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- PDB-8gt0: Structure of falcipain and human Stefin A complex -

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Basic information

Entry
Database: PDB / ID: 8gt0
TitleStructure of falcipain and human Stefin A complex
Components
  • Cystatin-A
  • Cysteine protease falcipain-2
KeywordsHYDROLASE / falcipain / stefin / complex
Function / homology
Function and homology information


MHC class II antigen presentation / negative regulation of peptidase activity / peptidase inhibitor complex / Neutrophil degranulation / food vacuole / Formation of the cornified envelope / peptide cross-linking / cornified envelope / cysteine-type endopeptidase inhibitor activity / keratinocyte differentiation ...MHC class II antigen presentation / negative regulation of peptidase activity / peptidase inhibitor complex / Neutrophil degranulation / food vacuole / Formation of the cornified envelope / peptide cross-linking / cornified envelope / cysteine-type endopeptidase inhibitor activity / keratinocyte differentiation / negative regulation of proteolysis / proteolysis involved in protein catabolic process / cell-cell adhesion / protease binding / Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases / lysosome / cysteine-type endopeptidase activity / proteolysis / extracellular space / nucleoplasm / membrane / cytosol / cytoplasm
Similarity search - Function
Proteinase inhibitor I25A, stefin / Proteinase inhibitor I25, cystatin, conserved site / Cysteine proteases inhibitors signature. / Cystatin domain / Cystatin-like domain / Cystatin domain / Cystatin superfamily / Cathepsin propeptide inhibitor domain (I29) / Cathepsin propeptide inhibitor domain (I29) / Cathepsin propeptide inhibitor domain (I29) ...Proteinase inhibitor I25A, stefin / Proteinase inhibitor I25, cystatin, conserved site / Cysteine proteases inhibitors signature. / Cystatin domain / Cystatin-like domain / Cystatin domain / 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 / Papain-like cysteine peptidase superfamily / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
3,6,9,12,15,18,21-HEPTAOXATRICOSANE-1,23-DIOL / DI(HYDROXYETHYL)ETHER / Cystatin-A / Falcipain-2a
Similarity search - Component
Biological speciesPlasmodium falciparum (malaria parasite P. falciparum)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.28 Å
AuthorsChakraborty, S. / Biswas, S.
Funding support India, 1items
OrganizationGrant numberCountry
Other government India
CitationJournal: To Be Published
Title: Structure of falcipain and human Stefin A complex
Authors: Chakraborty, S. / Biswas, S.
History
DepositionSep 7, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 13, 2023Provider: repository / Type: Initial release
Revision 1.1Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Cysteine protease falcipain-2
B: Cystatin-A
C: Cysteine protease falcipain-2
D: Cystatin-A
E: Cysteine protease falcipain-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)124,901181
Polymers103,6585
Non-polymers21,243176
Water2,594144
1
A: Cysteine protease falcipain-2
B: Cystatin-A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,51291
Polymers38,2262
Non-polymers11,28689
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13910 Å2
ΔGint-78 kcal/mol
Surface area27050 Å2
MethodPISA
2
C: Cysteine protease falcipain-2
D: Cystatin-A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,03575
Polymers38,2262
Non-polymers7,80873
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9780 Å2
ΔGint-68 kcal/mol
Surface area22470 Å2
MethodPISA
3
E: Cysteine protease falcipain-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,35415
Polymers27,2061
Non-polymers2,14814
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1460 Å2
ΔGint-7 kcal/mol
Surface area3610 Å2
MethodPISA
Unit cell
Length a, b, c (Å)65.100, 118.063, 119.340
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

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Protein , 2 types, 5 molecules ACEBD

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


Mass: 27205.672 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Plasmodium falciparum (malaria parasite P. falciparum)
Production host: Escherichia coli (E. coli)
References: UniProt: Q8I6U4, Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases
#2: Protein Cystatin-A / Cystatin-AS / Stefin-A


Mass: 11020.464 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CSTA, STF1, STFA / Production host: Escherichia coli (E. coli) / References: UniProt: P01040

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Non-polymers , 9 types, 320 molecules

#3: Chemical...
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 64 / Source method: obtained synthetically / Formula: C3H8O3 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical...
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 25 / Source method: obtained synthetically / Formula: Na
#5: Chemical...
ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 24 / Source method: obtained synthetically / Formula: C4H10O3 / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical
ChemComp-PE8 / 3,6,9,12,15,18,21-HEPTAOXATRICOSANE-1,23-DIOL


Mass: 370.436 Da / Num. of mol.: 13 / Source method: obtained synthetically / Formula: C16H34O9 / Feature type: SUBJECT OF INVESTIGATION
#7: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: C2H6O2 / Feature type: SUBJECT OF INVESTIGATION
#8: Chemical...
ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 31 / Source method: obtained synthetically / Formula: C8H18O5 / Feature type: SUBJECT OF INVESTIGATION / Comment: precipitant*YM
#9: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: SO4 / Feature type: SUBJECT OF INVESTIGATION
#10: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#11: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 144 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
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: 2.21 Å3/Da / Density % sol: 44.4 %
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop
Details: 0.05 M cadmium chloride, 0.1 M Na HEPES pH 7.5, 1.0 M sodium acetate and 5 mM MgSO4

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-3 / Wavelength: 0.9677 Å
DetectorType: DECTRIS EIGER X 4M / Detector: PIXEL / Date: Dec 9, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9677 Å / Relative weight: 1
ReflectionResolution: 3.28→43.99 Å / Num. obs: 14644 / % possible obs: 99.9 % / Redundancy: 8.6 % / Biso Wilson estimate: 75.1 Å2 / Rmerge(I) obs: 0.428 / Net I/σ(I): 6.1
Reflection shellResolution: 3.28→3.4 Å / Num. unique obs: 1449 / CC1/2: 0.568

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
XDSdata reduction
XDSdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.28→43.99 Å / SU ML: 0.5084 / Cross valid method: FREE R-VALUE / σ(F): 0.01 / Phase error: 32.0269
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2993 746 5.02 %
Rwork0.2783 25733 -
obs0.2794 14644 99.53 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 50.08 Å2
Refinement stepCycle: LAST / Resolution: 3.28→43.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5504 0 1386 144 7034
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00456824
X-RAY DIFFRACTIONf_angle_d1.00028717
X-RAY DIFFRACTIONf_chiral_restr0.0541803
X-RAY DIFFRACTIONf_plane_restr0.0056990
X-RAY DIFFRACTIONf_dihedral_angle_d26.98622815
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.28-3.40.37281540.32562601X-RAY DIFFRACTION99.93
3.4-3.530.38131320.30422567X-RAY DIFFRACTION99.89
3.53-3.690.36331320.2952580X-RAY DIFFRACTION99.96
3.69-3.890.30071270.28882584X-RAY DIFFRACTION99.85
3.89-4.130.31311040.26282606X-RAY DIFFRACTION99.6
4.13-4.450.27521450.24332535X-RAY DIFFRACTION99.33
4.45-4.90.27921420.26162561X-RAY DIFFRACTION98.72
4.9-5.610.27321360.28282570X-RAY DIFFRACTION98.62
5.61-7.060.30821160.30162589X-RAY DIFFRACTION99.89
7.06-43.990.27351710.26742540X-RAY DIFFRACTION99.6

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