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

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Basic information

Entry
Database: PDB / ID: 3tnx
TitleStructure of the precursor of a thermostable variant of papain at 2.6 Angstroem resolution
ComponentsPapain
KeywordsHYDROLASE / Cytoplasm for recombinant expression
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 / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.62 Å
AuthorsRoy, S. / Choudhury, D. / Dattagupta, J.K. / Biswas, S.
Citation
Journal: Acta Crystallogr.,Sect.D / Year: 2012
Title: The structure of a thermostable mutant of pro-papain reveals its activation mechanism
Authors: Roy, S. / Choudhury, D. / Aich, P. / Dattagupta, J.K. / Biswas, S.
#1: Journal: Acta Crystallogr.,Sect.F / Year: 2011
Title: Crystallization and preliminary X-ray diffraction studies of the precursor protein of a thermostable variant of papain
Authors: Roy, S. / Choudhury, D. / Chakrabarti, C. / Biswas, S. / Dattagupta, J.K.
History
DepositionSep 2, 2011Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Sep 12, 2012Provider: repository / Type: Initial release
Revision 1.1Sep 19, 2012Group: Database references
Revision 1.2Nov 28, 2012Group: Database references
Revision 1.3Nov 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 / pdbx_initial_refinement_model / 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_ref_seq_dif.details / _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

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Assembly

Deposited unit
A: Papain
C: Papain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)82,1713
Polymers82,1352
Non-polymers351
Water2,396133
1
A: Papain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,1032
Polymers41,0681
Non-polymers351
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
C: Papain


Theoretical massNumber of molelcules
Total (without water)41,0681
Polymers41,0681
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)42.925, 74.775, 116.510
Angle α, β, γ (deg.)90.00, 93.03, 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) / Plasmid: pET30 Ek/LIC / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P00784, papain
#2: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 133 / 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: 2.27 Å3/Da / Density % sol: 45.89 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 8.0% PEG 3350, 0.1M Na-acetate pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.9785 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Feb 10, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9785 Å / Relative weight: 1
ReflectionResolution: 2.6→50 Å / Num. all: 22356 / Num. obs: 21658 / % possible obs: 97 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1
Reflection shellResolution: 2.6→2.64 Å / % possible all: 94.6

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Processing

Software
NameVersionClassification
PXdata collection
MOLREPphasing
REFMAC5.5.0109refinement
HKL-2000data reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1pci

1pci


Resolution: 2.62→45.92 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.925 / SU B: 27.261 / SU ML: 0.256 / Cross valid method: THROUGHOUT / ESU R Free: 0.316 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23592 1110 5.1 %RANDOM
Rwork0.18296 ---
all0.1858 20562 --
obs0.1858 20562 96.5 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 65.18 Å2
Baniso -1Baniso -2Baniso -3
1-0.38 Å20 Å20.15 Å2
2---1.19 Å20 Å2
3---0.82 Å2
Refinement stepCycle: LAST / Resolution: 2.62→45.92 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4945 0 1 133 5079
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0225071
X-RAY DIFFRACTIONr_angle_refined_deg1.6431.9366878
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1575618
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.60724.241257
X-RAY DIFFRACTIONr_dihedral_angle_3_deg21.60115823
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.041530
X-RAY DIFFRACTIONr_chiral_restr0.1140.2706
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0213968
X-RAY DIFFRACTIONr_mcbond_it0.7411.53058
X-RAY DIFFRACTIONr_mcangle_it1.46424903
X-RAY DIFFRACTIONr_scbond_it2.30632013
X-RAY DIFFRACTIONr_scangle_it3.8334.51975
LS refinement shellResolution: 2.615→2.683 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.344 64 -
Rwork0.286 1421 -
obs--87.66 %
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)
12.34460.3189-0.4323.00610.39695.10550.0805-0.0865-0.05340.063-0.09410.12610.00590.27190.01370.132200.05380.4267-0.03640.1086-2.572-4.35312.822
22.80670.6143-0.27092.4551-0.23871.2169-0.00010.20850.0765-0.09580.0034-0.0424-0.00410.0146-0.00330.03340.0269-0.01720.34060.01150.0338.092.013-2.784
35.46210.5089-2.65961.9239-0.71425.699-0.0161-0.2766-0.1613-0.1344-0.07480.29860.1990.14480.0910.39370.05060.00620.6548-0.05490.112832.072-9.465-69.541
42.39960.0277-0.03726.5192-2.43713.48880.1441-0.3043-0.05660.7377-0.17960.0573-0.23640.01560.03550.3149-0.06660.06180.6703-0.0140.130328.372-15.949-50.541
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A10 - 84
2X-RAY DIFFRACTION1A85 - 107
3X-RAY DIFFRACTION2A108 - 319
4X-RAY DIFFRACTION3C10 - 84
5X-RAY DIFFRACTION3C85 - 107
6X-RAY DIFFRACTION4C108 - 319

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