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- PDB-8p3c: Full length structure of BpMIP with bound inhibitor NJS227. -

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Basic information

Entry
Database: PDB / ID: 8p3c
TitleFull length structure of BpMIP with bound inhibitor NJS227.
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 / protein folding / metal ion binding
Similarity search - Function
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
DI(HYDROXYETHYL)ETHER / : / Peptidyl-prolyl cis-trans isomerase
Similarity search - Component
Biological speciesBurkholderia pseudomallei (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.02 Å
AuthorsWhittaker, J.J. / Guskov, A. / Goretzki, B. / Hellmich, U.A.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research Foundation (DFG)390713860 Germany
CitationJournal: J.Med.Chem. / Year: 2025
Title: Structure and Dynamics of Macrophage Infectivity Potentiator Proteins from Pathogenic Bacteria and Protozoans Bound to Fluorinated Pipecolic Acid Inhibitors.
Authors: Perez Carrillo, V.H. / Whittaker, J.J. / Wiedemann, C. / Harder, J.M. / Lohr, T. / Jamithireddy, A.K. / Dajka, M. / Goretzki, B. / Joseph, B. / Guskov, A. / Harmer, N.J. / Holzgrabe, U. / Hellmich, U.A.
History
DepositionMay 17, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 12, 2024Provider: repository / Type: Initial release
Revision 1.1Mar 5, 2025Group: Database references / Structure summary / Category: citation / citation_author / pdbx_entry_details
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _pdbx_entry_details.has_protein_modification
Revision 1.2Mar 26, 2025Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID

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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)14,4695
Polymers13,6221
Non-polymers8474
Water1,44180
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: NMR relaxation study
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area440 Å2
ΔGint3 kcal/mol
Surface area7550 Å2
MethodPISA
Unit cell
Length a, b, c (Å)77.608, 77.608, 52.995
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: 13622.192 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Burkholderia pseudomallei (bacteria) / Gene: fbp, BPSS1823 / Production host: Escherichia coli (E. coli) / References: UniProt: Q63J95, peptidylprolyl isomerase
#2: Chemical ChemComp-WRX / (2~{S})-1-[(4-fluorophenyl)methylsulfonyl]-~{N}-[(2~{S})-3-(4-fluorophenyl)-1-oxidanylidene-1-(pyridin-3-ylmethylamino)propan-2-yl]piperidine-2-carboxamide


Mass: 556.624 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C28H30F2N4O4S
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 80 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationN

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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: 3.38 Å3/Da / Density % sol: 63.63 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 0.1 M BisTris pH 5.0 0.8 M Ammonium sulfate PEG3350 14 %

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.967 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 6, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.967 Å / Relative weight: 1
ReflectionResolution: 2.02→67.21 Å / Num. obs: 12368 / % possible obs: 99.76 % / Redundancy: 8 % / Biso Wilson estimate: 30.77 Å2 / CC1/2: 0.9 / Net I/σ(I): 9.5
Reflection shellResolution: 2.02→2.092 Å / Num. unique obs: 1234 / CC1/2: 0.78

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Processing

Software
NameVersionClassification
REFMAC5.8.0403refinement
XDSdata scaling
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.02→67.21 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.935 / SU B: 3.542 / SU ML: 0.096 / Cross valid method: THROUGHOUT / ESU R: 0.151 / ESU R Free: 0.146 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23525 529 4.2 %RANDOM
Rwork0.19398 ---
obs0.19582 11920 99.8 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 33.938 Å2
Baniso -1Baniso -2Baniso -3
1-0.03 Å20.02 Å20 Å2
2--0.03 Å20 Å2
3----0.11 Å2
Refinement stepCycle: 1 / Resolution: 2.02→67.21 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms961 0 58 80 1099
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0121038
X-RAY DIFFRACTIONr_bond_other_d0.0010.016930
X-RAY DIFFRACTIONr_angle_refined_deg2.4871.6831408
X-RAY DIFFRACTIONr_angle_other_deg0.6391.6042144
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.9975122
X-RAY DIFFRACTIONr_dihedral_angle_2_deg22.58659
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.50710142
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0980.2147
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.021207
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02245
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it4.1353.366485
X-RAY DIFFRACTIONr_mcbond_other4.1353.365485
X-RAY DIFFRACTIONr_mcangle_it6.5766.053605
X-RAY DIFFRACTIONr_mcangle_other6.5746.051606
X-RAY DIFFRACTIONr_scbond_it5.9614.051553
X-RAY DIFFRACTIONr_scbond_other5.9564.053554
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other8.7267.199803
X-RAY DIFFRACTIONr_long_range_B_refined11.64841.541076
X-RAY DIFFRACTIONr_long_range_B_other11.69940.521065
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.021→2.068 Å
RfactorNum. reflection% reflection
Rfree0.264 27 -
Rwork0.248 860 -
obs--99.89 %

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