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

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Basic information

Entry
Database: PDB / ID: 8bjc
TitleFull length structure of the apo-state LpMIP.
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
Peptidyl-prolyl cis-trans isomerase
Similarity search - Component
Biological speciesLegionella pneumophila (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.71 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 3, 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
B: Peptidyl-prolyl cis-trans isomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,9786
Polymers22,1481
Non-polymers8295
Water2,000111
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: NMR relaxation study
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1330 Å2
ΔGint13 kcal/mol
Surface area13240 Å2
Unit cell
Length a, b, c (Å)77.773, 77.773, 103.789
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

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Protein , 1 types, 1 molecules B

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


Mass: 22148.326 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

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Non-polymers , 5 types, 116 molecules

#2: 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
#3: Chemical ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES / HEPES


Mass: 238.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H18N2O4S / Comment: pH buffer*YM
#4: 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
#5: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 111 / 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: 3.43 Å3/Da / Density % sol: 64.15 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6
Details: 20 %(w/v) PEG 6000, 500 mM zinc acetate dihydrate, 100 mM MES, pH 6.0.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.9673 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: 0.9673 Å / Relative weight: 1
ReflectionResolution: 1.71→62.24 Å / Num. obs: 19488 / % possible obs: 76.74 % / Redundancy: 12 % / Rmerge(I) obs: 0.09 / Net I/σ(I): 12.2
Reflection shellResolution: 1.71→1.772 Å / Redundancy: 7 % / Num. unique obs: 14883 / Rrim(I) all: 0.09 / % possible all: 55.53

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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: 1.71→62.24 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 36.25 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2878 971 4.98 %RANDOM
Rwork0.2394 ---
obs0.2418 19486 55.41 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.71→62.24 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1602 0 1 111 1714
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0051625
X-RAY DIFFRACTIONf_angle_d0.9622190
X-RAY DIFFRACTIONf_dihedral_angle_d17.844243
X-RAY DIFFRACTIONf_chiral_restr0.043240
X-RAY DIFFRACTIONf_plane_restr0.007276
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.71-1.80.3054240.2758374X-RAY DIFFRACTION80
1.8-1.910.3176310.3095788X-RAY DIFFRACTION77
1.91-2.050.2549650.24651439X-RAY DIFFRACTION32
2.09-2.270.27421040.26842149X-RAY DIFFRACTION53
2.27-2.590.27722570.26584734X-RAY DIFFRACTION99
2.59-3.270.28582540.24764440X-RAY DIFFRACTION93
3.27-6.20.2992360.21924591X-RAY DIFFRACTION91

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