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- PDB-4yva: Cathepsin K co-crystallized with actinomycetes extract -

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Basic information

Entry
Database: PDB / ID: 4yva
TitleCathepsin K co-crystallized with actinomycetes extract
ComponentsCathepsin K
KeywordsHYDROLASE / cathepsin K / actinomycetes
Function / homology
Function and homology information


cathepsin K / mononuclear cell differentiation / intramembranous ossification / negative regulation of cartilage development / cellular response to zinc ion starvation / RUNX1 regulates transcription of genes involved in differentiation of keratinocytes / thyroid hormone generation / endolysosome lumen / Trafficking and processing of endosomal TLR / proteoglycan binding ...cathepsin K / mononuclear cell differentiation / intramembranous ossification / negative regulation of cartilage development / cellular response to zinc ion starvation / RUNX1 regulates transcription of genes involved in differentiation of keratinocytes / thyroid hormone generation / endolysosome lumen / Trafficking and processing of endosomal TLR / proteoglycan binding / Activation of Matrix Metalloproteinases / cysteine-type endopeptidase activator activity involved in apoptotic process / Collagen degradation / fibronectin binding / collagen catabolic process / mitophagy / extracellular matrix disassembly / bone resorption / cellular response to transforming growth factor beta stimulus / cysteine-type peptidase activity / collagen binding / MHC class II antigen presentation / Degradation of the extracellular matrix / lysosomal lumen / proteolysis involved in protein catabolic process / positive regulation of apoptotic signaling pathway / response to insulin / response to organic cyclic compound / cellular response to tumor necrosis factor / response to ethanol / lysosome / immune response / apical plasma membrane / external side of plasma membrane / cysteine-type endopeptidase activity / intracellular membrane-bounded organelle / serine-type endopeptidase activity / proteolysis / extracellular space / extracellular region / nucleoplasm
Similarity search - Function
Cathepsin propeptide inhibitor domain (I29) / Cathepsin propeptide inhibitor domain (I29) / Cathepsin propeptide inhibitor domain (I29) / Papain-like cysteine endopeptidase / 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 ...Cathepsin propeptide inhibitor domain (I29) / Cathepsin propeptide inhibitor domain (I29) / Cathepsin propeptide inhibitor domain (I29) / Papain-like cysteine endopeptidase / 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 / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsAguda, A.H. / Nguyen, N.T. / Bromme, D. / Brayer, G.D.
Funding support Canada, 1items
OrganizationGrant numberCountry
Canadian Institutes of Health Research (CIHR)FRN 111082 Canada
CitationJournal: J.Nat.Prod. / Year: 2016
Title: Affinity Crystallography: A New Approach to Extracting High-Affinity Enzyme Inhibitors from Natural Extracts.
Authors: Aguda, A.H. / Lavallee, V. / Cheng, P. / Bott, T.M. / Meimetis, L.G. / Law, S. / Nguyen, N.T. / Williams, D.E. / Kaleta, J. / Villanueva, I. / Davies, J. / Andersen, R.J. / Brayer, G.D. / Bromme, D.
History
DepositionMar 19, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 4, 2016Provider: repository / Type: Initial release
Revision 1.1Aug 24, 2016Group: Database references
Revision 1.2Sep 7, 2016Group: Database references
Revision 1.3Sep 27, 2017Group: Data collection / Derived calculations / Category: diffrn_detector / pdbx_struct_oper_list
Item: _diffrn_detector.detector / _pdbx_struct_oper_list.symmetry_operation
Revision 1.4Jan 8, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5Sep 27, 2023Group: 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.6Oct 30, 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: Cathepsin K
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,6202
Polymers23,5231
Non-polymers961
Water2,252125
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)56.720, 56.720, 129.910
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein Cathepsin K / Cathepsin O / Cathepsin O2 / Cathepsin X


Mass: 23523.480 Da / Num. of mol.: 1 / Fragment: UNP residues 115-329
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CTSK, CTSO, CTSO2 / Production host: Pichia (fungus) / References: UniProt: P43235, cathepsin K
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 125 / 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: 2.22 Å3/Da / Density % sol: 44.62 %
Crystal growTemperature: 294.15 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: 24% PEG 8000, 0.2M Ammonium sulfate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL7-1 / Wavelength: 0.97 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Feb 13, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 1.8→51.981 Å / Num. obs: 20402 / % possible obs: 99.7 % / Redundancy: 9.8 % / Rmerge(I) obs: 0.071 / Net I/σ(I): 18.2
Reflection shellResolution: 1.8→1.9 Å / Redundancy: 8.8 % / Rmerge(I) obs: 0.495 / Mean I/σ(I) obs: 4.2 / Num. unique all: 2913 / % possible all: 99.5

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3C9E

3c9e


Resolution: 1.8→51.98 Å / SU ML: 0.16 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 20.29 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.21 1005 4.93 %
Rwork0.183 --
obs0.184 20365 99.5 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.8→51.98 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1636 0 5 125 1766
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0041719
X-RAY DIFFRACTIONf_angle_d0.8012306
X-RAY DIFFRACTIONf_dihedral_angle_d13.889626
X-RAY DIFFRACTIONf_chiral_restr0.032233
X-RAY DIFFRACTIONf_plane_restr0.004301
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8001-1.8950.22161440.19742711X-RAY DIFFRACTION99
1.895-2.01370.22921260.18392708X-RAY DIFFRACTION99
2.0137-2.16920.24011420.18342698X-RAY DIFFRACTION99
2.1692-2.38750.20771420.18722732X-RAY DIFFRACTION100
2.3875-2.73290.24081520.1962741X-RAY DIFFRACTION100
2.7329-3.44310.21971530.18742793X-RAY DIFFRACTION100
3.4431-52.0030.18551460.17232977X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: -21.6299 Å / Origin y: 4.227 Å / Origin z: -12.6522 Å
111213212223313233
T0.1864 Å20.0364 Å20.01 Å2-0.1791 Å20.0171 Å2--0.1803 Å2
L0.6162 °20.3692 °20.1769 °2-0.9564 °20.2838 °2--1.3947 °2
S-0.0054 Å °-0.0427 Å °-0.0421 Å °-0.0936 Å °-0.0175 Å °-0.0653 Å °-0.1268 Å °-0.1646 Å °0 Å °
Refinement TLS groupSelection details: ALL

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