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- PDB-7avm: Crystal Structure of Pro-Rhodesain C150A -

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Basic information

Entry
Database: PDB / ID: 7avm
TitleCrystal Structure of Pro-Rhodesain C150A
ComponentsCysteine protease
KeywordsHYDROLASE / African trypanosomes / Sleeping Sickness / human african trypanosomiasis / cysteine protease / zymogen / pro-enzyme / rhodesain
Function / homology
Function and homology information


proteolysis involved in protein catabolic process / lysosome / cysteine-type endopeptidase activity / extracellular space
Similarity search - Function
Domain of unknown function DUF3586 / Protein of unknown function (DUF3586) / Cathepsin propeptide inhibitor domain (I29) / Cathepsin propeptide inhibitor domain (I29) / Cathepsin propeptide inhibitor domain (I29) / Papain-like cysteine endopeptidase / Cysteine peptidase, asparagine active site / Eukaryotic thiol (cysteine) proteases asparagine active site. / Cysteine peptidase, histidine active site / Eukaryotic thiol (cysteine) proteases histidine active site. ...Domain of unknown function DUF3586 / Protein of unknown function (DUF3586) / Cathepsin propeptide inhibitor domain (I29) / Cathepsin propeptide inhibitor domain (I29) / Cathepsin propeptide inhibitor domain (I29) / Papain-like cysteine endopeptidase / Cysteine peptidase, asparagine active site / Eukaryotic thiol (cysteine) proteases asparagine active site. / 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 peptidase, cysteine active site / Eukaryotic thiol (cysteine) proteases cysteine active site. / Papain-like cysteine peptidase superfamily / Prokaryotic membrane lipoprotein lipid attachment site profile.
Similarity search - Domain/homology
Biological speciesTrypanosoma brucei rhodesiense (eukaryote)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsJohe, P. / Jaenicke, E. / Neuweiler, H. / Schirmeister, T. / Kersten, C. / Hellmich, U.
Citation
Journal: J.Biol.Chem. / Year: 2021
Title: Structure, interdomain dynamics, and pH-dependent autoactivation of pro-rhodesain, the main lysosomal cysteine protease from African trypanosomes.
Authors: Johe, P. / Jaenicke, E. / Neuweiler, H. / Schirmeister, T. / Kersten, C. / Hellmich, U.A.
#1: Journal: Biorxiv / Year: 2020
Title: Structural basis of autoinhibition in the T. brucei rhodesiense cathepsin L zymogen pro-rhodesain and pH-dependent cleavage
Authors: Johe, P. / Jaenicke, E. / Neuweiler, H. / Schirmeister, T. / Kersten, C. / Hellmich, U.
#2: Journal: To Be Published
Title: Structural basis of autoinhibition in the T. brucei rhodesiense cathepsin L zymogen pro-rhodesain and pH-dependent cleavage
Authors: Johe, P. / Kersten, C. / Jaenicke, E. / Neuweiler, H. / Schirmeister, T. / Hellmich, U.
History
DepositionNov 5, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 25, 2020Provider: repository / Type: Initial release
Revision 1.1Nov 16, 2022Group: Database references / Category: citation / citation_author / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.3Nov 6, 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

Downloads & links

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Assembly

Deposited unit
A: Cysteine protease
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,9902
Polymers35,8981
Non-polymers921
Water68538
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area290 Å2
ΔGint-1 kcal/mol
Surface area14270 Å2
MethodPISA
Unit cell
Length a, b, c (Å)123.190, 123.190, 53.910
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number146
Space group name H-MH3
Space group name HallR3
Symmetry operation#1: x,y,z
#2: -y,x-y,z
#3: -x+y,-x,z
#4: x+1/3,y+2/3,z+2/3
#5: -y+1/3,x-y+2/3,z+2/3
#6: -x+y+1/3,-x+2/3,z+2/3
#7: x+2/3,y+1/3,z+1/3
#8: -y+2/3,x-y+1/3,z+1/3
#9: -x+y+2/3,-x+1/3,z+1/3

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Components

#1: Protein Cysteine protease / Pro-Rhodesain


Mass: 35897.926 Da / Num. of mol.: 1 / Mutation: C150A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Trypanosoma brucei rhodesiense (eukaryote)
Gene: rhodesain / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q95PM0, cathepsin L
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


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


Mass: 18.015 Da / Num. of mol.: 38 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
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: 2.07 Å3/Da / Density % sol: 40.48 %
Crystal growTemperature: 300 K / Method: vapor diffusion, hanging drop / pH: 3.5
Details: 40 mM sodium citrate, 30% PEG-6000, Lead(II) acetate (saturated),cryoprotection with glycerol 10%

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: BRUKER AXS MICROSTAR-H / Wavelength: 1.5417 Å
DetectorType: MAR scanner 300 mm plate / Detector: IMAGE PLATE / Date: Jul 11, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5417 Å / Relative weight: 1
ReflectionResolution: 2.8→37.92 Å / Num. obs: 7512 / % possible obs: 97.23 % / Redundancy: 20.6 % / Biso Wilson estimate: 41.24 Å2 / CC1/2: 0.919 / CC star: 0.979 / Net I/σ(I): 214.7
Reflection shellResolution: 2.8→2.9 Å / Num. unique obs: 729 / CC1/2: 0.905 / CC star: 0.975 / % possible all: 92.73

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Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
Coot0.9model building
XDSdata reduction
XDSdata scaling
PHENIX1.16_3549phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6EX8

6ex8


Resolution: 2.8→37.92 Å / SU ML: 0.265 / Cross valid method: FREE R-VALUE / σ(F): 1.97 / Phase error: 28.3682
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2618 --
Rwork0.2537 6581 -
obs0.2556 7306 97.23 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 47.97 Å2
Refinement stepCycle: LAST / Resolution: 2.8→37.92 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2335 0 6 38 2379
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01032392
X-RAY DIFFRACTIONf_angle_d1.59913243
X-RAY DIFFRACTIONf_chiral_restr0.1191340
X-RAY DIFFRACTIONf_plane_restr0.0059434
X-RAY DIFFRACTIONf_dihedral_angle_d23.5332842
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.8-3.010.38641410.35881244X-RAY DIFFRACTION93.2
3.02-3.320.31361410.32071321X-RAY DIFFRACTION96.18
3.32-3.80.25421500.26151333X-RAY DIFFRACTION98.8
3.8-4.780.23531460.22591328X-RAY DIFFRACTION98.27
4.79-37.920.23561470.21251355X-RAY DIFFRACTION99.93

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