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- PDB-4i07: Structure of mature form of cathepsin B1 from Schistosoma mansoni -

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Basic information

Entry
Database: PDB / ID: 4i07
TitleStructure of mature form of cathepsin B1 from Schistosoma mansoni
ComponentsCathepsin B-like peptidase (C01 family)
KeywordsHYDROLASE / peptidase / digestive tract
Function / homology
Function and homology information


cysteine-type endopeptidase activity / proteolysis
Similarity search - Function
Peptidase C1A, propeptide / Peptidase family C1 propeptide / : / 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 ...Peptidase C1A, propeptide / Peptidase family C1 propeptide / : / 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 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
ACETATE ION / Cathepsin B1 isotype 1
Similarity search - Component
Biological speciesSchistosoma mansoni (invertebrata)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.3 Å
AuthorsRezacova, P. / Jilkova, A. / Brynda, J. / Horn, M. / Mares, M.
CitationJournal: Structure / Year: 2014
Title: Activation route of the Schistosoma mansoni cathepsin B1 drug target: structural map with a glycosaminoglycan switch
Authors: Jilkova, A. / Horn, M. / Rezacova, P. / Maresova, L. / Fajtova, P. / Brynda, J. / Vondrasek, J. / McKerrow, J.H. / Caffrey, C.R. / Mares, M.
History
DepositionNov 16, 2012Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Feb 5, 2014Provider: repository / Type: Initial release
Revision 1.1Nov 12, 2014Group: Other
Revision 1.2May 25, 2016Group: Database references
Revision 1.3Dec 25, 2019Group: Data collection / Database references / Derived calculations
Category: reflns_shell / struct_conn / struct_ref_seq_dif
Item: _reflns_shell.Rmerge_I_obs / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details
Revision 1.4Nov 8, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Cathepsin B-like peptidase (C01 family)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,6343
Polymers28,5391
Non-polymers942
Water7,692427
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)33.143, 79.173, 90.483
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Cathepsin B-like peptidase (C01 family) / Cathepsin B1 isotype 1


Mass: 28539.256 Da / Num. of mol.: 1 / Fragment: UNP residues 87-340 / Mutation: T168A, T283A
Source method: isolated from a genetically manipulated source
Details: zeocin resistance / Source: (gene. exp.) Schistosoma mansoni (invertebrata) / Gene: cb1.1, Smp_103610 / Plasmid: pPICZalpha / Production host: Pichia pastoris (fungus) / Strain (production host): X33 / References: UniProt: Q8MNY2, cathepsin B
#2: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 427 / 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: 1

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Sample preparation

CrystalDensity Matthews: 2.08 Å3/Da / Density % sol: 40.86 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: Reservoir: 0.2M Ammonium Acetate, 0.1M Sodium Citrate, 30% PEG 4000. Protein buffer and concentration: 5mM Sodium Acetate, pH 5.5, Cpr=2.5mg/ml. Ratio Protein: Reservoir=1:1. Cryocooled in ...Details: Reservoir: 0.2M Ammonium Acetate, 0.1M Sodium Citrate, 30% PEG 4000. Protein buffer and concentration: 5mM Sodium Acetate, pH 5.5, Cpr=2.5mg/ml. Ratio Protein: Reservoir=1:1. Cryocooled in mother liquor, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.978 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Jul 10, 2008 / Details: mirrors
RadiationMonochromator: Si111 double-crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.978 Å / Relative weight: 1
ReflectionResolution: 1.3→50 Å / Num. all: 66361 / Num. obs: 59658 / % possible obs: 89.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.3 % / Biso Wilson estimate: 13.5 Å2 / Rmerge(I) obs: 0.077 / Net I/σ(I): 33.7
Reflection shellResolution: 1.3→1.32 Å / Redundancy: 5.7 % / Rmerge(I) obs: 0.438 / Mean I/σ(I) obs: 4 / % possible all: 49.3

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Processing

Software
NameVersionClassification
HKL-3000data collection
MOLREPphasing
REFMAC5.3.0037refinement
HKL-3000data reduction
HKL-3000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3QSD

3qsd


Resolution: 1.3→19.79 Å / Cor.coef. Fo:Fc: 0.973 / Cor.coef. Fo:Fc free: 0.959 / SU B: 1.487 / SU ML: 0.029 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.057 / ESU R Free: 0.054 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.17667 2711 5.1 %RANDOM
Rwork0.1374 ---
all0.13936 56496 --
obs0.13936 50812 89.95 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 11.512 Å2
Baniso -1Baniso -2Baniso -3
1-0.52 Å20 Å20 Å2
2---0.39 Å20 Å2
3----0.13 Å2
Refinement stepCycle: LAST / Resolution: 1.3→19.79 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1993 0 5 427 2425
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0222178
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.4371.9422972
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7995289
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.27924.02102
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.92415387
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.9421513
X-RAY DIFFRACTIONr_chiral_restr0.0980.2300
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.021695
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2010.21153
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3110.21501
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1910.2317
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2040.267
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.150.256
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.4731.51347
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.09622126
X-RAY DIFFRACTIONr_scbond_it2.7183974
X-RAY DIFFRACTIONr_scangle_it3.8574.5827
X-RAY DIFFRACTIONr_rigid_bond_restr1.53732321
X-RAY DIFFRACTIONr_sphericity_free6.2473428
X-RAY DIFFRACTIONr_sphericity_bonded4.44932100
LS refinement shellResolution: 1.3→1.334 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.215 116 -
Rwork0.171 2086 -
obs--50.7 %

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