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- PDB-5mbm: Cathepsin B in complex with DARPin 8h6 -

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Basic information

Entry
Database: PDB / ID: 5mbm
TitleCathepsin B in complex with DARPin 8h6
Components
  • Cathepsin B
  • DARPin 8h6
KeywordsHYDROLASE / protease / DARPin / complex
Function / homology
Function and homology information


cathepsin B / peptidase inhibitor complex / 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 ...cathepsin B / peptidase inhibitor complex / 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 / cysteine-type peptidase activity / epithelial cell differentiation / collagen binding / MHC class II antigen presentation / proteolysis involved in protein catabolic process / melanosome / peptidase activity / regulation of apoptotic process / collagen-containing extracellular matrix / 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
Similarity search - Function
Peptidase C1A, propeptide / Peptidase family C1 propeptide / Ankyrin repeat-containing domain / : / 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 ...Peptidase C1A, propeptide / Peptidase family C1 propeptide / Ankyrin repeat-containing domain / : / 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 / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / Alpha Horseshoe / Alpha-Beta Complex / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.76 Å
AuthorsTurk, D. / Kramer, L. / Renko, M. / Turk, B.
Funding support Slovenia, 1items
OrganizationGrant numberCountry
Slovenian Research AgencyP1000048 Slovenia
CitationJournal: To Be Published
Title: Cathepsin B in complex with DARPin 8h6
Authors: Turk, D. / Kramer, L.
History
DepositionNov 8, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 20, 2017Provider: repository / Type: Initial release
Revision 1.1Feb 20, 2019Group: Advisory / Data collection / Derived calculations
Category: pdbx_data_processing_status / pdbx_validate_symm_contact / struct_conn
Revision 1.2May 1, 2024Group: 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
B: Cathepsin B
C: DARPin 8h6
D: DARPin 8h6


Theoretical massNumber of molelcules
Total (without water)92,5774
Polymers92,5774
Non-polymers00
Water2,576143
1
A: Cathepsin B
C: DARPin 8h6


Theoretical massNumber of molelcules
Total (without water)46,2882
Polymers46,2882
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Cathepsin B
D: DARPin 8h6


Theoretical massNumber of molelcules
Total (without water)46,2882
Polymers46,2882
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)101.45, 201.52, 46.86
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein Cathepsin B / / APP secretase / APPS / Cathepsin B1


Mass: 28131.408 Da / Num. of mol.: 2 / Fragment: UNP residues 78-333
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CTSB, CPSB / Production host: Escherichia coli (E. coli) / References: UniProt: P07858, cathepsin B
#2: Protein DARPin 8h6


Mass: 18156.984 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Production host: Escherichia coli (E. coli)
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 143 / 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: 2.65 Å3/Da / Density % sol: 53.56 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4 / Details: 0,1 M Na-citrate 15% PEG6000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.918007 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jan 24, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.918007 Å / Relative weight: 1
ReflectionResolution: 2.76→46.8 Å / Num. obs: 25129 / % possible obs: 98.6 % / Observed criterion σ(F): 1 / Redundancy: 6.2 % / CC1/2: 0.99 / Rmerge(I) obs: 0.17 / Rsym value: 0.18 / Net I/σ(I): 10.9
Reflection shellResolution: 2.76→2.93 Å / Redundancy: 6.4 % / Rmerge(I) obs: 1.01 / Mean I/σ(I) obs: 1.6 / CC1/2: 0.67 / % possible all: 93

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Processing

Software
NameVersionClassification
MAIN2016refinement
XDS2016data reduction
XDS2016data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: cathepsin B and ankirin

Resolution: 2.76→46.7 Å / Cor.coef. Fo:Fc: 0.8869 / Cor.coef. Fo:Fc free: 0.868 / Cross valid method: NONE / σ(F): 0 / Phase error: 27.2
Details: free kick refinement target was used in combination with NCS and secondary structure hydrogen bonds restraints
RfactorNum. reflection% reflectionSelection details
Rfree0.2808 25128 -all
Rwork0.2556 ---
obs0.2808 25126 100 %-
Solvent computationBsol: 20.76 Å2 / ksol: 0.31 e/Å3
Displacement parametersBiso max: 99.82 Å2 / Biso mean: 63.33 Å2 / Biso min: 5.17 Å2
Baniso -1Baniso -2Baniso -3
1-2.474 Å20 Å20 Å2
2--3.1 Å20 Å2
3----5.574 Å2
Refinement stepCycle: LAST / Resolution: 2.76→46.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6356 0 0 143 6499
LS refinement shellResolution: 2.76→2.81 Å
RfactorNum. reflection% reflection
Rfree0.4645 953 100 %
Rwork0.4422 953 -
obs--93 %

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