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- PDB-2cio: The high resolution x-ray structure of papain complexed with frag... -

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Basic information

Entry
Database: PDB / ID: 2cio
TitleThe high resolution x-ray structure of papain complexed with fragments of the Trypanosoma brucei cysteine protease inhibitor ICP.
Components
  • INHIBITOR OF CYSTEINE PEPTIDASE
  • PAPAIN
KeywordsHYDROLASE/INHIBITOR / COMPLEX HYDROLASE-INHIBITOR / ICP / CYSTEINE PROTEASE / INHIBITOR / TRYPANOSOMA BRUCEI / ALLERGEN / PROTEASE / THIOL PROTEASE / ZYMOGEN / HYDROLASE / HYDROLASE-INHIBITOR complex
Function / homology
Function and homology information


papain / serpin family protein binding / cysteine-type peptidase activity / proteolysis
Similarity search - Function
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. ...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 / Alpha Beta
Similarity search - Domain/homology
ACETATE ION / Papain / Inhibitor of cysteine peptidase
Similarity search - Component
Biological speciesTRYPANOSOMA BRUCEI (eukaryote)
CARICA PAPAYA (papaya)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsAlphey, M.S. / Hunter, W.N.
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2006
Title: High-Resolution Complex of Papain with Remnants of a Cysteine Protease Inhibitor Derived from Trypanosoma Brucei
Authors: Alphey, M.S. / Hunter, W.N.
History
DepositionMar 24, 2006Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 18, 2006Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jan 24, 2018Group: Source and taxonomy / Category: entity_src_gen
Item: _entity_src_gen.pdbx_host_org_ncbi_taxonomy_id / _entity_src_gen.pdbx_host_org_scientific_name ..._entity_src_gen.pdbx_host_org_ncbi_taxonomy_id / _entity_src_gen.pdbx_host_org_scientific_name / _entity_src_gen.pdbx_host_org_strain / _entity_src_gen.pdbx_host_org_variant
Revision 1.4Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_conn.pdbx_leaving_atom_flag
Remark 700 SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: PAPAIN
B: INHIBITOR OF CYSTEINE PEPTIDASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,3107
Polymers36,9492
Non-polymers3615
Water2,900161
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)42.323, 46.118, 95.697
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein PAPAIN / / PAPAYA PROTEINASE I / PPI / ALLERGEN / CARP1PAPAIN


Mass: 23499.314 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: PURCHASED FROM SIGMA / Source: (natural) CARICA PAPAYA (papaya) / References: UniProt: P00784, papain
#2: Protein INHIBITOR OF CYSTEINE PEPTIDASE / CYSTEINE PROTEASE INHIBITOR / ICP


Mass: 13449.203 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: TWO PEPTIDE FRAGMENTS FROM DIGESTION OF ICP / Source: (gene. exp.) TRYPANOSOMA BRUCEI (eukaryote) / Plasmid: PBP117 / Production host: ESCHERICHIA COLI BL21(DE3) (bacteria) / Variant (production host): C43 / References: UniProt: Q868H0
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H3O2
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 161 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsPROTEIN USED IN EXPERIMENT WAS COMMERCIALLY AVAILABLE AND ALREADY HAD REMOVED SIGNAL AND PROPEPTIDE ...PROTEIN USED IN EXPERIMENT WAS COMMERCIALLY AVAILABLE AND ALREADY HAD REMOVED SIGNAL AND PROPEPTIDE SEQUENCE FROM N- TERMINUS.

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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: 2.2 Å3/Da / Density % sol: 44 %
Crystal growpH: 7.5 / Details: 50% ETHANOL, 0.01M NA ACETATE, pH 7.50

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.9756
DetectorType: ADSC CCD / Detector: CCD / Date: Dec 8, 2005 / Details: TOROIDAL MIRRORS
RadiationMonochromator: SI(III) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9756 Å / Relative weight: 1
ReflectionResolution: 1.5→95.7 Å / Num. obs: 60928 / % possible obs: 100 % / Observed criterion σ(I): 2 / Redundancy: 13.6 % / Biso Wilson estimate: 16.24 Å2 / Rmerge(I) obs: 0.1 / Net I/σ(I): 21.4
Reflection shellResolution: 1.5→1.58 Å / Redundancy: 13.8 % / Rmerge(I) obs: 0.63 / Mean I/σ(I) obs: 3.7 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 9PAP

9pap


Resolution: 1.5→95.7 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.942 / SU B: 3.23 / SU ML: 0.056 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.112 / ESU R Free: 0.089 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. LYS211-ASN212 IS AT THE C-TERMINUS OF THE PROTEIN CHAIN WHERE ELECTRON DENSITY WAS POORLY DEFINED
RfactorNum. reflection% reflectionSelection details
Rfree0.225 1551 5.02 %RANDOM
Rwork0.177 ---
obs0.179 30823 100 %-
Solvent computationIon probe radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 19.83 Å2
Baniso -1Baniso -2Baniso -3
1--0.739 Å20 Å20 Å2
2--0.764 Å20 Å2
3----0.025 Å2
Refinement stepCycle: LAST / Resolution: 1.5→95.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1690 0 24 161 1875
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0221870
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.4161.9562562
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6175246
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.33923.44490
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.9715291
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.9491514
X-RAY DIFFRACTIONr_chiral_restr0.0980.2261
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.021496
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2340.2940
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.320.21270
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2050.2185
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.230.267
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2210.219
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.3661.51158
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.06521817
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.9113839
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.4244.5729
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
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: 6.69→95.7 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.348 23
Rwork0.252 395

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