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- PDB-6yce: Structure the bromelain protease from Ananas comosus with a thiom... -

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Basic information

Entry
Database: PDB / ID: 6yce
TitleStructure the bromelain protease from Ananas comosus with a thiomethylated active cysteine
ComponentsFBSB
KeywordsHYDROLASE / cysteine protease / stem bromelain protein
Function / homology
Function and homology information


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
ISOPROPYL ALCOHOL / Ananain / FBSB
Similarity search - Component
Biological speciesAnanas comosus (pineapple)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.8 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 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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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)47,8735
Polymers46,7272
Non-polymers1,1463
Water5,909328
1
A: FBSB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,2282
Polymers23,3631
Non-polymers8651
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: FBSB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,6453
Polymers23,3631
Non-polymers2812
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)91.260, 137.660, 81.990
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: 0 / Ens-ID: 1 / Beg auth comp-ID: VAL / Beg label comp-ID: VAL / End auth comp-ID: GLU / End label comp-ID: GLU / Refine code: 0 / Auth seq-ID: 2 - 216 / Label seq-ID: 2 - 216

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

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Components

#1: Protein FBSB


Mass: 23363.434 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
#2: Polysaccharide alpha-D-xylopyranose-(1-2)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4) ...alpha-D-xylopyranose-(1-2)-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: 864.797 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DXylpa1-2DManpb1-4DGlcpNAcb1-4[LFucpa1-3]DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/4,5,4/[a2122h-1b_1-5_2*NCC/3=O][a1221m-1a_1-5][a1122h-1b_1-5][a212h-1a_1-5]/1-2-1-3-4/a3-b1_a4-c1_c4-d1_d2-e1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(3+1)][b-L-Fucp]{}[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(2+1)][b-D-Xylp]{}}}}}LINUCSPDB-CARE
#3: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE / N-Acetylglucosamine


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#4: Chemical ChemComp-IPA / ISOPROPYL ALCOHOL / 2-PROPANOL / Isopropyl alcohol


Mass: 60.095 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C3H8O / Comment: alkaloid*YM
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 328 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.76 Å3/Da / Density % sol: 55.5 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.5 / Details: 20% PEG 4000, 20% 2-propanol, 0.1 M citrate pH 5.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.97911 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: 0.97911 Å / Relative weight: 1
ReflectionResolution: 1.79→52.72 Å / Num. obs: 48667 / % possible obs: 99.4 % / Redundancy: 12.7 % / CC1/2: 0.999 / Rmerge(I) obs: 0.074 / Rpim(I) all: 0.022 / Rrim(I) all: 0.077 / Net I/σ(I): 19.2
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
1.79-1.8410.91.05832670.8360.3221.10892
8.02-52.7211.10.0316230.9990.010.03399.3

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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: 1IWD

1iwd


Resolution: 1.8→52.72 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.95 / SU B: 5.256 / SU ML: 0.079 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.112 / ESU R Free: 0.111 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2062 2411 5.1 %RANDOM
Rwork0.17 ---
obs0.1719 44750 98.01 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 69.05 Å2 / Biso mean: 25.011 Å2 / Biso min: 12.67 Å2
Baniso -1Baniso -2Baniso -3
1-0.09 Å20 Å20 Å2
2--0.01 Å20 Å2
3----0.1 Å2
Refinement stepCycle: final / Resolution: 1.8→52.72 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3314 0 76 328 3718
Biso mean--32.56 34.98 -
Num. residues----430
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0123583
X-RAY DIFFRACTIONr_angle_refined_deg1.5031.6634909
X-RAY DIFFRACTIONr_dihedral_angle_1_deg13.9955.209479
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.87222.792154
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.35415541
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.3131514
X-RAY DIFFRACTIONr_chiral_restr0.1250.2489
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.022806
Refine LS restraints NCS

Ens-ID: 1 / Number: 7002 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.1 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 1.8→1.847 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.26 160 -
Rwork0.294 3182 -
all-3342 -
obs--95.49 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.23570.38690.20870.97420.08270.67690.0245-0.0140.064-0.019-0.03630.06870.02030.02350.01180.0103-0.0030.00180.0055-0.00510.0095-15.628120.617310.7204
21.6999-0.28820.64881.2336-0.08161.1186-0.02160.1241-0.0041-0.0478-0.01370.0350.0170.09220.03530.0072-0.0009-0.00620.01370.00450.0136-32.46216.8603-14.2968
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 216
2X-RAY DIFFRACTION2B2 - 216

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