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- PDB-6jw9: Crystal structure of E-64 inhibited falcipain 2 from Plasmodium f... -

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Basic information

Entry
Database: PDB / ID: 6jw9
TitleCrystal structure of E-64 inhibited falcipain 2 from Plasmodium falciparum, strain 3D7
ComponentsCysteine protease falcipain-2
KeywordsHYDROLASE / Cysteine protease / haemoglobinase / drug-target / Plasmodium falciparum
Function / homology
Function and homology information


MHC class II antigen presentation / Neutrophil degranulation / food vacuole / proteolysis involved in protein catabolic process / Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases / lysosome / cysteine-type endopeptidase activity / proteolysis / extracellular space / 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-E64 / Falcipain-2a
Similarity search - Component
Biological speciesPlasmodium falciparum (malaria parasite P. falciparum)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.5 Å
AuthorsChakraborty, S. / Alam, B. / Biswas, S.
CitationJournal: Biochem.Biophys.Res.Commun. / Year: 2022
Title: New insights of falcipain 2 structure from Plasmodium falciparum 3D7 strain.
Authors: Chakraborty, S. / Alam, B. / Biswas, S.
History
DepositionApr 18, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 22, 2020Provider: repository / Type: Initial release
Revision 1.1Oct 19, 2022Group: Database references / Category: citation / database_2
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _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 / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id ..._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
Revision 1.3Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Cysteine protease falcipain-2
B: Cysteine protease falcipain-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,7723
Polymers54,4112
Non-polymers3601
Water55831
1
A: Cysteine protease falcipain-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,5662
Polymers27,2061
Non-polymers3601
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Cysteine protease falcipain-2


Theoretical massNumber of molelcules
Total (without water)27,2061
Polymers27,2061
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)115.269, 115.269, 242.005
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 1 through 8 or resid 13...
21(chain B and (resid 1 through 8 or resid 13...

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11GLNGLNILEILE(chain A and (resid 1 through 8 or resid 13...AA1 - 81 - 8
12GLYGLYGLYGLY(chain A and (resid 1 through 8 or resid 13...AA1313
13PHEPHELEULEU(chain A and (resid 1 through 8 or resid 13...AA17 - 13617 - 136
14GLUGLUSERSER(chain A and (resid 1 through 8 or resid 13...AA138 - 153138 - 153
15ASPASPGLYGLY(chain A and (resid 1 through 8 or resid 13...AA155 - 166155 - 166
16CYSCYSGLUGLU(chain A and (resid 1 through 8 or resid 13...AA168 - 241168 - 241
21GLNGLNILEILE(chain B and (resid 1 through 8 or resid 13...BB1 - 81 - 8
22GLYGLYGLYGLY(chain B and (resid 1 through 8 or resid 13...BB1313
23PHEPHELEULEU(chain B and (resid 1 through 8 or resid 13...BB17 - 13617 - 136
24GLUGLUSERSER(chain B and (resid 1 through 8 or resid 13...BB138 - 153138 - 153
25ASPASPGLYGLY(chain B and (resid 1 through 8 or resid 13...BB155 - 166155 - 166
26CYSCYSGLUGLU(chain B and (resid 1 through 8 or resid 13...BB168 - 241168 - 241

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Components

#1: Protein Cysteine protease falcipain-2 / Cysteine proteinase falcipain 2a


Mass: 27205.672 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Plasmodium falciparum (malaria parasite P. falciparum)
Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21DE3
References: UniProt: Q8I6U4, Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases
#2: Chemical ChemComp-E64 / N-[N-[1-HYDROXYCARBOXYETHYL-CARBONYL]LEUCYLAMINO-BUTYL]-GUANIDINE


Mass: 360.429 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H30N5O5
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 31 / Source method: isolated from a natural source / Formula: H2O
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: 7.49 Å3/Da / Density % sol: 83.45 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5
Details: 0.4 M Ammonium Sulfate, 0.1 M Sodium Citrate, 25% Ethylene Glycol, 5 mM MgSO4

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: RRCAT INDUS-2 / Beamline: PX-BL21 / Wavelength: 0.97947 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Mar 8, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97947 Å / Relative weight: 1
ReflectionResolution: 3.5→48.58 Å / Num. obs: 21387 / % possible obs: 100 % / Redundancy: 9 % / Biso Wilson estimate: 108.11 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.214 / Rpim(I) all: 0.074 / Rrim(I) all: 0.227 / Net I/σ(I): 11.7 / Num. measured all: 193056 / Scaling rejects: 11
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
3.5-3.788.71.79442990.6890.6281.903100
9.26-48.588.40.026130410.0090.02799.2

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Processing

Software
NameVersionClassification
XDSdata reduction
Aimless0.7.2data scaling
PHENIX1.12_2829refinement
PDB_EXTRACT3.25data extraction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3BPF

3bpf


Resolution: 3.5→48.58 Å / SU ML: 0.65 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 39.09
RfactorNum. reflection% reflection
Rfree0.3278 1023 4.81 %
Rwork0.294 --
obs0.2957 21288 99.82 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 472.36 Å2 / Biso mean: 121.7684 Å2 / Biso min: 44.94 Å2
Refinement stepCycle: final / Resolution: 3.5→48.58 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3778 0 25 31 3834
Biso mean--119.49 130.94 -
Num. residues----482
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0063893
X-RAY DIFFRACTIONf_angle_d1.0235261
X-RAY DIFFRACTIONf_chiral_restr0.089548
X-RAY DIFFRACTIONf_plane_restr0.006688
X-RAY DIFFRACTIONf_dihedral_angle_d14.0212308
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A2552X-RAY DIFFRACTION14.853TORSIONAL
12B2552X-RAY DIFFRACTION14.853TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 7

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.5001-3.68450.44131320.398328292961100
3.6845-3.91530.40531430.382228292972100
3.9153-4.21740.38341480.340728472995100
4.2174-4.64160.38131470.301228613008100
4.6416-5.31250.37091500.285128743024100
5.3125-6.69040.30621500.302929373087100
6.6904-48.58510.2511530.23743088324199

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