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- PDB-8bjd: Full length structure of LpMIP with bound inhibitor JK095 -

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Basic information

Entry
Database: PDB / ID: 8bjd
TitleFull length structure of LpMIP with bound inhibitor JK095
ComponentsPeptidyl-prolyl cis-trans isomeraseProlyl 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
Chem-9QN / Peptidyl-prolyl cis-trans isomerase
Similarity search - Component
Biological speciesLegionella pneumophila (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 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)23,3126
Polymers22,4101
Non-polymers9035
Water27015
1
A: Peptidyl-prolyl cis-trans isomerase
hetero molecules

A: Peptidyl-prolyl cis-trans isomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,62412
Polymers44,8192
Non-polymers1,80510
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_555-y,-x,-z+1/21
Buried area4660 Å2
ΔGint-137 kcal/mol
Surface area24200 Å2
MethodPISA
Unit cell
Length a, b, c (Å)76.752, 76.752, 103.597
Angle α, β, γ (deg.)90, 90, 90
Int Tables number96
Space group name H-MP43212

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Peptidyl-prolyl cis-trans isomerase / Prolyl isomerase


Mass: 22409.562 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 (E. coli) / Strain (production host): BL23 (DE3) / References: UniProt: A0A2S6FAG4, peptidylprolyl isomerase

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Non-polymers , 5 types, 20 molecules

#2: Chemical ChemComp-9QN / (1~{S},5~{S},6~{R})-10-[3,5-bis(chloranyl)phenyl]sulfonyl-5-(hydroxymethyl)-3-(pyridin-2-ylmethyl)-3,10-diazabicyclo[4.3.1]decan-2-one


Mass: 484.396 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H23Cl2N3O4S
#3: Chemical ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID / MES (buffer)


Mass: 195.237 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#4: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 15 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 3.32 Å3/Da / Density % sol: 62.9 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 15 %(w/v) PEG 6000, 500 mM zinc acetate dihydrate, 100 mM MES, 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: 2.4→61.67 Å / Num. obs: 19644 / % possible obs: 99.91 % / Redundancy: 8 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 11.1
Reflection shellResolution: 2.4→2.486 Å / Rmerge(I) obs: 0.08 / Num. unique obs: 1218 / % possible all: 99.75

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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: 2.4→52.24 Å / Cross valid method: FREE R-VALUE
RfactorNum. reflection% reflectionSelection details
Rfree0.2943 --RANDOM
Rwork0.2455 ---
obs-19488 55.53 %-
Refinement stepCycle: LAST / Resolution: 2.4→52.24 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1573 0 51 15 1639

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