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- PDB-6ycd: Structure the ananain protease from Ananas comosus covalently bou... -

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Basic information

Entry
Database: PDB / ID: 6ycd
TitleStructure the ananain protease from Ananas comosus covalently bound to the TLCK inhibitor
ComponentsAnanain
KeywordsHYDROLASE / cysteine protease / stem bromelain protein
Function / homology
Function and homology information


ananain / proteolysis involved in protein catabolic process / lysosome / cysteine-type endopeptidase activity / extracellular space
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 peptidase, cysteine active site / Eukaryotic thiol (cysteine) proteases cysteine active site. / Papain-like cysteine peptidase superfamily
Similarity search - Domain/homology
Biological speciesAnanas comosus (pineapple)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.35 Å
AuthorsAzarkan, M. / Charlier, P. / Herman, R. / Delbrassine, F. / Sauvage, E. / M Rabet, N. / Calvo Esposito, R. / Kerff, F.
CitationJournal: Sci Rep / Year: 2020
Title: Structures of the free and inhibitors-bound forms of bromelain and ananain from Ananas comosus stem and in vitro study of their cytotoxicity.
Authors: Azarkan, M. / Maquoi, E. / Delbrassine, F. / Herman, R. / M'Rabet, N. / Calvo Esposito, R. / Charlier, P. / Kerff, F.
History
DepositionMar 18, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 25, 2020Provider: repository / Type: Initial release
Revision 1.1Jan 24, 2024Group: 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 1.2Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Ananain
B: Ananain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,9518
Polymers46,9052
Non-polymers1,0466
Water8,089449
1
A: Ananain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,9784
Polymers23,4531
Non-polymers5253
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Ananain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,9744
Polymers23,4531
Non-polymers5213
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)34.390, 58.420, 119.160
Angle α, β, γ (deg.)90.000, 92.620, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Ananain


Mass: 23452.572 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Ananas comosus (pineapple) / References: UniProt: P80884, ananain
#2: Chemical ChemComp-TCK / N-[(1S)-5-amino-1-(chloroacetyl)pentyl]-4-methylbenzenesulfonamide / Tos-Lys-CH2Cl


Type: peptide-like / Mass: 332.846 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C14H21ClN2O3S / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-SO4 / SULFATE ION


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


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 449 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

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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: 2.55 Å3/Da / Density % sol: 51.75 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.6 / Details: 0.5 M Li2SO4, 0.1 M citrate pH 5.6

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.98011 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 23, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98011 Å / Relative weight: 1
ReflectionResolution: 1.344→119.256 Å / Num. all: 104486 / Num. obs: 104486 / % possible obs: 99.2 % / Redundancy: 6.5 % / Rpim(I) all: 0.023 / Rrim(I) all: 0.059 / Rsym value: 0.055 / Net I/av σ(I): 7 / Net I/σ(I): 15.7 / Num. measured all: 674749
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsRpim(I) allRrim(I) allRsym value% possible all
1.344-1.425.40.5991.3147230.2810.6640.59996
1.42-1.56.50.382144840.1610.4130.3899.8
1.5-1.616.60.2333.3135260.0980.2530.23399.7
1.61-1.746.70.1485126980.0610.160.14899.8
1.74-1.96.70.17.2116580.0420.1080.199.8
1.9-2.136.70.0679.7105540.0280.0730.06799.9
2.13-2.456.60.05411.793680.0230.0590.05499.9
2.45-3.016.60.04712.578810.020.0510.04799.9
3.01-4.256.50.03914.561680.0160.0420.03999.8
4.25-41.7566.50.03315.334260.0140.0360.03399.6

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
XDSdata reduction
SCALA3.3.16data scaling
PHASERphasing
PHENIX1.14_3260refinement
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6Y6L

6y6l


Resolution: 1.35→39.678 Å / SU ML: 0.12 / Cross valid method: THROUGHOUT / σ(F): 1.4 / Phase error: 13.31
RfactorNum. reflection% reflection
Rfree0.1488 5169 5 %
Rwork0.1188 --
obs0.1203 103368 99.79 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 94.43 Å2 / Biso mean: 20.2641 Å2 / Biso min: 8.71 Å2
Refinement stepCycle: final / Resolution: 1.35→39.678 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3284 0 111 449 3844
Biso mean--30.3 32.24 -
Num. residues----430
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.35-1.36530.281610.2239314995
1.3653-1.38140.24361740.1991326399
1.3814-1.39820.22861550.17353209100
1.3982-1.41590.20741790.16473287100
1.4159-1.43460.1911750.15513281100
1.4346-1.45420.18851750.14443224100
1.4542-1.4750.18711650.13053289100
1.475-1.4970.16551610.12443323100
1.497-1.52040.16711580.11563184100
1.5204-1.54530.15481850.10553281100
1.5453-1.5720.17361550.11053300100
1.572-1.60060.15351570.10563244100
1.6006-1.63130.16571800.10113305100
1.6313-1.66460.13521590.09443253100
1.6646-1.70080.13411880.09173272100
1.7008-1.74040.14171830.09453263100
1.7404-1.78390.12671520.0933278100
1.7839-1.83220.1211780.08723283100
1.8322-1.88610.13131810.08783262100
1.8861-1.94690.10221720.08623272100
1.9469-2.01650.12811660.08673306100
2.0165-2.09730.11551760.08613255100
2.0973-2.19270.11691740.09093279100
2.1927-2.30830.11061920.09453276100
2.3083-2.45290.13331940.10063284100
2.4529-2.64230.12981590.11093297100
2.6423-2.90810.15481820.12443281100
2.9081-3.32870.13511610.133304100
3.3287-4.19310.15981620.12723350100
4.1931-39.6780.19072100.1774334599

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