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- PDB-6y6l: Structure the ananain protease from Ananas comosus with a thiomet... -

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Basic information

Entry
Database: PDB / ID: 6y6l
TitleStructure the ananain protease from Ananas comosus with a thiomethylated catalytic cysteine
ComponentsAnanain
KeywordsHYDROLASE / cysteine protease / stem bromelain protein
Function / homology
Function and homology information


ananain / 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 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: 1.3 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
DepositionFeb 26, 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Ananain
B: Ananain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,12614
Polymers46,9972
Non-polymers1,12912
Water8,521473
1
A: Ananain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,0637
Polymers23,4991
Non-polymers5646
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Ananain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,0637
Polymers23,4991
Non-polymers5646
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)34.482, 57.861, 119.913
Angle α, β, γ (deg.)90.000, 93.000, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Ananain


Mass: 23498.664 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Ananas comosus (pineapple) / References: UniProt: P80884, ananain
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: SO4
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 473 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.54 Å3/Da / Density % sol: 51.61 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6 / Details: NaK tartrate 1 M, MES 0.1M at pH6

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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: 1.3→119.749 Å / Num. all: 112222 / Num. obs: 112222 / % possible obs: 97.1 % / Redundancy: 6.8 % / Rpim(I) all: 0.033 / Rrim(I) all: 0.087 / Rsym value: 0.08 / Net I/av σ(I): 4.6 / Net I/σ(I): 11.2 / Num. measured all: 768537
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique obsRpim(I) allRrim(I) allRsym valueNet I/σ(I) obs% possible all
1.3-1.376.70.6581.2107560159550.2710.7120.6582.794.9
1.37-1.456.80.4261.8103256151890.1750.4610.426495.6
1.45-1.556.80.2782.698028144180.1150.3010.2785.896.3
1.55-1.686.80.1983.491812134810.0820.2150.198896.9
1.68-1.8470.1434.587167125050.0590.1550.1431197.5
1.84-2.066.90.1075.779226114010.0440.1150.10715.298
2.06-2.3770.0857.170320101030.0350.0920.08519.398.6
2.37-2.916.90.0718.25959886610.0290.0770.07121.699.2
2.91-4.116.90.0569.64610667180.0230.060.05626.199.6
4.11-39.9166.70.0489.82546437910.020.0520.04825.299.8

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Phasing

PhasingMethod: molecular replacement

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Processing

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

6yce


Resolution: 1.3→39.916 Å / SU ML: 0.12 / Cross valid method: THROUGHOUT / σ(F): 0.05 / Phase error: 12.47 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1397 5628 5.02 %
Rwork0.1201 106479 -
obs0.121 112107 96.81 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 192.85 Å2 / Biso mean: 20.7422 Å2 / Biso min: 9.26 Å2
Refinement stepCycle: final / Resolution: 1.3→39.916 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3288 0 113 473 3874
Biso mean--38.81 31.71 -
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 (%)
1.3-1.31480.26411690.2232346694
1.3148-1.33020.24951760.2167348195
1.3302-1.34650.24151780.1916345995
1.3465-1.36350.21061690.1726343395
1.3635-1.38150.17441770.1612351895
1.3815-1.40040.17151890.149343195
1.4004-1.42040.16572020.1371344495
1.4204-1.44160.16681890.1317352595
1.4416-1.46410.15871900.1247347696
1.4641-1.48810.15911870.1179349696
1.4881-1.51380.13251900.116347196
1.5138-1.54130.14831920.1154349096
1.5413-1.5710.14871780.1152360296
1.571-1.6030.13381730.1011351196
1.603-1.63790.14011990.1024355297
1.6379-1.6760.13311810.0977347897
1.676-1.71790.14041980.0943359997
1.7179-1.76430.12342060.0954349297
1.7643-1.81630.131920.0973360797
1.8163-1.87490.12892000.0982351397
1.8749-1.94190.13151800.0975358198
1.9419-2.01960.10831950.0974360798
2.0196-2.11160.11292020.0944357298
2.1116-2.22290.10661700.0945362498
2.2229-2.36210.12212080.1359498
2.3621-2.54450.12341960.1106360699
2.5445-2.80050.15152050.1205367399
2.8005-3.20560.15121490.1297372699
3.2056-4.03810.12861740.1246368899
4.0381-39.9160.15712140.1592376499

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