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- PDB-5z5o: Structure of Pycnonodysostosis disease related I249T mutant of hu... -

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Basic information

Entry
Database: PDB / ID: 5z5o
TitleStructure of Pycnonodysostosis disease related I249T mutant of human cathepsin K
Components(Cathepsin K) x 2
KeywordsHYDROLASE / cathepsin k / cysteine protease / lysosomal / Bone disorder / Pycnodysostosis
Function / homology
Function and homology information


cathepsin K / negative regulation of cartilage development / RUNX1 regulates transcription of genes involved in differentiation of keratinocytes / endolysosome lumen / thyroid hormone generation / Trafficking and processing of endosomal TLR / proteoglycan binding / Activation of Matrix Metalloproteinases / Collagen degradation / collagen catabolic process ...cathepsin K / negative regulation of cartilage development / RUNX1 regulates transcription of genes involved in differentiation of keratinocytes / endolysosome lumen / thyroid hormone generation / Trafficking and processing of endosomal TLR / proteoglycan binding / Activation of Matrix Metalloproteinases / Collagen degradation / collagen catabolic process / fibronectin binding / extracellular matrix disassembly / bone resorption / mitophagy / collagen binding / Degradation of the extracellular matrix / cysteine-type peptidase activity / MHC class II antigen presentation / lysosomal lumen / proteolysis involved in protein catabolic process / lysosome / apical plasma membrane / serine-type endopeptidase activity / external side of plasma membrane / cysteine-type endopeptidase activity / intracellular membrane-bounded organelle / 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
DI(HYDROXYETHYL)ETHER / Cathepsin K
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.92 Å
AuthorsBiswas, S. / Roy, S.
Funding support India, 1items
OrganizationGrant numberCountry
DST India
CitationJournal: FEBS J. / Year: 2018
Title: Not all pycnodysostosis-related mutants of human cathepsin K are inactive - crystal structure and biochemical studies of an active mutant I249T.
Authors: Roy, S. / Das Chakraborty, S. / Biswas, S.
History
DepositionJan 19, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 26, 2018Provider: repository / Type: Initial release
Revision 1.1Dec 12, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title
Revision 1.2Nov 22, 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Cathepsin K
B: Cathepsin K
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,30543
Polymers48,9392
Non-polymers3,36641
Water3,711206
1
A: Cathepsin K
hetero molecules

B: Cathepsin K
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,30543
Polymers48,9392
Non-polymers3,36641
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_756-x+2,y+1/2,-z+11
Buried area8010 Å2
ΔGint-70 kcal/mol
Surface area21610 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.100, 67.270, 82.870
Angle α, β, γ (deg.)90.000, 91.830, 90.000
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 2 types, 2 molecules AB

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


Mass: 37786.508 Da / Num. of mol.: 1 / Mutation: C139S/I249T
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CTSK, CTSO, CTSO2 / Production host: Escherichia coli (E. coli) / References: UniProt: P43235, cathepsin K
#2: Protein Cathepsin K / Cathepsin O / Cathepsin O2 / Cathepsin X


Mass: 11152.578 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CTSK, CTSO, CTSO2 / Production host: Escherichia coli (E. coli) / References: UniProt: P43235, cathepsin K

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Non-polymers , 8 types, 247 molecules

#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#6: Chemical
ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C4H10O3
#7: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#8: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#9: Chemical ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#10: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 206 / 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: 2.86 Å3/Da / Density % sol: 57.02 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 100mM Na-K Phosphate 6.2, 20 % MPD, 12mM (NH4)2SO4, 10% PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.984 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 14, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.984 Å / Relative weight: 1
ReflectionResolution: 1.92→82 Å / Num. obs: 40362 / % possible obs: 96 % / Redundancy: 2.8 % / CC1/2: 0.999 / Net I/σ(I): 12.6
Reflection shellResolution: 1.92→1.99 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.795 / CC1/2: 0.493 / % possible all: 95.2

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Processing

Software
NameVersionClassification
PHENIXrefinement
XDSdata reduction
PDB_EXTRACT3.24data extraction
pointlessdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1BY8

