[English] 日本語
Yorodumi
- PDB-6jw9: Crystal structure of E-64 inhibited falcipain 2 from Plasmodium f... -

+
Open data


ID or keywords:

Loading...

-
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 / 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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

-
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

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
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

-
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

-
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

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbjlc1.pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more