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- PDB-2dc8: X-ray crystal structure analysis of bovine spleen cathepsin B-CA0... -

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Basic information

Entry
Database: PDB / ID: 2dc8
TitleX-ray crystal structure analysis of bovine spleen cathepsin B-CA059 complex
ComponentsCATHEPSIN B
KeywordsHYDROLASE / Cathepsin B / Cysteine Protease / CA059 / EC 3.4.22.1
Function / homology
Function and homology information


Trafficking and processing of endosomal TLR / Collagen degradation / cathepsin B / MHC class II antigen presentation / Neutrophil degranulation / proteolysis involved in protein catabolic process / melanosome / endopeptidase activity / lysosome / apical plasma membrane ...Trafficking and processing of endosomal TLR / Collagen degradation / cathepsin B / MHC class II antigen presentation / Neutrophil degranulation / proteolysis involved in protein catabolic process / melanosome / endopeptidase activity / lysosome / apical plasma membrane / cysteine-type endopeptidase activity / extracellular space
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
Chem-59A / PHOSPHATE ION / : / Cathepsin B
Similarity search - Component
Biological speciesBos taurus (cattle)
MethodX-RAY DIFFRACTION / ISOMORPHOUS REPLACEMENT / Resolution: 1.94 Å
AuthorsWatanabe, D.
CitationJournal: To be Published
Title: Quantitative estimation of each active subsite of cathepsin B for the inhibitory activity, based on the inhibitory activitybinding mode relationship of a series of epoxysuccinyl inhibitors by ...Title: Quantitative estimation of each active subsite of cathepsin B for the inhibitory activity, based on the inhibitory activitybinding mode relationship of a series of epoxysuccinyl inhibitors by X-ray crystal structure analyses of the complexes
Authors: Watanabe, D. / Yamamoto, A. / Matsumoto, K. / Murata, M. / Kitamura, K. / Tomoo, K. / Ishida, T.
History
DepositionDec 31, 2005Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 24, 2006Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software
Revision 1.4Oct 25, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / struct_site
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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 1.5Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: CATHEPSIN B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,3794
Polymers27,9191
Non-polymers4603
Water4,450247
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)72.320, 72.320, 140.110
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein CATHEPSIN B


Mass: 27919.037 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / Tissue: SPLEEN
References: GenBank: 27806671, UniProt: P07688*PLUS, cathepsin B
#2: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#3: Chemical ChemComp-59A / N-{[(2S,3S)-3-(ETHOXYCARBONYL)OXIRAN-2-YL]CARBONYL}-L-ISOLEUCINE / CA059 / N-(L-3-TRANS-ETHOXYCARBONYLOXIRANE-2-CARBONYL)-L-ISOLEUCINE


Mass: 273.282 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H19NO6
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


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


Mass: 18.015 Da / Num. of mol.: 247 / Source method: isolated from a natural source / Formula: H2O
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: 3.28 Å3/Da / Density % sol: 62.49 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 3.5
Details: 50mM sodium citrate, 2.4M sodium phosphate, pH 3.5, VAPOR DIFFUSION, HANGING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 120 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IIC / Detector: IMAGE PLATE / Date: Oct 19, 2005
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.94→64.24 Å / Num. obs: 28249 / % possible obs: 99.9 % / Redundancy: 9.89 % / Biso Wilson estimate: 10.2 Å2 / Rmerge(I) obs: 0.062
Reflection shellResolution: 1.94→2.01 Å / Redundancy: 9.65 % / Rmerge(I) obs: 0.224 / % possible all: 100

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Processing

Software
NameVersionClassification
CNS1refinement
CNSphasing
RefinementMethod to determine structure: ISOMORPHOUS REPLACEMENT
Starting model: PDB ENTRY 1ITO

1ito


Resolution: 1.94→9.99 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 2039747.07 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.21 1434 5 %RANDOM
Rwork0.183 ---
obs0.183 28249 99.8 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 54.0312 Å2 / ksol: 0.502863 e/Å3
Displacement parametersBiso mean: 16.8 Å2
Baniso -1Baniso -2Baniso -3
1-0.5 Å20 Å20 Å2
2--0.5 Å20 Å2
3----1 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.21 Å0.19 Å
Luzzati d res low-5 Å
Luzzati sigma a0.1 Å0.03 Å
Refinement stepCycle: LAST / Resolution: 1.94→9.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1908 0 30 247 2185
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d23.9
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.7
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.191.5
X-RAY DIFFRACTIONc_mcangle_it1.832
X-RAY DIFFRACTIONc_scbond_it2.092
X-RAY DIFFRACTIONc_scangle_it2.852.5
LS refinement shellResolution: 1.94→2.02 Å / Rfactor Rfree error: 0.017 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.23 181 5 %
Rwork0.194 3419 -
obs--73.9 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater.top
X-RAY DIFFRACTION3ion.paramion.top
X-RAY DIFFRACTION459a.param59a.top
X-RAY DIFFRACTION5gol.paramgol.top

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