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- PDB-3lfy: CTD of Tarocystatin in complex with papain -

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Basic information

Entry
Database: PDB / ID: 3lfy
TitleCTD of Tarocystatin in complex with papain
ComponentsPapain
KeywordsHYDROLASE / CYSTATIN / TAROCYSTATIN / CECPI / PAPAIN / PHYTOCYSTATIN
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
ASPARAGINE / GLYCINE / SERINE / Papain
Similarity search - Component
Biological speciesCarica papaya (papaya)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsChu, M.H. / Liu, K.L. / Yeh, K.W. / Cheng, Y.S.
CitationJournal: Planta / Year: 2011
Title: Crystal structure of tarocystatin-papain complex: implications for the inhibition property of group-2 phytocystatins.
Authors: Chu, M.H. / Liu, K.L. / Wu, H.Y. / Yeh, K.W. / Cheng, Y.S.
History
DepositionJan 19, 2010Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jul 21, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 18, 2020Group: Database references / Derived calculations
Category: citation / citation_author ...citation / citation_author / struct_conn / struct_site
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Nov 1, 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.4Nov 22, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Papain
C: Papain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,5507
Polymers47,0012
Non-polymers5495
Water3,081171
1
A: Papain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,7383
Polymers23,5001
Non-polymers2372
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
C: Papain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,8134
Polymers23,5001
Non-polymers3123
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)48.890, 48.890, 200.870
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number144
Space group name H-MP31

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Components

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


Mass: 23500.299 Da / Num. of mol.: 2 / Fragment: Papain DOMAIN / Source method: isolated from a natural source
Details: Papain was purchased from SIGMA co. for co-crystallization.
Source: (natural) Carica papaya (papaya) / References: UniProt: P00784, papain
#2: Chemical ChemComp-SER / SERINE / Serine


Type: L-peptide linking / Mass: 105.093 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H7NO3
#3: Chemical ChemComp-ASN / ASPARAGINE / Asparagine


Type: L-peptide linking / Mass: 132.118 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H8N2O3
#4: Chemical ChemComp-GLY / GLYCINE / Glycine


Type: peptide linking / Mass: 75.067 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H5NO2
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 171 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsRESIDUES A 213-214, C 213-215 WERE FROM C-TERMINAL OF CYSTEINE PROTEINASE INHIBITOR (CECPI; ...RESIDUES A 213-214, C 213-215 WERE FROM C-TERMINAL OF CYSTEINE PROTEINASE INHIBITOR (CECPI; SEQUENCE: TPADLGVKRDAHEAEWLEIPTHDPVVQDAANHAVKSIQQRSNTLFPYELLEILHAKAKVLEDLAKIHLLLKLKRGSREEKFKVEVHKNIEGTFHLNQMEQDHSDSGN; SOURCE: COCOCASIA ESCULENTA; DATABASE: UNIPROTKB/TREMBL Q8L5J8; OVEREXPRESSED IN E. COLI BL21(DE3); PLASMID NAME: PGEX-4T-1). THE C-TERMINAL DOMAIN OF CSCPI WAS CO-CRYSTALLIZED WITH PAPAIN, BUT WAS DIGESTED BY PAPAIN. ONLY 2 OR 3 RESIDUES REMAINED.

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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: 2.95 Å3/Da / Density % sol: 58.29 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.1M Hepes pH 7.5, 70% v/v MPD, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: BL13C1 / Wavelength: 0.97315 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Mar 26, 2008 / Details: mirrors
RadiationMonochromator: Si(111) double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97315 Å / Relative weight: 1
ReflectionResolution: 2.56→30 Å / Num. obs: 17482 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.2 % / Biso Wilson estimate: 39.8 Å2 / Rmerge(I) obs: 0.076 / Net I/σ(I): 45.6
Reflection shellResolution: 2.56→2.75 Å / Rmerge(I) obs: 0.517 / Mean I/σ(I) obs: 3.08 / Num. unique all: 3483 / % possible all: 99.5

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
CNSrefinement
HKL-2000data reduction
HKL-2000data scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1PPN

1ppn


Resolution: 2.6→29.14 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 211835.05 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.267 1476 9.9 %RANDOM
Rwork0.213 ---
obs0.213 14897 90.3 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 58.5002 Å2 / ksol: 0.322757 e/Å3
Displacement parametersBiso mean: 59.3 Å2
Baniso -1Baniso -2Baniso -3
1-14.68 Å214.44 Å20 Å2
2--14.68 Å20 Å2
3----29.36 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.47 Å0.35 Å
Luzzati d res low-5 Å
Luzzati sigma a0.67 Å0.54 Å
Refinement stepCycle: LAST / Resolution: 2.6→29.14 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3316 0 34 171 3521
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d24.1
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.75
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.281.5
X-RAY DIFFRACTIONc_mcangle_it2.152
X-RAY DIFFRACTIONc_scbond_it1.882
X-RAY DIFFRACTIONc_scangle_it2.852.5
Refine LS restraints NCSNCS model details: NONE
LS refinement shellResolution: 2.6→2.76 Å / Rfactor Rfree error: 0.03 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.448 226 10.9 %
Rwork0.371 1852 -
obs--75.9 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater.top

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