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- PDB-8p42: Full length structure of TcMIP with bound inhibitor NJS227. -

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Basic information

Entry
Database: PDB / ID: 8p42
TitleFull length structure of TcMIP with bound inhibitor NJS227.
ComponentsMacrophage infectivity potentiator
KeywordsSTRUCTURAL PROTEIN / Macrophage / potentiator / soluble / protein
Function / homology
Function and homology information


peptidylprolyl isomerase / peptidyl-prolyl cis-trans isomerase activity / extracellular region
Similarity search - Function
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
DI(HYDROXYETHYL)ETHER / : / Macrophage infectivity potentiator
Similarity search - Component
Biological speciesTrypanosoma cruzi (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.64 Å
AuthorsWhittaker, J.J. / Guskov, A. / Goretzki, B. / Hellmich, U.A.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research Foundation (DFG)390713860 Germany
CitationJournal: To Be Published
Title: Structural dynamics of macrophage infectivity potentiator proteins (MIPs) are differentially modulated by inhibitors and appendage domains
Authors: Whittaker, J.J. / Guskov, A. / Goretzki, B. / Hellmich, U.A.
History
DepositionMay 19, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 12, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Macrophage infectivity potentiator
D: Macrophage infectivity potentiator
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,9118
Polymers36,3732
Non-polymers1,5386
Water1,27971
1
A: Macrophage infectivity potentiator
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,0625
Polymers18,1871
Non-polymers8754
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
D: Macrophage infectivity potentiator
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,8493
Polymers18,1871
Non-polymers6632
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)87.744, 87.744, 57.505
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number76
Space group name H-MP41

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Components

#1: Protein Macrophage infectivity potentiator / Peptidyl-prolyl cis-trans isomerase / PPIase / Rotamase


Mass: 18186.549 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Trypanosoma cruzi (eukaryote) / Gene: MIP / Production host: Escherichia coli (E. coli) / References: UniProt: Q09734, 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.: 2 / Source method: obtained synthetically / Formula: C28H30F2N4O4S
#3: Chemical
ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C4H10O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 71 / Source method: isolated from a natural source / Formula: H2O
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: 3.09 Å3/Da / Density % sol: 60.22 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 5mM TRIS pH 7.5 150mM NaCl PEG2000 12 %

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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: Sep 10, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.967 Å / Relative weight: 1
ReflectionResolution: 2.64→34.9 Å / Num. obs: 12330 / % possible obs: 94.84 % / Redundancy: 9 % / CC1/2: 0.92 / Net I/σ(I): 13.2
Reflection shellResolution: 2.64→2.74 Å / Num. unique obs: 1225 / CC1/2: 0.84

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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: 2.64→34.88 Å / SU ML: 0.38 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 26.01 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2819 649 5.27 %
Rwork0.2241 --
obs0.227 12326 94.9 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.64→34.88 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2522 0 106 71 2699
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0032674
X-RAY DIFFRACTIONf_angle_d0.6843587
X-RAY DIFFRACTIONf_dihedral_angle_d9.207404
X-RAY DIFFRACTIONf_chiral_restr0.056361
X-RAY DIFFRACTIONf_plane_restr0.006475
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.64-2.850.35541350.31332303X-RAY DIFFRACTION95
2.85-3.130.30291170.26522359X-RAY DIFFRACTION96
3.13-3.590.33071580.25562350X-RAY DIFFRACTION97
3.59-4.510.25961260.21012291X-RAY DIFFRACTION93
4.52-34.880.22431130.17222374X-RAY DIFFRACTION93

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