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- PDB-3bcn: Crystal structure of a papain-like cysteine protease Ervatamin-A ... -

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Basic information

Entry
Database: PDB / ID: 3bcn
TitleCrystal structure of a papain-like cysteine protease Ervatamin-A complexed with irreversible inhibitor E-64
ComponentsErvatamin-A
KeywordsHYDROLASE / protease-inhibitor complex / papain-like fold / plant cysteine protease / Ervatamin / Thiol protease
Function / homology
Function and homology information


cysteine-type peptidase activity / Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases
Similarity search - Function
Papain-like cysteine endopeptidase / 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 endopeptidase / 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
BETA-MERCAPTOETHANOL / Chem-E64 / Ervatamin-A
Similarity search - Component
Biological speciesTabernaemontana divaricata (crepe jasmine)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.85 Å
AuthorsGhosh, R. / Chakrabarti, C. / Dattagupta, J.K. / Biswas, S.
CitationJournal: Febs J. / Year: 2008
Title: Structural insights into the substrate specificity and activity of ervatamins, the papain-like cysteine proteases from a tropical plant, Ervatamia coronaria
Authors: Ghosh, R. / Chakraborty, S. / Chakrabarti, C. / Dattagupta, J.K. / Biswas, S.
History
DepositionNov 13, 2007Deposition site: RCSB / Processing site: PDBJ
SupersessionNov 27, 2007ID: 2PSC
Revision 1.0Nov 27, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 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_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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: Ervatamin-A
B: Ervatamin-A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,5055
Polymers45,7062
Non-polymers7993
Water72140
1
A: Ervatamin-A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,2923
Polymers22,8531
Non-polymers4392
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Ervatamin-A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,2142
Polymers22,8531
Non-polymers3601
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)31.168, 105.587, 73.927
Angle α, β, γ (deg.)90.00, 101.96, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Ervatamin-A / papain-like cysteine protease


Mass: 22853.143 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Tabernaemontana divaricata (crepe jasmine)
References: UniProt: A5YVK8, Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases
#2: Chemical ChemComp-E64 / N-[N-[1-HYDROXYCARBOXYETHYL-CARBONYL]LEUCYLAMINO-BUTYL]-GUANIDINE


Mass: 360.429 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C15H30N5O5
#3: Chemical ChemComp-BME / BETA-MERCAPTOETHANOL / 2-Mercaptoethanol


Mass: 78.133 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6OS
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 40 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHIS PROTEIN IS ISOLATED FROM THE NATIVE SOURCE. THE RESIDUE 12 TO 195 IS FROM CDNA SEQUENCE. CDNA ...THIS PROTEIN IS ISOLATED FROM THE NATIVE SOURCE. THE RESIDUE 12 TO 195 IS FROM CDNA SEQUENCE. CDNA SEQUENCE IS EF591130. 144TH RESIDUE IS GLY FROM THE ELECTRON DENSITY MAP.

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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: 2.6 Å3/Da / Density % sol: 52.76 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 7.5
Details: 0.2M Lithium acetate dihydrate, 20%(w/v) PEG 3350, 12% Glycerol, pH 7.5, VAPOR DIFFUSION, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: BRUKER AXS MICROSTAR / Wavelength: 1.5418 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Oct 10, 2007 / Details: Mar multilayer confocal system
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.5→100 Å / Num. all: 14392 / Num. obs: 13929 / % possible obs: 85.8 % / Redundancy: 1.97 % / Biso Wilson estimate: 42.7 Å2 / Rmerge(I) obs: 0.0743 / Net I/σ(I): 5.4
Reflection shellResolution: 2.5→2.56 Å / Redundancy: 2.04 % / Rmerge(I) obs: 0.1463 / Mean I/σ(I) obs: 3 / Num. unique all: 914 / % possible all: 81.4

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Processing

Software
NameVersionClassification
CNS1.1refinement
MAR345dtbdata collection
AUTOMARdata reduction
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2PNS

2pns


Resolution: 2.85→30 Å / Data cutoff high absF: 1788723.6 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.27 460 4.2 %CNS SCRIPT MAKE_CV_TWIN.INP, ENSURES THAT TWIN-RELATED PAIRS OF REFLECTIONS ARE EITHER BOTH IN TEST OR BOTH IN WORK SET
Rwork0.2398 ---
obs0.2398 8207 75 %-
all-10943 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 35.0984 Å2 / ksol: 0.356501 e/Å3
Refine analyze
FreeObs
Luzzati coordinate error0.44 Å0.35 Å
Luzzati d res low-5 Å
Luzzati sigma a0.44 Å0.47 Å
Refinement stepCycle: LAST / Resolution: 2.85→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3208 0 54 40 3302
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.009
X-RAY DIFFRACTIONc_angle_deg1.5
X-RAY DIFFRACTIONc_dihedral_angle_d25.5
X-RAY DIFFRACTIONc_improper_angle_d1.16
LS refinement shellResolution: 2.85→2.98 Å / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.302 66 -
Rwork0.341 1046 -
obs-1046 84.2 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater.top
X-RAY DIFFRACTION3e64.parame64.top
X-RAY DIFFRACTION4bme.parambme.top

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