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- PDB-3e1z: Crystal structure of the parasite protesase inhibitor chagasin in... -

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Basic information

Entry
Database: PDB / ID: 3e1z
TitleCrystal structure of the parasite protesase inhibitor chagasin in complex with papain
Components
  • Chagasin
  • Papain
KeywordsHYDROLASE INHIBITOR/HYDROLASE / chagasin-papain complex / papain / Chagas disease / cysteine proteinases / protein inhibitors / Cytoplasmic vesicle / Protease inhibitor / Thiol protease inhibitor / Allergen / Hydrolase / Protease / Thiol protease / Zymogen / HYDROLASE INHIBITOR-HYDROLASE COMPLEX
Function / homology
Function and homology information


ciliary pocket / papain / cysteine-type endopeptidase inhibitor activity / serpin family protein binding / proteolysis involved in protein catabolic process / cytoplasmic vesicle / lysosome / cysteine-type endopeptidase activity / cell surface / extracellular space
Similarity search - Function
Immunoglobulin-like - #2020 / Proteinase inhibitor I42, chagasin / Chagasin-like superfamily / Chagasin family peptidase inhibitor I42 / Cathepsin propeptide inhibitor domain (I29) / Cathepsin propeptide inhibitor domain (I29) / Cathepsin propeptide inhibitor domain (I29) / Papain-like cysteine endopeptidase / : / Cysteine peptidase, asparagine active site ...Immunoglobulin-like - #2020 / Proteinase inhibitor I42, chagasin / Chagasin-like superfamily / Chagasin family peptidase inhibitor I42 / Cathepsin propeptide inhibitor domain (I29) / Cathepsin propeptide inhibitor domain (I29) / Cathepsin propeptide inhibitor domain (I29) / Papain-like cysteine endopeptidase / : / Cysteine peptidase, asparagine active site / Eukaryotic thiol (cysteine) proteases asparagine active site. / Cysteine peptidase, histidine active site / Eukaryotic thiol (cysteine) proteases histidine active site. / Peptidase C1A, papain C-terminal / Papain family cysteine protease / Papain family cysteine protease / Cysteine proteinases / Cysteine peptidase, cysteine active site / Eukaryotic thiol (cysteine) proteases cysteine active site. / Cathepsin B; Chain A / Papain-like cysteine peptidase superfamily / Alpha-Beta Complex / Immunoglobulin-like / Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
ACETIC ACID / FORMIC ACID / Papain / Chagasin
Similarity search - Component
Biological speciesTrypanosoma cruzi (eukaryote)
Carica papaya (papaya)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.86 Å
AuthorsRedzynia, I. / Bujacz, G. / Bujacz, A. / Ljunggren, A. / Abrahamson, M. / Jaskolski, M.
CitationJournal: Febs J. / Year: 2009
Title: Crystal structure of the parasite inhibitor chagasin in complex with papain allows identification of structural requirements for broad reactivity and specificity determinants for target proteases.
Authors: Redzynia, I. / Ljunggren, A. / Bujacz, A. / Abrahamson, M. / Jaskolski, M. / Bujacz, G.
History
DepositionAug 5, 2008Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jan 27, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_source / pdbx_initial_refinement_model / pdbx_struct_special_symmetry / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_source.pdbx_synchrotron_site / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Chagasin
B: Papain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,09214
Polymers35,5072
Non-polymers58612
Water5,368298
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1710 Å2
ΔGint-12 kcal/mol
Surface area13940 Å2
MethodPISA
Unit cell
Length a, b, c (Å)99.13, 99.13, 159.49
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number97
Space group name H-MI422
Components on special symmetry positions
IDModelComponents
11B-313-

HOH

21B-428-

HOH

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Components

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Protein , 2 types, 2 molecules AB

#1: Protein Chagasin / cysteine protease inhibitor


Mass: 12054.476 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Trypanosoma cruzi (eukaryote) / Gene: cha / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: Q966X9
#2: Protein Papain / cysteine protease / Papaya proteinase I / PPI


Mass: 23452.301 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Carica papaya (papaya) / Strain: papaya / References: UniProt: P00784, papain

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Non-polymers , 4 types, 310 molecules

#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#4: Chemical
ChemComp-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: CH2O2
#5: Chemical ChemComp-ACY / ACETIC ACID


Mass: 60.052 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H4O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 298 / 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: 2.76 Å3/Da / Density % sol: 55.41 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 2.0M ammonium formate, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X13 / Wavelength: 0.8086 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Dec 7, 2007 / Details: mirrors
RadiationMonochromator: Si [111], horizontally focussing / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8086 Å / Relative weight: 1
ReflectionResolution: 1.86→84.22 Å / Num. all: 33803 / Num. obs: 33263 / % possible obs: 98.4 % / Observed criterion σ(I): -1 / Redundancy: 10.5 % / Biso Wilson estimate: 22.36 Å2 / Rmerge(I) obs: 0.09 / Net I/σ(I): 22.1
Reflection shellResolution: 1.86→1.93 Å / Redundancy: 6.8 % / Rmerge(I) obs: 0.557 / Mean I/σ(I) obs: 2.1 / Num. unique all: 2946 / % possible all: 88.8

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Processing

Software
NameVersionClassification
REFMAC5.4.0062refinement
HKL-2000data collection
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2NQD

2nqd


Resolution: 1.86→60 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.942 / SU B: 5.322 / SU ML: 0.082 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / ESU R: 0.119 / ESU R Free: 0.12 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20777 1694 5.1 %RANDOM
Rwork0.16423 ---
all0.16645 33803 --
obs0.16639 31568 98.35 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 27.6 Å2
Baniso -1Baniso -2Baniso -3
1--0.97 Å20 Å20 Å2
2---0.97 Å20 Å2
3---1.94 Å2
Refinement stepCycle: LAST / Resolution: 1.86→60 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2557 0 1 332 2890
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0222665
X-RAY DIFFRACTIONr_angle_refined_deg1.6141.943623
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3845336
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.50923.548124
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.88215402
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.2011515
X-RAY DIFFRACTIONr_chiral_restr0.1150.2372
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0212095
X-RAY DIFFRACTIONr_mcbond_it0.9741.51634
X-RAY DIFFRACTIONr_mcangle_it1.60422601
X-RAY DIFFRACTIONr_scbond_it2.70231031
X-RAY DIFFRACTIONr_scangle_it4.1614.51014
LS refinement shellResolution: 1.858→1.907 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.335 115 -
Rwork0.272 2026 -
obs--86.96 %
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)
12.0290.72781.37581.72381.01112.29480.0676-0.1126-0.0634-0.1237-0.1217-0.02530.0854-0.30760.0541-0.0765-0.04210.00660.0212-0.0578-0.1737.1744.777215.2074
21.0809-0.0583-0.03870.6506-0.05080.68180.02370.05450.0201-0.0558-0.02220.00670.0112-0.0712-0.0016-0.041-0.00970.0016-0.0298-0.0146-0.018154.760523.35732.2084
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA2 - 1102 - 110
2X-RAY DIFFRACTION2BB1 - 2121 - 212

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