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- PDB-1yal: CARICA PAPAYA CHYMOPAPAIN AT 1.7 ANGSTROMS RESOLUTION -

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Basic information

Entry
Database: PDB / ID: 1yal
TitleCARICA PAPAYA CHYMOPAPAIN AT 1.7 ANGSTROMS RESOLUTION
ComponentsCHYMOPAPAIN
KeywordsHYDROLASE / THIOL PROTEASE
Function / homology
Function and homology information


chymopapain / 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
Biological speciesCarica papaya (papaya)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsMaes, D. / Bouckaert, J. / Poortmans, F. / Wyns, L. / Looze, Y.
Citation
Journal: Biochemistry / Year: 1996
Title: Structure of chymopapain at 1.7 A resolution.
Authors: Maes, D. / Bouckaert, J. / Poortmans, F. / Wyns, L. / Looze, Y.
#1: Journal: To be Published
Title: Preparation of Crystals of Chymopapain Diffracting to 1.4 Angstroms Resolution
Authors: Azarkan, M. / Maes, D. / Bouckaert, J. / Thi, M.-H.D. / Wyns, L. / Looze, Y.
History
DepositionJun 20, 1996Processing site: BNL
Revision 1.0Dec 23, 1996Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Apr 4, 2018Group: Advisory / Data collection / Other
Category: diffrn_source / pdbx_database_status / pdbx_unobs_or_zero_occ_atoms
Item: _diffrn_source.type / _pdbx_database_status.process_site
Revision 1.4Apr 18, 2018Group: Data collection / Category: diffrn_detector / Item: _diffrn_detector.detector
Revision 1.5Aug 9, 2023Group: Advisory / Database references ...Advisory / Database references / Derived calculations / Refinement description
Category: database_2 / pdbx_initial_refinement_model ...database_2 / pdbx_initial_refinement_model / pdbx_unobs_or_zero_occ_atoms / struct_conn / struct_ref_seq_dif
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_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_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: CHYMOPAPAIN


Theoretical massNumber of molelcules
Total (without water)23,7781
Polymers23,7781
Non-polymers00
Water3,999222
1
A: CHYMOPAPAIN

A: CHYMOPAPAIN


Theoretical massNumber of molelcules
Total (without water)47,5562
Polymers47,5562
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_556-x,y,-z+11
Unit cell
Length a, b, c (Å)145.180, 32.350, 47.420
Angle α, β, γ (deg.)90.00, 98.37, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein CHYMOPAPAIN


Mass: 23777.971 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Details: THE ACTIVE SITE CYS 25 AS WELL AS CYS 117 ARE PROTECTED WITH A THIOMETHYL GROUP
Source: (natural) Carica papaya (papaya) / Organ: FRUIT / References: UniProt: P14080, chymopapain
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 222 / 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: 2

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Sample preparation

CrystalDensity Matthews: 2.32 Å3/Da / Density % sol: 46.88 %
Crystal growpH: 7.6 / Details: pH 7.6
Crystal grow
*PLUS
Temperature: 20 ℃ / Method: unknown
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
16 mg/mlenzyme11
22 Msodium acetate11

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: ROTATING ANODE / Type: OTHER / Wavelength: 1.5418
DetectorType: ENRAF-NONIUS FAST / Detector: DIFFRACTOMETER / Date: Dec 13, 1995
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.7→19 Å / Num. obs: 20199 / % possible obs: 84 % / Observed criterion σ(I): 0 / Biso Wilson estimate: 18.33 Å2 / Rmerge(I) obs: 0.066 / Net I/σ(I): 7.6
Reflection shellResolution: 1.7→1.79 Å / Redundancy: 1.3 % / Rmerge(I) obs: 0.22 / Mean I/σ(I) obs: 5.5 / % possible all: 69
Reflection
*PLUS
Num. measured all: 39180
Reflection shell
*PLUS
% possible obs: 68.8 % / Num. unique obs: 2374 / Rmerge(I) obs: 0.222

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Processing

Software
NameVersionClassification
MADNESdata collection
CCP4data reduction
X-PLOR3.1model building
X-PLOR3.1refinement
MADNESdata reduction
CCP4data scaling
X-PLOR3.1phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1PPO

1ppo


Resolution: 1.7→9.5 Å / σ(F): 0
RfactorNum. reflection% reflection
Rwork0.1923 --
obs0.1923 20060 84 %
Displacement parametersBiso mean: 16.74 Å2
Refine analyzeLuzzati coordinate error obs: 0.1 Å / Luzzati d res low obs: 9.5 Å
Refinement stepCycle: LAST / Resolution: 1.7→9.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1667 0 4 222 1893
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.011
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_deg1.54
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d24.63
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.44
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
LS refinement shellResolution: 1.7→1.79 Å
RfactorNum. reflection% reflection
Rwork0.3 2017 -
obs--69 %
Software
*PLUS
Name: X-PLOR / Version: 3.1 / Classification: refinement
Refinement
*PLUS
Rfactor obs: 0.192
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_angle_deg1.57
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg24.63
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.46
LS refinement shell
*PLUS
Rfactor Rwork: 0.3

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