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- PDB-2pbh: CRYSTAL STRUCTURE OF HUMAN PROCATHEPSIN B AT 3.3 ANGSTROM RESOLUTION -

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Basic information

Entry
Database: PDB / ID: 2pbh
TitleCRYSTAL STRUCTURE OF HUMAN PROCATHEPSIN B AT 3.3 ANGSTROM RESOLUTION
ComponentsPROCATHEPSIN B
KeywordsTHIOL PROTEASE / CATHEPSIN B / CYSTEINE PROTEASE / PROENZYME / PAPAIN
Function / homology
Function and homology information


cathepsin B / peptidase inhibitor complex / endolysosome lumen / thyroid hormone generation / cellular response to thyroid hormone stimulus / Trafficking and processing of endosomal TLR / proteoglycan binding / Assembly of collagen fibrils and other multimeric structures / decidualization / Collagen degradation ...cathepsin B / peptidase inhibitor complex / endolysosome lumen / thyroid hormone generation / cellular response to thyroid hormone stimulus / Trafficking and processing of endosomal TLR / proteoglycan binding / Assembly of collagen fibrils and other multimeric structures / decidualization / Collagen degradation / collagen catabolic process / collagen binding / epithelial cell differentiation / MHC class II antigen presentation / cysteine-type peptidase activity / proteolysis involved in protein catabolic process / melanosome / peptidase activity / : / regulation of apoptotic process / ficolin-1-rich granule lumen / lysosome / apical plasma membrane / external side of plasma membrane / cysteine-type endopeptidase activity / Neutrophil degranulation / symbiont entry into host cell / perinuclear region of cytoplasm / proteolysis / extracellular space / extracellular exosome / extracellular region
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
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 3.3 Å
AuthorsPodobnik, M. / Turk, D. / Kuhelj, R. / Turk, V.
CitationJournal: FEBS Lett. / Year: 1996
Title: Crystal structures of human procathepsin B at 3.2 and 3.3 Angstroms resolution reveal an interaction motif between a papain-like cysteine protease and its propeptide.
Authors: Turk, D. / Podobnik, M. / Kuhelj, R. / Dolinar, M. / Turk, V.
History
DepositionFeb 14, 1997Processing site: BNL
Revision 1.0Feb 25, 1998Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Apr 3, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.4Oct 9, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: PROCATHEPSIN B


Theoretical massNumber of molelcules
Total (without water)35,2261
Polymers35,2261
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)78.750, 78.750, 153.640
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522

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Components

#1: Protein PROCATHEPSIN B


Mass: 35226.391 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line: BL21 / Plasmid: PET3A / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) PLYSS / References: UniProt: P07858, cathepsin B
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 2

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Sample preparation

CrystalDensity Matthews: 2.35 Å3/Da / Density % sol: 48 %
Crystal growpH: 7.2
Details: PROTEIN WAS CRYSTALLIZED FROM 2 M AMMONIUM SULFATE, 700 MM TRIS, PH 7.2
Crystal grow
*PLUS
Temperature: 20 ℃ / pH: 7.1 / Method: vapor diffusion, sitting drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
12 Mammonium sulphate1reservoir
2700 mMTris-HCl1reservoir

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Data collection

DiffractionMean temperature: 283 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH2R / Wavelength: 1.5418
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Oct 1, 1995 / Details: COLLIMATOR
RadiationMonochromator: NI FILTER / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 3.3→8 Å / Num. obs: 4297 / % possible obs: 94.2 % / Observed criterion σ(I): 2 / Redundancy: 8.5 % / Rmerge(I) obs: 0.186 / Rsym value: 0.08 / Net I/σ(I): 3.9
Reflection shellResolution: 3.3→3.4 Å / Redundancy: 4.2 % / Rmerge(I) obs: 0.066 / Mean I/σ(I) obs: 2.4 / Rsym value: 0.316 / % possible all: 96.7

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Processing

Software
NameClassification
MOSFLMdata reduction
CCP4data reduction
MAINmodel building
MAINrefinement
CCP4data scaling
MAINphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY

Resolution: 3.3→10 Å / σ(F): 2
RfactorNum. reflection% reflection
Rfree0.269 -8 %
Rwork0.2313 --
obs-4011 -
Refinement stepCycle: LAST / Resolution: 3.3→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2342 0 0 0 2342
Software
*PLUS
Name: MAIN / Classification: refinement
Refinement
*PLUS
Num. reflection all: 4297 / Rfactor Rfree: 0.269
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.0119
X-RAY DIFFRACTIONx_angle_deg1.83

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