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- PDB-8bk4: Full length structure of the apo-state LpMIP. -

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Basic information

Entry
Database: PDB / ID: 8bk4
TitleFull length structure of the apo-state LpMIP.
ComponentsMacrophage infectivity potentiator
KeywordsSTRUCTURAL PROTEIN / Macrophage / potentiator / soluble / protein.
Function / homology
Function and homology information


peptidylprolyl isomerase / peptidyl-prolyl cis-trans isomerase activity / extracellular region
Similarity search - Function
Chitinase A; domain 3 - #40 / Chitinase A; domain 3 / 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 / Roll / Alpha Beta
Similarity search - Domain/homology
PHOSPHATE ION / Chem-WRL / Macrophage infectivity potentiator
Similarity search - Component
Biological speciesTrypanosoma cruzi (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.34 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 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: Macrophage infectivity potentiator
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,1584
Polymers18,4731
Non-polymers6853
Water2,576143
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: NMR relaxation study
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area370 Å2
ΔGint-5 kcal/mol
Surface area9040 Å2
MethodPISA
Unit cell
Length a, b, c (Å)42.493, 57.529, 67.712
Angle α, β, γ (deg.)90, 90, 90
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Macrophage infectivity potentiator / Peptidyl-prolyl cis-trans isomerase / PPIase / Rotamase


Mass: 18472.855 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Trypanosoma cruzi (eukaryote) / Gene: MIP / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q09734, peptidylprolyl isomerase
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / 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: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 143 / 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: 2.21 Å3/Da / Density % sol: 44.36 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 5.6
Details: 30 %(v/v) MPD, 0.2 M ammonium acetate, 0.1 M sodium citrate, pH 5.6

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.9795 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: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.34→43.84 Å / Num. obs: 28364 / % possible obs: 74.79 % / Redundancy: 8.5 % / Rrim(I) all: 0.08 / Net I/σ(I): 15.56
Reflection shellResolution: 1.342→1.39 Å / Num. unique obs: 209 / 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: 1JVW

1jvw


Resolution: 1.34→43.83 Å / Cross valid method: FREE R-VALUE
RfactorNum. reflection% reflectionSelection details
Rfree0.2205 --RANDOM
Rwork0.1968 ---
obs-28364 99 %-
Refinement stepCycle: LAST / Resolution: 1.34→43.83 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1298 0 43 143 1484

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