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- PDB-3pbh: REFINED CRYSTAL STRUCTURE OF HUMAN PROCATHEPSIN B AT 2.5 ANGSTROM... -

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Basic information

Entry
Database: PDB / ID: 3pbh
TitleREFINED CRYSTAL STRUCTURE OF HUMAN PROCATHEPSIN B AT 2.5 ANGSTROM RESOLUTION
ComponentsPROCATHEPSIN B
KeywordsTHIOL PROTEASE / CATHEPSIN B / CYSTEINE PROTEASE / PROENZYME / PAPAIN
Function / homology
Function and homology information


cathepsin B / peptidase inhibitor complex / regulation of catalytic activity / thyroid hormone generation / endolysosome lumen / cellular response to thyroid hormone stimulus / Trafficking and processing of endosomal TLR / proteoglycan binding / Assembly of collagen fibrils and other multimeric structures / Collagen degradation ...cathepsin B / peptidase inhibitor complex / regulation of catalytic activity / thyroid hormone generation / endolysosome lumen / cellular response to thyroid hormone stimulus / Trafficking and processing of endosomal TLR / proteoglycan binding / Assembly of collagen fibrils and other multimeric structures / Collagen degradation / decidualization / collagen catabolic process / collagen binding / cysteine-type peptidase activity / MHC class II antigen presentation / epithelial cell differentiation / proteolysis involved in protein catabolic process / melanosome / peptidase activity / collagen-containing extracellular matrix / regulation of apoptotic process / ficolin-1-rich granule lumen / lysosome / apical plasma membrane / symbiont entry into host cell / external side of plasma membrane / cysteine-type endopeptidase activity / Neutrophil degranulation / 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 peptidase, cysteine active site / Eukaryotic thiol (cysteine) proteases cysteine active site. / Cysteine proteinases / 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: 2.5 Å
AuthorsPodobnik, M. / Turk, D. / Kuhelj, R. / Turk, V.
CitationJournal: J.Mol.Biol. / Year: 1997
Title: Crystal structure of the wild-type human procathepsin B at 2.5 A resolution reveals the native active site of a papain-like cysteine protease zymogen.
Authors: Podobnik, M. / Kuhelj, R. / Turk, V. / Turk, D.
History
DepositionFeb 13, 1997Processing site: BNL
Revision 1.0Feb 25, 1998Provider: repository / Type: Initial release
Revision 1.1Mar 4, 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 16, 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
Water2,072115
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)77.550, 77.550, 153.160
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
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 115 / 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: 2.27 Å3/Da / Density % sol: 46 %
Crystal growpH: 5.72
Details: PROTEIN WAS CRYSTALLIZED FROM 2 M AMMONIUM SULFATE, PH 5.72
Crystal
*PLUS
Crystal grow
*PLUS
Temperature: 22 ℃ / pH: 8 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
120 mMTris-HCl1drop
210 mg/mlprotein1drop
32 Mammonium sulfate1reservoir

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Data collection

DiffractionMean temperature: 285 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH2R / Wavelength: 1.5418
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Jun 1, 1996 / Details: YALE MIRRORS
RadiationMonochromator: YALE MIRRORS / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionHighest resolution: 2.5 Å / Num. obs: 9306 / % possible obs: 92.1 % / Observed criterion σ(I): 2 / Rmerge(I) obs: 0.129
Reflection shellResolution: 2.5→2.6 Å / % possible all: 90.4
Reflection
*PLUS
Lowest resolution: 100 Å / Num. measured all: 54009
Reflection shell
*PLUS
% possible obs: 90.4 % / Rmerge(I) obs: 0.4

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Processing

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

Resolution: 2.5→10 Å / σ(F): 2
RfactorNum. reflection% reflection
Rfree0.234 -8 %
Rwork0.179 --
obs-9119 -
Refinement stepCycle: LAST / Resolution: 2.5→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2270 0 0 115 2385
Software
*PLUS
Name: MAIN / Classification: refinement
Refinement
*PLUS
Num. reflection all: 9306 / Rfactor obs: 0.179 / Rfactor Rfree: 0.2342
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.012
X-RAY DIFFRACTIONx_angle_deg1.64

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