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- PDB-3u8e: Crystal Structure of Cysteine Protease from Bulbs of Crocus sativ... -

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Basic information

Entry
Database: PDB / ID: 3u8e
TitleCrystal Structure of Cysteine Protease from Bulbs of Crocus sativus at 1.3 A Resolution
ComponentsPapain-like Cysteine Protease
KeywordsHYDROLASE / Papain-like Cysteine Peptidase / Peptidase_C1A / Inactive form
Function / homology
Function and homology information


cysteine-type peptidase activity
Similarity search - Function
Papain-like cysteine endopeptidase / Cysteine peptidase, asparagine active site / Eukaryotic thiol (cysteine) proteases asparagine 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 endopeptidase / Cysteine peptidase, asparagine active site / Eukaryotic thiol (cysteine) proteases asparagine 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
Papain-like Cysteine Protease
Similarity search - Component
Biological speciesCrocus sativus (saffron crocus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.31 Å
AuthorsIqbal, S. / Akrem, A. / Buck, F. / Perbandt, M. / Banumathi, S. / Betzel, C.
CitationJournal: To be Published
Title: Crystal Structure of A Papain-like Cysteine Protease from Bulbs of Crocus sativum at 1.3 A resolution
Authors: Iqbal, S. / Akrem, A. / Buck, F. / Perbandt, M. / Banumathi, S. / Betzel, C.
History
DepositionOct 17, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 26, 2011Provider: repository / Type: Initial release
Revision 1.1Sep 13, 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 / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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_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-like Cysteine Protease
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,6327
Polymers23,2101
Non-polymers4226
Water3,459192
1
A: Papain-like Cysteine Protease
hetero molecules

A: Papain-like Cysteine Protease
hetero molecules

A: Papain-like Cysteine Protease
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,89621
Polymers69,6293
Non-polymers1,26718
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
Buried area6570 Å2
ΔGint-191 kcal/mol
Surface area24620 Å2
MethodPISA
Unit cell
Length a, b, c (Å)97.970, 97.970, 48.780
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number146
Space group name H-MH3

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Components

#1: Protein Papain-like Cysteine Protease


Mass: 23209.557 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: Bulbs of the plant / Source: (natural) Crocus sativus (saffron crocus) / References: UniProt: G8JLU6*PLUS
#2: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#3: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 192 / 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: 1.94 Å3/Da / Density % sol: 36.63 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: 0.085M tri-Sodium citrate, 0.85M Lithium sulphate, 0.425M Ammonium sulfate, 15% (v/v) Glycerol, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 0.9774 Å
DetectorDetector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9774 Å / Relative weight: 1
ReflectionResolution: 1.31→40 Å / Num. obs: 41920 / % possible obs: 99.9499 % / Observed criterion σ(F): 2.5 / Observed criterion σ(I): 1
Reflection shellHighest resolution: 1.31 Å / % possible all: 97.3

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Processing

Software
NameVersionClassification
HKL-2000data collection
MOLREPin CCP4iphasing
REFMACrefinement
HKL-2000data reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 2B1M

2b1m


Resolution: 1.31→24.49 Å / σ(F): 1.31 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.1893 39803 RANDOM
Rwork0.1437 --
obs0.1893 41920 -
Refinement stepCycle: LAST / Resolution: 1.31→24.49 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1596 0 24 192 1812

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