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- PDB-1meg: CRYSTAL STRUCTURE OF A CARICAIN D158E MUTANT IN COMPLEX WITH E-64 -

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Basic information

Entry
Database: PDB / ID: 1meg
TitleCRYSTAL STRUCTURE OF A CARICAIN D158E MUTANT IN COMPLEX WITH E-64
ComponentsCARICAIN
KeywordsHYDROLASE / CYSTEINE PROTEINASE / THIOL PROTEASE
Function / homology
Function and homology information


caricain / cysteine-type peptidase activity / proteolysis
Similarity search - Function
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 ...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
Chem-E64 / ETHANOL / Caricain
Similarity search - Component
Biological speciesCarica papaya (papaya)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2 Å
AuthorsKaterelos, N.A.
Citation
Journal: FEBS Lett. / Year: 1996
Title: Crystal structure of a caricain D158E mutant in complex with E-64.
Authors: Katerelos, N.A. / Taylor, M.A. / Scott, M. / Goodenough, P.W. / Pickersgill, R.W.
#1: Journal: To be Published
Title: Rapid Kinetics Studies and Structural Determination of a Cysteine Proteinase Mutant Implies that Residue Asp 158 in Caricain Has a Major Effect Upon the Ability of the Active Site Histidine to ...Title: Rapid Kinetics Studies and Structural Determination of a Cysteine Proteinase Mutant Implies that Residue Asp 158 in Caricain Has a Major Effect Upon the Ability of the Active Site Histidine to Protonate a Dipyridyl Probe
Authors: Katerelos, A. / Goodenough, P.W.
#2: Journal: Protein Eng. / Year: 1994
Title: An Unequivocal Example of Cysteine Proteinase Activity Affected by Multiple Electrostatic Interactions
Authors: Taylor, M.A. / Baker, K.C. / Connerton, I.F. / Cummings, N.J. / Harris, G.W. / Henderson, I.M. / Jones, S.T. / Pickersgill, R.W. / Sumner, I.G. / Warwicker, J. / al., et
#3: Journal: Gene / Year: 1993
Title: Nucleotide Sequence and Expression in Escherichia Coli of Cdnas Encoding Papaya Proteinase Omega from Carica Papaya
Authors: Revell, D.F. / Cummings, N.J. / Baker, K.C. / Collins, M.E. / Taylor, M.A. / Sumner, I.G. / Pickersgill, R.W. / Connerton, I.F. / Goodenough, P.W.
#4: Journal: Protein Eng. / Year: 1992
Title: Active Papain Renatured and Processed from Insoluble Recombinant Propapain Expressed in Escherichia Coli
Authors: Taylor, M.A. / Pratt, K.A. / Revell, D.F. / Baker, K.C. / Sumner, I.G. / Goodenough, P.W.
History
DepositionMay 4, 1996Processing site: BNL
Revision 1.0Jan 11, 1997Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 3, 2021Group: Database references / Derived calculations
Category: database_2 / struct_conn ...database_2 / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Nov 20, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: CARICAIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,7463
Polymers23,3401
Non-polymers4062
Water1,69394
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)53.450, 65.330, 64.370
Angle α, β, γ (deg.)90.00, 111.60, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein CARICAIN / PAPAYA PROTEINASE / PROTEASE OMEGA


Mass: 23339.770 Da / Num. of mol.: 1 / Mutation: D158E
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Carica papaya (papaya) / Plasmid: PLYSS / Production host: Escherichia coli (E. coli) / Strain (production host): PET / References: UniProt: P10056, caricain
#2: Chemical ChemComp-E64 / N-[N-[1-HYDROXYCARBOXYETHYL-CARBONYL]LEUCYLAMINO-BUTYL]-GUANIDINE


Mass: 360.429 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H30N5O5
#3: Chemical ChemComp-EOH / ETHANOL


Mass: 46.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 94 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.24 Å3/Da / Density % sol: 34.2 %
Crystal
*PLUS
Crystal grow
*PLUS
Temperature: 18 ℃ / pH: 8 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
113 mg/mlprotein1drop
210 mMTris1drop
329 %PEG10001reservoir
40.3 M1reservoir(NH4)2SO4

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-6A / Wavelength: 1
DetectorType: FUJI / Detector: IMAGE PLATE / Date: Nov 10, 1994
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionNum. obs: 12010 / % possible obs: 86 % / Redundancy: 3.5 % / Rmerge(I) obs: 0.06
Reflection
*PLUS
Highest resolution: 2 Å / Lowest resolution: 7.72 Å / % possible obs: 86 % / Num. measured all: 42446 / Rmerge(I) obs: 0.06

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Processing

Software
NameClassification
DENZOdata reduction
X-PLORmodel building
X-PLORrefinement
X-PLORphasing
RefinementResolution: 2→10 Å / σ(F): 2
Details: ATOMS C13, C14, C15, N3, C16, N4 AND N5 OF E64 WERE NOT VISIBLE IN DENSITY BECAUSE OF THE HIGH MOBILITY OF THAT PART OF THE E-64 MOLECULE WHICH ACCOUNTS FOR THEIR HIGH TEMPERATURE FACTORS.
RfactorNum. reflection
Rwork0.193 -
obs0.193 11858
Displacement parametersBiso mean: 10.15 Å2
Refinement stepCycle: LAST / Resolution: 2→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1642 0 1 94 1737
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.012
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.74
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d25.56
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Software
*PLUS
Name: X-PLOR / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_angle_deg1.7
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg25.6
X-RAY DIFFRACTIONx_improper_angle_d1.7

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