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- PDB-1jvw: TRYPANOSOMA CRUZI MACROPHAGE INFECTIVITY POTENTIATOR (TCMIP) -

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Basic information

Entry
Database: PDB / ID: 1jvw
TitleTRYPANOSOMA CRUZI MACROPHAGE INFECTIVITY POTENTIATOR (TCMIP)
ComponentsMACROPHAGE INFECTIVITY POTENTIATOR
KeywordsISOMERASE / Macrophage Infectivity Potentiator / Trypanosoma cruzi / Chagas disease / X-ray crystal structure / rotamase
Function / homology
Function and homology information


peptidylprolyl isomerase / peptidyl-prolyl cis-trans isomerase activity / extracellular region
Similarity search - Function
Chitinase A; domain 3 - #40 / Chitinase A; domain 3 / 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 / Roll / Alpha Beta
Similarity search - Domain/homology
Macrophage infectivity potentiator
Similarity search - Component
Biological speciesTrypanosoma cruzi (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsPereira, P.J.B. / Vega, M.C. / Gonzalez-Rey, E. / Fernandez-Carazo, R. / Macedo-Ribeiro, S. / Gomis-Rueth, F.X. / Gonzalez, A. / Coll, M.
CitationJournal: EMBO Rep. / Year: 2002
Title: Trypanosoma cruzi macrophage infectivity potentiator has a rotamase core and a highly exposed alpha-helix.
Authors: Pereira, P.J. / Vega, M.C. / Gonzalez-Rey, E. / Fernandez-Carazo, R. / Macedo-Ribeiro, S. / Gomis-Ruth, F.X. / Gonzalez, A. / Coll, M.
History
DepositionAug 31, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 5, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 7, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_source
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_source.pdbx_synchrotron_site

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: MACROPHAGE INFECTIVITY POTENTIATOR


Theoretical massNumber of molelcules
Total (without water)18,8631
Polymers18,8631
Non-polymers00
Water4,882271
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)46.034, 34.587, 50.412
Angle α, β, γ (deg.)90.00, 91.57, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein MACROPHAGE INFECTIVITY POTENTIATOR / TCMIP / Peptidyl-prolyl cis-trans isomerase / PPiase / Rotamase


Mass: 18863.271 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Trypanosoma cruzi (eukaryote) / Production host: Escherichia coli (E. coli) / References: UniProt: Q09734, peptidylprolyl isomerase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 271 / Source method: isolated from a natural source / Formula: H2O

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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: 2.13 Å3/Da / Density % sol: 42.14 %
Crystal growTemperature: 277 K / Method: small tubes / pH: 7.5
Details: PMSF, Tris/HCl, pH 7.5, SMALL TUBES, temperature 277K
Crystal grow
*PLUS
Temperature: 4 ℃ / Method: microdialysis
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
15 mMTris-HCl11pH7.5
21 mMPMSF11

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: BW7B / Wavelength: 0.885 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Dec 20, 1997
RadiationMonochromator: SAGITALLY FOCUSED Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.885 Å / Relative weight: 1
ReflectionResolution: 1.7→19.2 Å / Num. obs: 17009 / % possible obs: 95.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0
Reflection shellResolution: 1.7→1.79 Å / % possible all: 89.8
Reflection
*PLUS
Highest resolution: 1.7 Å / Redundancy: 3.6 % / Num. measured all: 60547 / Rmerge(I) obs: 0.081
Reflection shell
*PLUS
Highest resolution: 1.7 Å / % possible obs: 89.8 % / Rmerge(I) obs: 0.097

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Processing

Software
NameVersionClassification
AMoREphasing
SHELXL-97refinement
MOSFLMdata reduction
CCP4(SCALA)data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.7→19 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.231 863 RANDOM
Rwork0.176 --
all0.179 16999 -
obs0.179 16999 -
Refinement stepCycle: LAST / Resolution: 1.7→19 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1286 0 0 271 1557
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_angle_d1.572
X-RAY DIFFRACTIONs_bond_d0.005
Software
*PLUS
Name: SHELXL / Version: 97 / Classification: refinement
Refinement
*PLUS
% reflection Rfree: 5 % / Rfactor all: 0.179 / Rfactor Rfree: 0.231 / Rfactor Rwork: 0.176
Solvent computation
*PLUS
Displacement parameters
*PLUS

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