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- PDB-3usv: Structure of the precursor of a thermostable variant of papain at... -

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Basic information

Entry
Database: PDB / ID: 3usv
TitleStructure of the precursor of a thermostable variant of papain at 3.8 A resolution from a crystal soaked at pH 4
ComponentsPapain
KeywordsHYDROLASE / protease
Function / homology
Function and homology information


papain / serpin family protein binding / 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: 3.8 Å
AuthorsRoy, S. / Choudhury, D. / Biswas, S. / Dattagupta, J.K.
CitationJournal: To be Published
Title: Crystallographic analysis of pro-papain variant elucidates the structural basis of the step-wise activation mechanism of the zymogen
Authors: Roy, S. / Choudhury, D. / Biswas, S. / Dattagupta, J.K.
History
DepositionNov 24, 2011Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Nov 28, 2012Provider: repository / Type: Initial release
Revision 1.1Nov 8, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Papain
C: Papain


Theoretical massNumber of molelcules
Total (without water)82,1352
Polymers82,1352
Non-polymers00
Water0
1
A: Papain


Theoretical massNumber of molelcules
Total (without water)41,0681
Polymers41,0681
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: Papain


Theoretical massNumber of molelcules
Total (without water)41,0681
Polymers41,0681
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)42.853, 75.970, 109.711
Angle α, β, γ (deg.)90.00, 97.71, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Papain / / Papaya proteinase I / PPI


Mass: 41067.570 Da / Num. of mol.: 2 / Fragment: UNP residues 27-345 / Mutation: C132A, V139S, G143S, K281R
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Carica papaya (papaya) / Production host: Escherichia coli (E. coli) / References: UniProt: P00784, papain

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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: 2.15 Å3/Da / Density % sol: 42.91 %
Crystal growMethod: vapor diffusion, hanging drop / pH: 4
Details: CS37 of Hampton Research, soaked overnight in NaOAc buffer pH 4.0, VAPOR DIFFUSION, HANGING DROP

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: Cu FINE FOCUS / Wavelength: 1.54 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: May 23, 2011 / Details: Osmic
RadiationMonochromator: Ni / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 3.8→50 Å / Num. all: 7008 / Num. obs: 6069 / % possible obs: 86.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Rmerge(I) obs: 0.121 / Net I/σ(I): 1.4
Reflection shellResolution: 3.8→3.94 Å / % possible all: 88.1

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Processing

Software
NameClassification
MAR345dtbdata collection
MOLREPphasing
CNSrefinement
AUTOMARdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3TNX

3tnx


Resolution: 3.8→29.6 Å / Occupancy max: 1 / Occupancy min: 1 / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.408 562 RANDOM
Rwork0.358 --
obs0.358 5245 -
all-5807 -
Solvent computationBsol: 4294.29 Å2
Displacement parametersBiso max: 60.1 Å2 / Biso mean: 44.4991 Å2 / Biso min: 0.01 Å2
Baniso -1Baniso -2Baniso -3
1--42.167 Å20 Å2-3.633 Å2
2---8.797 Å20 Å2
3---50.964 Å2
Refine analyzeLuzzati coordinate error obs: 0.62 Å
Refinement stepCycle: LAST / Resolution: 3.8→29.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3020 0 0 0 3020
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.012
X-RAY DIFFRACTIONc_angle_deg2.4
LS refinement shellResolution: 3.8→4.04 Å / Rfactor Rfree error: 0.044
RfactorNum. reflection% reflection
Rfree0.424 91 -
Rwork0.407 --
obs-742 73.3 %

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