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- PDB-6ssz: Structure of the Plasmodium falciparum falcipain 2 protease in co... -

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Basic information

Entry
Database: PDB / ID: 6ssz
TitleStructure of the Plasmodium falciparum falcipain 2 protease in complex with an (E)-chalcone inhibitor.
ComponentsCysteine proteinase falcipain 2a
KeywordsHYDROLASE / Inhibitor / complex / malaria / haemoglobin / proteolysis
Function / homology
Function and homology information


cysteine-type peptidase activity / Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases / proteolysis / membrane
Similarity search - Function
Cathepsin propeptide inhibitor domain (I29) / Cathepsin propeptide inhibitor domain (I29) / Cathepsin propeptide inhibitor domain (I29) / 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 ...Cathepsin propeptide inhibitor domain (I29) / Cathepsin propeptide inhibitor domain (I29) / Cathepsin propeptide inhibitor domain (I29) / 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
Chem-JV1 / Falcipain 2
Similarity search - Component
Biological speciesPlasmodium falciparum (malaria parasite P. falciparum)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.45 Å
AuthorsMachin, J. / Kantsadi, A. / Vakonakis, I.
CitationJournal: Malar.J. / Year: 2019
Title: The complex of Plasmodium falciparum falcipain-2 protease with an (E)-chalcone-based inhibitor highlights a novel, small, molecule-binding site.
Authors: Machin, J.M. / Kantsadi, A.L. / Vakonakis, I.
History
DepositionSep 9, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 4, 2019Provider: repository / Type: Initial release
Revision 1.1Dec 11, 2019Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.name
Revision 1.2Jan 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 / software
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _software.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Cysteine proteinase falcipain 2a
B: Cysteine proteinase falcipain 2a
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,9544
Polymers54,3592
Non-polymers5952
Water0
1
A: Cysteine proteinase falcipain 2a
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,4772
Polymers27,1801
Non-polymers2971
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Cysteine proteinase falcipain 2a
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,4772
Polymers27,1801
Non-polymers2971
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)109.431, 109.431, 107.254
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein Cysteine proteinase falcipain 2a / / Falcipain 2


Mass: 27179.660 Da / Num. of mol.: 2 / Mutation: C25A
Source method: isolated from a genetically manipulated source
Details: Features a C25A mutation using the numbering system of the entry.
Source: (gene. exp.) Plasmodium falciparum (malaria parasite P. falciparum)
Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: Q9N6S8, Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases
#2: Chemical ChemComp-JV1 / (~{E})-3-(1,3-benzodioxol-5-yl)-1-(3-nitrophenyl)prop-2-en-1-one


Mass: 297.262 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C16H11NO5 / Feature type: SUBJECT OF INVESTIGATION
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: 3.43 Å3/Da / Density % sol: 64.15 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: Mother liquor comprising 0.12 M of monosaccharides mixture (D-glucose; D-mannose; D-galactose; L-fucose; D-xylose; N-acetyl-D-glucosamine), 0.1 M Tris/Bicine (pH 8.5); 20% v/v glycerol, 10% ...Details: Mother liquor comprising 0.12 M of monosaccharides mixture (D-glucose; D-mannose; D-galactose; L-fucose; D-xylose; N-acetyl-D-glucosamine), 0.1 M Tris/Bicine (pH 8.5); 20% v/v glycerol, 10% w/v PEG 4000. Crystal soaked for 2 hours with (E)-chalcone #48 inhibitor. Inhibitor prepared in 100% DMSO, 100 mM concentration and then diluted to 1 mM in mother liquor for crystal soaking.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9763 Å
DetectorType: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Jan 27, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 3.45→94.77 Å / Num. obs: 6001 / % possible obs: 90.2 % / Redundancy: 18.9 % / Biso Wilson estimate: 147.87 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.204 / Rpim(I) all: 0.048 / Rrim(I) all: 0.209 / Net I/σ(I): 10.7
Reflection shellResolution: 3.45→3.85 Å / Redundancy: 17.6 % / Rmerge(I) obs: 2.31 / Mean I/σ(I) obs: 1.5 / Num. unique obs: 301 / CC1/2: 0.44 / Rpim(I) all: 0.554 / Rrim(I) all: 2.378 / % possible all: 66.9

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Processing

Software
NameClassification
BUSTERrefinement
XDSdata reduction
autoPROCdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2OUL

2oul


Resolution: 3.45→94.77 Å / Cross valid method: THROUGHOUT
Details: Automatically applied NCS and TLS restraints. Refined using RCSB 2OUL as external target restraint.
RfactorNum. reflection% reflectionSelection details
Rfree0.308 288 4.8 %Random selection
Rwork0.255 ---
obs0.258 5712 59.2 %-
Refinement stepCycle: LAST / Resolution: 3.45→94.77 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3793 0 44 0 3837

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