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- PDB-3k9m: Cathepsin B in complex with stefin A -

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Basic information

Entry
Database: PDB / ID: 3k9m
TitleCathepsin B in complex with stefin A
Components
  • Cathepsin B
  • Cystatin-A
KeywordsHYDROLASE/HYDROLASE INHIBITOR / Disulfide bond / Glycoprotein / Lysosome / Protease / Thiol protease / Zymogen / Thiol protease inhibitor / HYDROLASE-HYDROLASE INHIBITOR complex
Function / homology
Function and homology information


cathepsin B / negative regulation of peptidase activity / peptidase inhibitor complex / Formation of the cornified envelope / peptide cross-linking / cornified envelope / thyroid hormone generation / endolysosome lumen / cellular response to thyroid hormone stimulus / Trafficking and processing of endosomal TLR ...cathepsin B / negative regulation of peptidase activity / peptidase inhibitor complex / Formation of the cornified envelope / peptide cross-linking / cornified envelope / 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 / cysteine-type endopeptidase inhibitor activity / Collagen degradation / decidualization / collagen catabolic process / keratinocyte differentiation / cysteine-type peptidase activity / epithelial cell differentiation / collagen binding / MHC class II antigen presentation / proteolysis involved in protein catabolic process / negative regulation of proteolysis / cell-cell adhesion / melanosome / peptidase activity / regulation of apoptotic process / collagen-containing extracellular matrix / protease binding / ficolin-1-rich granule lumen / lysosome / symbiont entry into host cell / apical plasma membrane / external side of plasma membrane / cysteine-type endopeptidase activity / Neutrophil degranulation / perinuclear region of cytoplasm / proteolysis / extracellular space / extracellular exosome / extracellular region / nucleoplasm / cytosol / cytoplasm
Similarity search - Function
Proteinase inhibitor I25A, stefin / Peptidase C1A, propeptide / Peptidase family C1 propeptide / Proteinase inhibitor I25, cystatin, conserved site / Cysteine proteases inhibitors signature. / Cystatin domain / Cystatin-like domain / Cystatin domain / Nuclear Transport Factor 2; Chain: A, - #10 / Cystatin superfamily ...Proteinase inhibitor I25A, stefin / Peptidase C1A, propeptide / Peptidase family C1 propeptide / Proteinase inhibitor I25, cystatin, conserved site / Cysteine proteases inhibitors signature. / Cystatin domain / Cystatin-like domain / Cystatin domain / Nuclear Transport Factor 2; Chain: A, - #10 / Cystatin superfamily / : / 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 / Nuclear Transport Factor 2; Chain: A, / Papain-like cysteine peptidase superfamily / Roll / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
Cystatin-A / Cathepsin B
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.61 Å
AuthorsRenko, M. / Turk, D.
CitationJournal: Febs J. / Year: 2010
Title: Stefin A displaces the occluding loop of cathepsin B only by as much as required to bind to the active site cleft
Authors: Renko, M. / Pozgan, U. / Majera, D. / Turk, D.
History
DepositionOct 16, 2009Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Nov 3, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 5, 2011Group: Database references / Structure summary
Revision 1.3Nov 1, 2017Group: Advisory / Refinement description
Category: pdbx_unobs_or_zero_occ_atoms / pdbx_unobs_or_zero_occ_residues / software
Revision 1.4Nov 1, 2023Group: Advisory / Data collection ...Advisory / 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 / pdbx_unobs_or_zero_occ_atoms / pdbx_unobs_or_zero_occ_residues
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Cathepsin B
C: Cystatin-A
B: Cathepsin B
D: Cystatin-A


Theoretical massNumber of molelcules
Total (without water)77,7274
Polymers77,7274
Non-polymers00
Water2,288127
1
A: Cathepsin B
C: Cystatin-A


Theoretical massNumber of molelcules
Total (without water)38,8632
Polymers38,8632
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2440 Å2
ΔGint-14 kcal/mol
Surface area15060 Å2
MethodPISA
2
B: Cathepsin B
D: Cystatin-A


Theoretical massNumber of molelcules
Total (without water)38,8632
Polymers38,8632
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2430 Å2
ΔGint-14 kcal/mol
Surface area15260 Å2
MethodPISA
Unit cell
Length a, b, c (Å)62.122, 31.078, 70.937
Angle α, β, γ (deg.)89.950, 104.450, 89.900
Int Tables number1
Space group name H-MP1

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Components

#1: Protein Cathepsin B / / Cathepsin B1 / APP secretase / APPS / Cathepsin B light chain / Cathepsin B heavy chain


Mass: 27842.977 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CTSB, CPSB / Plasmid: PET3a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21DE3 / References: UniProt: P07858, cathepsin B
#2: Protein Cystatin-A / Cystatin-AS / Stefin-A


Mass: 11020.464 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CSTA, STF1, STFA / Plasmid: PET3a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21DE3 / References: UniProt: P01040
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 127 / 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: 1.71 Å3/Da / Density % sol: 27.9 % / Mosaicity: 1.294 °
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 0.2M ammonium suphate, 24% PEG3350, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ELETTRA / Beamline: 5.2R / Wavelength: 0.99988 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Mar 31, 2009 / Details: Double Crystal Si111
RadiationMonochromator: Double Crystal Si111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99988 Å / Relative weight: 1
ReflectionResolution: 2.6→50 Å / Num. all: 15513 / Num. obs: 14361 / % possible obs: 92.6 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 2.6 % / Rmerge(I) obs: 0.084 / Χ2: 0.858 / Net I/σ(I): 6
Reflection shellResolution: 2.6→2.64 Å / Redundancy: 2.2 % / Rmerge(I) obs: 0.206 / Num. unique all: 564 / Χ2: 0.491 / % possible all: 71.2

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACT3.005data extraction
HKL-2000data collection
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1NB3 and 1SP4

1nb3

1sp4


Resolution: 2.61→40.52 Å / Cor.coef. Fo:Fc: 0.932 / Cor.coef. Fo:Fc free: 0.895 / WRfactor Rfree: 0.185 / WRfactor Rwork: 0.191 / Occupancy max: 1 / Occupancy min: 0 / FOM work R set: 0.885 / SU Rfree: 0.343 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.343 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: The structure was refined also with MAIN
RfactorNum. reflection% reflectionSelection details
Rfree0.25 713 5 %RANDOM
Rwork0.198 ---
obs0.201 14360 92.1 %-
all-15513 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 96.22 Å2 / Biso mean: 42.42 Å2 / Biso min: 3.44 Å2
Baniso -1Baniso -2Baniso -3
1--3.46 Å2-1.31 Å2-4.29 Å2
2--4.54 Å2-1.65 Å2
3----3.22 Å2
Refinement stepCycle: LAST / Resolution: 2.61→40.52 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5454 0 0 127 5581
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0225506
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.7091.9437484
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.1975689
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.57224.72250
X-RAY DIFFRACTIONr_dihedral_angle_3_deg22.51315851
X-RAY DIFFRACTIONr_dihedral_angle_4_deg24.3311520
X-RAY DIFFRACTIONr_chiral_restr0.1190.2773
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0214290
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.791.53437
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.47825514
X-RAY DIFFRACTIONr_scbond_it1.58632069
X-RAY DIFFRACTIONr_scangle_it2.7234.51970
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.61→2.68 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.292 45 -
Rwork0.277 711 -
all-756 -
obs--66.67 %

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