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- PDB-1yvb: the Plasmodium falciparum Cysteine Protease Falcipain-2 -

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Basic information

Entry
Database: PDB / ID: 1yvb
Titlethe Plasmodium falciparum Cysteine Protease Falcipain-2
Components
  • Cystatin
  • falcipain 2
KeywordsHYDROLASE/HYDROLASE INHIBITOR / cysteine protease-inhibitor complex / HYDROLASE-HYDROLASE INHIBITOR COMPLEX
Function / homology
Function and homology information


cysteine-type endopeptidase inhibitor activity / cysteine-type peptidase activity / vesicle / Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases / proteolysis / extracellular space / membrane / cytoplasm
Similarity search - Function
Proteinase inhibitor I25, cystatin, conserved site / Cysteine proteases inhibitors signature. / Cystatin domain / Cystatin-like domain / Cystatin domain / Nuclear Transport Factor 2; Chain: A, - #10 / Cystatin superfamily / Cathepsin propeptide inhibitor domain (I29) / Cathepsin propeptide inhibitor domain (I29) / Cathepsin propeptide inhibitor domain (I29) ...Proteinase inhibitor I25, cystatin, conserved site / Cysteine proteases inhibitors signature. / Cystatin domain / Cystatin-like domain / Cystatin domain / Nuclear Transport Factor 2; Chain: A, - #10 / Cystatin superfamily / 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 / Nuclear Transport Factor 2; Chain: A, / Papain-like cysteine peptidase superfamily / Roll / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
Cystatin / Falcipain 2
Similarity search - Component
Biological speciesPlasmodium falciparum (malaria parasite P. falciparum)
Gallus gallus (chicken)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsWang, S.X.
CitationJournal: Proc.Natl.Acad.Sci.Usa / Year: 2006
Title: Structural basis for unique mechanisms of folding and hemoglobin binding by a malarial protease.
Authors: Wang, S.X. / Pandey, K.C. / Somoza, J.R. / Sijwali, P.S. / Kortemme, T. / Brinen, L.S. / Fletterick, R.J. / Rosenthal, P.J. / McKerrow, J.H.
History
DepositionFeb 15, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 28, 2006Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.3Jul 28, 2021Group: Advisory / Data collection ...Advisory / Data collection / Derived calculations / Refinement description
Category: pdbx_unobs_or_zero_occ_atoms / refine ...pdbx_unobs_or_zero_occ_atoms / refine / refine_ls_shell / reflns / reflns_shell / struct_conn / struct_site
Item: _refine.ls_percent_reflns_obs / _refine_ls_shell.percent_reflns_obs ..._refine.ls_percent_reflns_obs / _refine_ls_shell.percent_reflns_obs / _reflns.percent_possible_obs / _reflns_shell.number_unique_all / _reflns_shell.number_unique_obs / _reflns_shell.percent_possible_all / _struct_conn.pdbx_leaving_atom_flag / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Oct 20, 2021Group: Advisory / Database references
Category: database_2 / pdbx_unobs_or_zero_occ_atoms / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.5Aug 23, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: falcipain 2
I: Cystatin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,8673
Polymers39,7752
Non-polymers921
Water25214
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1900 Å2
ΔGint-13 kcal/mol
Surface area17210 Å2
MethodPISA
Unit cell
Length a, b, c (Å)96.036, 96.036, 124.164
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Cell settingtetragonal
Space group name H-MP43212

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Components

#1: Protein falcipain 2 / E.C.3.4.22.-


Mass: 27186.672 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Plasmodium falciparum (malaria parasite P. falciparum)
Strain: 3D7 / Gene: AF239801 / Plasmid: pQE30 / Production host: Escherichia coli (E. coli) / Strain (production host): m15 pREP4
References: UniProt: Q9N6S8, Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases
#2: Protein Cystatin / / Egg-white cystatin


Mass: 12588.377 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Gallus gallus (chicken) / References: UniProt: P01038
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 14 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 2

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Sample preparation

CrystalDensity Matthews: 3.6 Å3/Da / Density % sol: 65.9 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6
Details: 0.1 M HEPES pH 7.5 and 4.3 M NaCl , pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 200 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.115875 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Feb 8, 2004
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.115875 Å / Relative weight: 1
ReflectionResolution: 2.7→41 Å / Num. obs: 16071 / % possible obs: 96.5 % / Observed criterion σ(I): 2 / Redundancy: 6 % / Biso Wilson estimate: 46 Å2 / Rmerge(I) obs: 0.148 / Net I/σ(I): 8.9
Reflection shellResolution: 2.7→2.8 Å / Redundancy: 2.6 % / Rmerge(I) obs: 0.423 / Mean I/σ(I) obs: 2 / Num. unique obs: 1426 / Rsym value: 0.443 / % possible all: 85

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1ATK

1atk


Resolution: 2.7→40 Å / Data cutoff high absF: 1000 / Data cutoff low absF: 0 / Cross valid method: THROUGHOUT / σ(F): 2 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2641 769 -Random
Rwork0.2322 ---
all0.2322 ---
obs0.2322 15720 95 %-
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--4.123 Å20 Å20 Å2
2---4.123 Å20 Å2
3---8.246 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.41 Å0.37 Å
Luzzati d res low-5 Å
Luzzati sigma a0.65 Å0.73 Å
Refinement stepCycle: LAST / Resolution: 2.7→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2789 0 6 14 2809
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.019
X-RAY DIFFRACTIONc_angle_deg1.5
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkRefine-IDNum. reflection obs% reflection obs (%)
2.7-2.80.37490.41X-RAY DIFFRACTION115772
2.8-2.910.29620.34X-RAY DIFFRACTION151092
2.91-3.040.35650.32X-RAY DIFFRACTION155196

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