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- PDB-1mir: RAT PROCATHEPSIN B -

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Basic information

Entry
Database: PDB / ID: 1mir
TitleRAT PROCATHEPSIN B
ComponentsPROCATHEPSIN B
KeywordsHYDROLASE / THIOL PROTEASE / CYSTEINE PROTEASE
Function / homology
Function and homology information


Trafficking and processing of endosomal TLR / Assembly of collagen fibrils and other multimeric structures / kininogen binding / cathepsin B / Collagen degradation / response to interleukin-4 / peptidase inhibitor complex / MHC class II antigen presentation / thyroid hormone generation / cellular response to thyroid hormone stimulus ...Trafficking and processing of endosomal TLR / Assembly of collagen fibrils and other multimeric structures / kininogen binding / cathepsin B / Collagen degradation / response to interleukin-4 / peptidase inhibitor complex / MHC class II antigen presentation / thyroid hormone generation / cellular response to thyroid hormone stimulus / proteoglycan binding / Neutrophil degranulation / response to dexamethasone / response to amine / decidualization / collagen catabolic process / response to glucose / response to mechanical stimulus / cysteine-type peptidase activity / skeletal muscle tissue development / epithelial cell differentiation / collagen binding / proteolysis involved in protein catabolic process / response to cytokine / peptide binding / protein catabolic process / sarcolemma / response to organic cyclic compound / response to peptide hormone / autophagy / cellular response to mechanical stimulus / : / melanosome / peptidase activity / spermatogenesis / neuron apoptotic process / response to ethanol / endopeptidase activity / lysosome / symbiont entry into host cell / apical plasma membrane / external side of plasma membrane / cysteine-type endopeptidase activity / protein-containing complex binding / perinuclear region of cytoplasm / cell surface / proteolysis / extracellular space / 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 speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / Resolution: 2.8 Å
AuthorsCygler, M. / Sivaraman, J. / Grochulski, P. / Coulombe, R. / Storer, A.C. / Mort, J.S.
Citation
Journal: Structure / Year: 1996
Title: Structure of rat procathepsin B: model for inhibition of cysteine protease activity by the proregion.
Authors: Cygler, M. / Sivaraman, J. / Grochulski, P. / Coulombe, R. / Storer, A.C. / Mort, J.S.
#1: Journal: To be Published
Title: Crystallization of Rat Procathepsin B
Authors: Sivaraman, J. / Coulombe, R. / Magny, M.-C. / Mason, P. / Mort, J.S. / Cygler, M.
History
DepositionJan 12, 1996Processing site: BNL
Revision 1.0Jan 11, 1997Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 12, 2020Group: Advisory / Database references ...Advisory / Database references / Derived calculations / Other
Category: pdbx_database_status / pdbx_struct_assembly ...pdbx_database_status / pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_unobs_or_zero_occ_atoms / struct_ref_seq_dif
Item: _pdbx_database_status.process_site / _struct_ref_seq_dif.details
Revision 1.4Nov 3, 2021Group: Advisory / Database references
Category: database_2 / pdbx_unobs_or_zero_occ_atoms / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: PROCATHEPSIN B
B: PROCATHEPSIN B


Theoretical massNumber of molelcules
Total (without water)71,2672
Polymers71,2672
Non-polymers00
Water59433
1
A: PROCATHEPSIN B


Theoretical massNumber of molelcules
Total (without water)35,6341
Polymers35,6341
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: PROCATHEPSIN B


Theoretical massNumber of molelcules
Total (without water)35,6341
Polymers35,6341
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)99.600, 99.600, 141.400
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (0.2123, 0.6981, -0.6839), (0.7037, -0.5948, -0.3887), (-0.6781, -0.3987, -0.6175)
Vector: 15.374, 43.711, 72.106)

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Components

#1: Protein PROCATHEPSIN B


Mass: 35633.625 Da / Num. of mol.: 2 / Mutation: C29S, S115A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Variant: NATURALLY OCCURRING VARIANT V223A / Production host: Pichia pastoris (fungus) / References: UniProt: P00787, cathepsin B
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 33 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.84 Å3/Da / Density % sol: 56 %
Crystal
*PLUS
Crystal grow
*PLUS
Method: unknown

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Data collection

Diffraction sourceWavelength: 1.5418
DetectorType: RIGAKU / Detector: IMAGE PLATE / Date: Jul 7, 1995
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.8→74 Å / Num. obs: 19015 / % possible obs: 91 % / Observed criterion σ(I): 1 / Redundancy: 4.4 % / Rmerge(I) obs: 0.097

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Processing

Software
NameVersionClassification
R-AXISSOFTWAREdata collection
X-PLOR3.1model building
X-PLOR3.1refinement
R-AXISdata reduction
X-PLOR3.1phasing
RefinementResolution: 2.8→8 Å / σ(F): 2
RfactorNum. reflection% reflection
Rfree0.27 -10 %
Rwork0.22 --
obs0.22 18037 92 %
Displacement parametersBiso mean: 32.4 Å2
Refinement stepCycle: LAST / Resolution: 2.8→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4856 0 0 33 4889
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.009
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.44
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d22.89
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.04
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it2
X-RAY DIFFRACTIONx_mcangle_it3
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Software
*PLUS
Name: X-PLOR / Version: 3.1 / Classification: refinement
Refinement
*PLUS
Rfactor all: 0.22 / Rfactor obs: 0.19
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg22.89
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.04

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