1by8


Resolution: 1.92→52.218 Å / SU ML: 0.22 / Cross valid method: THROUGHOUT / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2036 1995 4.94 %
Rwork0.1621 38365 -
obs0.1641 40360 96.21 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 286.84 Å2 / Biso mean: 57.5072 Å2 / Biso min: 20.28 Å2
Refinement stepCycle: LAST / Resolution: 1.92→52.218 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3094 0 212 206 3512
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0113356
X-RAY DIFFRACTIONf_angle_d1.134477
X-RAY DIFFRACTIONf_chiral_restr0.061454
X-RAY DIFFRACTIONf_plane_restr0.006551
X-RAY DIFFRACTIONf_dihedral_angle_d15.5171966
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.9233-1.97140.3321290.30192635276494
1.9714-2.02470.33931490.28282758290797
2.0247-2.08430.28441380.26012785292397
2.0843-2.15160.26491370.23222700283797
2.1516-2.22850.26131440.20552778292298
2.2285-2.31770.22651500.18662781293197
2.3177-2.42320.22361410.17342756289797
2.4232-2.5510.20461530.16332699285296
2.551-2.71080.22041400.16292774291497
2.7108-2.92010.19871440.15462771291597
2.9201-3.21390.2051500.14472730288096
3.2139-3.67880.16291390.13062718285795
3.6788-4.63450.15441460.11982726287295
4.6345-52.23690.2141350.17162754288994
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
13.2299-1.18091.29016.04731.59184.2024-0.0503-0.171-0.18580.79340.3738-0.7638-0.22650.2256-0.19480.4833-0.0272-0.0880.3632-0.09670.355255.957750.096970.5935
25.99034.78744.40464.69735.08076.2797-0.0271-0.1515-0.10720.10660.3262-0.0808-0.0686-0.0789-0.16770.5603-0.0111-0.01830.34560.03240.26145.261645.708969.7571
30.4735-0.05650.12711.790.01880.7693-0.0113-0.17450.05190.11540.11070.2233-0.0713-0.2812-0.16720.4313-0.02340.00180.36460.01860.264539.883952.807360.2842
43.8908-3.2453-0.23335.8759-0.34030.65590.12160.1878-0.0365-0.4781-0.04290.88430.0394-0.39780.02210.3440.0244-0.09820.37270.01520.410129.409352.924934.1813
51.41580.2394-0.1472.1850.34022.37350.11360.04690.2375-0.158-0.1038-0.0843-0.32620.0376-0.02260.27960.00360.02640.24260.03630.29542.739265.466941.393
61.99692.48290.4173.71081.17150.8-0.14780.30180.172-0.54070.07970.184-0.4373-0.09820.03650.49710.00790.00570.39120.03210.411843.840575.827143.136
77.50951.7622-3.35277.0137-4.33837.4029-0.1082-0.0032-0.035-0.19720.08850.78840.0819-0.49390.13240.16210.0241-0.13120.35450.01220.337226.84655.782637.5313
80.9964-0.07170.72761.3037-0.18872.26070.1642-0.093-0.030.1569-0.0170.19730.0684-0.2007-0.11320.2599-0.02970.01610.29220.03140.321535.263749.906249.0862
92.1232-0.2303-0.56984.9917-1.76235.79740.01540.0763-0.11750.59770.81040.60830.5672-0.6348-0.76760.7577-0.0996-0.04640.49930.14320.43637.351525.750474.2194
102.43511.5969-2.11433.4039-2.28743.5285-0.1535-0.0301-0.50630.20290.1673-0.38060.4648-0.1113-0.11410.6565-0.0144-0.06440.3874-0.01780.315648.139627.967.6492
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 24 )A1 - 24
2X-RAY DIFFRACTION2chain 'A' and (resid 25 through 51 )A25 - 51
3X-RAY DIFFRACTION3chain 'A' and (resid 52 through 81 )A52 - 81
4X-RAY DIFFRACTION4chain 'A' and (resid 85 through 109 )A85 - 109
5X-RAY DIFFRACTION5chain 'A' and (resid 110 through 186 )A110 - 186
6X-RAY DIFFRACTION6chain 'A' and (resid 187 through 206 )A187 - 206
7X-RAY DIFFRACTION7chain 'A' and (resid 207 through 226 )A207 - 226
8X-RAY DIFFRACTION8chain 'A' and (resid 227 through 314 )A227 - 314
9X-RAY DIFFRACTION9chain 'B' and (resid -3 through 24 )B-3 - 24
10X-RAY DIFFRACTION10chain 'B' and (resid 25 through 73 )B25 - 73

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