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- PDB-9ibn: Crystal structure of the peptidyl-prolyl isomerase (PPIase) from ... -

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Basic information

Entry
Database: PDB / ID: 9ibn
TitleCrystal structure of the peptidyl-prolyl isomerase (PPIase) from E. faecium
ComponentsFoldase protein PrsA
KeywordsISOMERASE / peptidyl-prolyl isomerase / gram-positive bacteria / Protein folding
Function / homology
Function and homology information


peptidylprolyl isomerase / peptidyl-prolyl cis-trans isomerase activity / protein folding / plasma membrane
Similarity search - Function
Foldase protein PrsA / : / Trigger factor/SurA domain superfamily / PPIC-type PPIASE domain / PpiC-type peptidyl-prolyl cis-trans isomerase family profile. / Peptidyl-prolyl cis-trans isomerase, PpiC-type / Peptidyl-prolyl cis-trans isomerase domain superfamily / Prokaryotic membrane lipoprotein lipid attachment site profile.
Similarity search - Domain/homology
: / Foldase protein PrsA
Similarity search - Component
Biological speciesEnterococcus faecium (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.48 Å
AuthorsNapolitano, V. / Kramarska, E. / Berisio, R.
Funding supportEuropean Union, 1items
OrganizationGrant numberCountry
H2020 Marie Curie Actions of the European Commission860325European Union
CitationJournal: Febs J. / Year: 2025
Title: Crystal structure and biophysical characterisation of the enterococcal foldase PpiC, a cross-opsonic antigen against gram-positive nosocomial pathogens.
Authors: Napolitano, V. / Kramarska, E. / Ghilardi, O. / Romero-Saavedra, F. / Del Vecchio, P. / Squeglia, F. / Huebner, J. / Berisio, R.
History
DepositionFeb 12, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 16, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Foldase protein PrsA
B: Foldase protein PrsA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,71520
Polymers74,7522
Non-polymers1,96218
Water1,964109
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: light scattering
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5280 Å2
ΔGint-95 kcal/mol
Surface area31380 Å2
Unit cell
Length a, b, c (Å)67.486, 69.674, 87.413
Angle α, β, γ (deg.)90.00, 102.81, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Foldase protein PrsA


Mass: 37376.219 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterococcus faecium (bacteria)
Gene: prsA, B1P95_07975, CUN04_03160, CUS10_12795, CYQ77_09495, EB01_00008, EB12_02080, GBM44_12185, GBM73_11745, KYX88_03295, P6Z85_01695
Production host: Escherichia coli (E. coli) / References: UniProt: A0A132Z550, peptidylprolyl isomerase
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical
ChemComp-CD / CADMIUM ION


Mass: 112.411 Da / Num. of mol.: 15 / Source method: obtained synthetically / Formula: Cd
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 109 / 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: 2.68 Å3/Da / Density % sol: 54.12 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop
Details: 0.1 M Sodium acetate trihydrate pH 4.6, 0.1 M Cadmium chloride hydrate, 30% v/v Polyethylene glycol 400.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID30B / Wavelength: 0.8731 Å
DetectorType: DECTRIS EIGER X 4M / Detector: PIXEL / Date: Mar 10, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8731 Å / Relative weight: 1
ReflectionResolution: 2.479→65.81 Å / Num. obs: 17572 / % possible obs: 86.7 % / Redundancy: 2.8 % / CC1/2: 0.823 / Net I/σ(I): 5.1
Reflection shellResolution: 2.479→7.958 Å / Num. unique obs: 879 / CC1/2: 0.02

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Processing

Software
NameVersionClassification
REFMAC5.8.0430refinement
XDSdata reduction
PHASERphasing
AutoProcessdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.48→65.81 Å / Cor.coef. Fo:Fc: 0.918 / Cor.coef. Fo:Fc free: 0.872 / SU B: 25.343 / SU ML: 0.304 / Cross valid method: THROUGHOUT / ESU R Free: 0.378 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.2501 872 5 %RANDOM
Rwork0.20691 ---
obs0.20916 16697 62.12 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 46.424 Å2
Baniso -1Baniso -2Baniso -3
1-0.64 Å20 Å2-0.21 Å2
2--0.78 Å20 Å2
3----1.2 Å2
Refinement stepCycle: 1 / Resolution: 2.48→65.81 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4189 0 33 109 4331
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0124293
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.9281.8255794
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5915552
X-RAY DIFFRACTIONr_dihedral_angle_2_deg9.03155
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.88810784
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.1320.2673
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.023178
X-RAY DIFFRACTIONr_gen_planes_other
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_it2.6592.7752202
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it4.5944.9732756
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it3.2932.912091
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined8.68730.496421
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.48→2.543 Å
RfactorNum. reflection% reflection
Rfree0.267 5 -
Rwork0.286 76 -
obs--3.93 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.3181.0429-1.14530.9605-0.76222.0677-0.12160.2390.2106-0.23380.18340.1694-0.1984-0.3964-0.06180.17550.019-0.03010.07940.00630.12718.9562-5.3915-20.4051
20.6110.80410.94051.12911.06411.8971-0.04590.1084-0.1076-0.17890.0924-0.19890.1820.3246-0.04650.16680.08180.09050.07550.01240.1044-18.5443-33.6824-20.2909
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A29 - 401
2X-RAY DIFFRACTION2B30 - 402

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