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- PDB-8r39: Full-length LpMIP mutant Y16F -

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Basic information

Entry
Database: PDB / ID: 8r39
TitleFull-length LpMIP mutant Y16F
ComponentsPeptidyl-prolyl cis-trans isomerase
KeywordsSTRUCTURAL PROTEIN / Potentiator Mutant Legionalla
Function / homology
Function and homology information


peptidyl-prolyl cis-trans isomerase activity / peptidylprolyl isomerase / 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 / FKBP-type peptidyl-prolyl cis-trans isomerase domain / Peptidyl-prolyl cis-trans isomerase domain superfamily
Similarity search - Domain/homology
DI(HYDROXYETHYL)ETHER / Peptidyl-prolyl cis-trans isomerase
Similarity search - Component
Biological speciesLegionella pneumophila (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsWhittaker, J.J. / Guskov, A.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research Foundation (DFG)390713860 Germany
CitationJournal: To Be Published
Title: Full-length LpMIP mutant Y16F
Authors: Whittaker, J.J. / Guskov, A.
History
DepositionNov 8, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 20, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
C: Peptidyl-prolyl cis-trans isomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,1008
Polymers22,3941
Non-polymers7077
Water1,15364
1
C: Peptidyl-prolyl cis-trans isomerase
hetero molecules

C: Peptidyl-prolyl cis-trans isomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,20116
Polymers44,7872
Non-polymers1,41314
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation1
Buried area5800 Å2
ΔGint-38 kcal/mol
Surface area24670 Å2
Unit cell
Length a, b, c (Å)78.444, 78.444, 105.176
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 C

#1: Protein Peptidyl-prolyl cis-trans isomerase


Mass: 22393.562 Da / Num. of mol.: 1 / Mutation: Y16F
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Legionella pneumophila (bacteria) / Gene: C3927_03235 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A2S6FAG4

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Non-polymers , 5 types, 71 molecules

#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-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID


Mass: 195.237 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#4: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3
#5: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: Na
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 64 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 3.6 Å3/Da / Density % sol: 65.82 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: MES 50mM NaCl 150mM PEG3350 14%

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-1 / Wavelength: 0.9677 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Sep 28, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9677 Å / Relative weight: 1
ReflectionResolution: 2.2→49.06 Å / Num. obs: 25869 / % possible obs: 99.9 % / Redundancy: 8 % / CC1/2: 0.95 / Net I/σ(I): 14
Reflection shellResolution: 2.2→4.9 Å / Num. unique obs: 3405 / CC1/2: 0.78

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Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
XDSdata scaling
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.2→49.06 Å / SU ML: 0.24 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 26.32 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.271 838 4.85 %
Rwork0.2178 --
obs0.2203 17281 99.93 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.2→49.06 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1572 0 45 64 1681
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0141644
X-RAY DIFFRACTIONf_angle_d1.4742203
X-RAY DIFFRACTIONf_dihedral_angle_d14.223239
X-RAY DIFFRACTIONf_chiral_restr0.061243
X-RAY DIFFRACTIONf_plane_restr0.01280
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2-2.340.28421310.23892696X-RAY DIFFRACTION100
2.34-2.520.26541370.23452685X-RAY DIFFRACTION100
2.52-2.770.32721260.2432708X-RAY DIFFRACTION100
2.77-3.170.3031410.25352705X-RAY DIFFRACTION100
3.17-40.25431510.21652740X-RAY DIFFRACTION100
4-4.90.25861520.19582909X-RAY DIFFRACTION100

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