Domain/homology
DI(HYDROXYETHYL)ETHER / Peptidyl-prolyl cis-trans isomerase
Similarity search - Component
Biological speciesLegionella pneumophila (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.263 Å
AuthorsWhittaker, J.J. / Guskov, A. / Hellmich, A.U. / Goretzki, B.
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 8, 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
B: Peptidyl-prolyl cis-trans isomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,5057
Polymers23,8852
Non-polymers6205
Water23413
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: NMR relaxation study
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)73.557, 73.557, 103.286
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein Peptidyl-prolyl cis-trans isomerase


Mass: 11942.639 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Legionella pneumophila (bacteria) / Gene: mip / Production host: Escherichia coli (E. coli) / References: UniProt: Q933L8
#2: Chemical
ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C4H10O3
#3: Chemical ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID


Mass: 195.237 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 13 / 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: 2.9 Å3/Da / Density % sol: 57.64 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 20 %(v/v) 2-propanol, 0.2 M sodium citrate tribasic dihydrate, 0.1 M HEPES, pH 7.5

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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: 2.263→59.92 Å / Num. obs: 13801 / % possible obs: 99.63 % / Redundancy: 7.5 % / Rrim(I) all: 0.06 / Net I/σ(I): 8
Reflection shellResolution: 2.263→5.5 Å / Num. unique obs: 1334 / Rrim(I) all: 0.09

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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: 2.263→59.92 Å / SU ML: 0.42 / Cross valid method: FREE R-VALUE / σ(F): 2.263 / Phase error: 36.19 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.3482 --RANDOM
Rwork0.2868 ---
obs0.2868 13801 99.93 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.263→59.92 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1684 0 40 13 1737
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0111760
X-RAY DIFFRACTIONf_angle_d1.7972386
X-RAY DIFFRACTIONf_dihedral_angle_d14.927257
X-RAY DIFFRACTIONf_chiral_restr0.085274
X-RAY DIFFRACTIONf_plane_restr0.015296
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.263-2.440.41671240.31662566X-RAY DIFFRACTION100
2.44-2.680.35791390.29792553X-RAY DIFFRACTION100
2.68-3.070.3541330.30142594X-RAY DIFFRACTION100
3.07-3.870.40631350.29192639X-RAY DIFFRACTION100
3.87-5.50.28971340.25342784X-RAY DIFFRACTION100

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