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- PDB-1ito: Crystal Structure Analysis of Bovine Spleen Cathepsin B-E64c complex -

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Basic information

Entry
Database: PDB / ID: 1ito
TitleCrystal Structure Analysis of Bovine Spleen Cathepsin B-E64c complex
ComponentsCathepsin B
KeywordsHYDROLASE / Cathepsin B / Cysteine Protease / E64c
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-E6C / Cathepsin B
Similarity search - Component
Biological speciesBos taurus (cattle)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.286 Å
AuthorsYamamoto, A. / Tomoo, T. / Matsugi, K. / Hara, T. / In, Y. / Murata, M. / Kitamura, K. / Ishida, T.
CitationJournal: BIOCHIM.BIOPHYS.ACTA / Year: 2002
Title: Structural basis for development of cathepsin B-specific noncovalent-type inhibitor: crystal structure of cathepsin B-E64c complex
Authors: Yamamoto, A. / Tomoo, T. / Matsugi, K. / Hara, T. / In, Y. / Murata, M. / Kitamura, K. / Ishida, T.
History
DepositionJan 19, 2002Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 19, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 4, 2017Group: Refinement description / Category: software
Revision 1.4Oct 25, 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_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._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

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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)28,2352
Polymers27,9191
Non-polymers3161
Water2,342130
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)72.578, 72.578, 141.835
Angle α, β, γ (deg.)90, 90, 90
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: UniProt: P07688, cathepsin B
#2: Chemical ChemComp-E6C / N-[1-HYDROXYCARBOXYETHYL-CARBONYL]LEUCYLAMINO-2-METHYL-BUTANE


Mass: 316.393 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H28N2O5
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 130 / 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: 3.34 Å3/Da / Density % sol: 63.21 %
Crystal growTemperature: 288 K / Method: vapor diffusion, hanging drop / pH: 3.5
Details: Sodium phosphate, pH 3.5, VAPOR DIFFUSION, HANGING DROP, temperature 288K
Crystal grow
*PLUS
Temperature: 15 ℃ / pH: 4.5
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
19 mg/mlprotein1drop
250 mMacetate1reservoirpH4.5
32.8 Msodium phosphate1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IIC / Detector: IMAGE PLATE
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.29→30 Å / Num. all: 17925 / Num. obs: 15102 / % possible obs: 84.3 % / Rmerge(I) obs: 0.092
Reflection shellResolution: 2.286→2.3 Å / Rmerge(I) obs: 0.211 / % possible all: 62.1
Reflection
*PLUS
Highest resolution: 2.3 Å / Num. measured all: 58117
Reflection shell
*PLUS
% possible obs: 62.1 %

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Processing

Software
NameClassification
CNSrefinement
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1QDQ

1qdq


Resolution: 2.286→10 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.239 1494 -RANDOM
Rwork0.197 ---
all-17290 --
obs-14759 85.4 %-
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-2.326 Å20 Å20 Å2
2--2.326 Å20 Å2
3----4.653 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.3 Å0.24 Å
Luzzati d res low-5 Å
Luzzati sigma a0.23 Å0.2 Å
Refinement stepCycle: LAST / Resolution: 2.286→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1908 0 22 130 2060
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.23
X-RAY DIFFRACTIONc_dihedral_angle_d24.97
X-RAY DIFFRACTIONc_improper_angle_d0.76
LS refinement shellResolution: 2.3→2.38 Å
RfactorNum. reflection% reflection
Rfree0.2486 117 -
Rwork0.2178 --
obs-1278 75.7 %
Refinement
*PLUS
Highest resolution: 2.3 Å
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg24.97
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.76

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