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- PDB-6ycg: Structure the bromelain protease from Ananas comosus in complex w... -

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Basic information

Entry
Database: PDB / ID: 6ycg
TitleStructure the bromelain protease from Ananas comosus in complex with the TLCK inhibitor
ComponentsFBSB
KeywordsHYDROLASE / cysteine protease / stem bromelain protein
Function / homology
Function and homology information


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
CITRIC ACID / ISOPROPYL ALCOHOL / Chem-TCK / Ananain / FBSB
Similarity search - Component
Biological speciesAnanas comosus (pineapple)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.45 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 ...Data collection / Database references / Derived calculations / Refinement description
Category: atom_type / chem_comp_atom ...atom_type / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z ..._atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Oct 23, 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: FBSB
B: FBSB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,8778
Polymers46,6352
Non-polymers2,2436
Water7,927440
1
A: FBSB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,6575
Polymers23,3171
Non-polymers1,3394
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: FBSB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,2213
Polymers23,3171
Non-polymers9032
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)91.240, 137.230, 82.600
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein FBSB


Mass: 23317.342 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Ananas comosus (pineapple)
Plasmid details: residues G84, N99 and S210 were refined in alternate conformation with A1084, D1099 and P1210 in accordance with electron density and mass spectrometry results
References: UniProt: O23799, UniProt: A0A199VSS3*PLUS

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Sugars , 2 types, 2 molecules

#2: Polysaccharide alpha-D-xylopyranose-(1-2)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2- ...alpha-D-xylopyranose-(1-2)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-3)]2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 1026.938 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DXylpa1-2[DManpa1-6]DManpb1-4DGlcpNAcb1-4[LFucpa1-3]DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/5,6,5/[a2122h-1b_1-5_2*NCC/3=O][a1221m-1a_1-5][a1122h-1b_1-5][a212h-1a_1-5][a1122h-1a_1-5]/1-2-1-3-4-5/a3-b1_a4-c1_c4-d1_d2-e1_d6-f1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(3+1)][a-L-Fucp]{}[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(2+1)][b-D-Xylp]{}[(6+1)][a-D-Manp]{}}}}}LINUCSPDB-CARE
#3: Polysaccharide alpha-L-fucopyranose-(1-3)-[2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)]2-acetamido-2-deoxy-beta- ...alpha-L-fucopyranose-(1-3)-[2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)]2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 570.542 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
LFucpa1-3[DGlcpNAcb1-4]DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1221m-1a_1-5]/1-2-1/a3-b1_a4-c1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(3+1)][a-L-Fucp]{}[(4+1)][b-D-GlcpNAc]{}}}LINUCSPDB-CARE

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Non-polymers , 4 types, 444 molecules

#4: Chemical ChemComp-IPA / ISOPROPYL ALCOHOL / 2-PROPANOL


Mass: 60.095 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C3H8O / Comment: alkaloid*YM
#5: Chemical ChemComp-CIT / CITRIC ACID


Mass: 192.124 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C6H8O7
#6: 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.: 1
Source method: isolated from a genetically manipulated source
Formula: C14H21ClN2O3S / Feature type: SUBJECT OF INVESTIGATION
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 440 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.77 Å3/Da / Density % sol: 55.63 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6 / Details: 20% PEG 4000, 20% 2-propanol, 0.1 M citrate pH 6

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.9793 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 20, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 1.44→45.7 Å / Num. obs: 93157 / % possible obs: 99.6 % / Redundancy: 12.7 % / CC1/2: 1 / Rmerge(I) obs: 0.045 / Rpim(I) all: 0.013 / Rrim(I) all: 0.047 / Net I/σ(I): 27.3 / Num. measured all: 1186942 / Scaling rejects: 1
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
1.44-1.489.60.7926167764530.8860.2610.8362.494.2
6.46-45.711.70.02313542115610.0070.02474.399.6

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
REFMAC5.8.0258refinement
XDSdata reduction
Aimless0.7.4data scaling
PHASERphasing
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6YCE

6yce


Resolution: 1.45→45.62 Å / Cor.coef. Fo:Fc: 0.98 / Cor.coef. Fo:Fc free: 0.968 / SU B: 1.762 / SU ML: 0.03 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.047 / ESU R Free: 0.049 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1548 4590 5 %RANDOM
Rwork0.1146 ---
obs0.1166 87083 99.92 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 101.78 Å2 / Biso mean: 17.38 Å2 / Biso min: 8.61 Å2
Baniso -1Baniso -2Baniso -3
1-0.08 Å20 Å20 Å2
2---0.16 Å20 Å2
3---0.08 Å2
Refinement stepCycle: final / Resolution: 1.45→45.62 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3310 0 168 440 3918
Biso mean--27.26 33.45 -
Num. residues----430
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0133697
X-RAY DIFFRACTIONr_bond_other_d0.0020.0183298
X-RAY DIFFRACTIONr_angle_refined_deg1.9351.6995073
X-RAY DIFFRACTIONr_angle_other_deg1.7291.6327722
X-RAY DIFFRACTIONr_dihedral_angle_1_deg19.5465.393496
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.8122.745153
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.90615545
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.3551515
X-RAY DIFFRACTIONr_chiral_restr0.3110.2515
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.024566
X-RAY DIFFRACTIONr_gen_planes_other0.010.02795
X-RAY DIFFRACTIONr_rigid_bond_restr3.37836993
LS refinement shellResolution: 1.45→1.488 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.23 335 -
Rwork0.191 6363 -
all-6698 -
obs--99.97 %

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