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- PDB-6jd8: Structure of a proline specific mutant of human cathepsin L -

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Basic information

Entry
Database: PDB / ID: 6jd8
TitleStructure of a proline specific mutant of human cathepsin L
ComponentsCathepsin L1
KeywordsHYDROLASE / protease / proline-specific / engineered
Function / homology
Function and homology information


enkephalin processing / cathepsin L / CD4-positive, alpha-beta T cell lineage commitment / macrophage apoptotic process / chromaffin granule / elastin catabolic process / antigen processing and presentation of peptide antigen / RUNX1 regulates transcription of genes involved in differentiation of keratinocytes / endolysosome lumen / cellular response to thyroid hormone stimulus ...enkephalin processing / cathepsin L / CD4-positive, alpha-beta T cell lineage commitment / macrophage apoptotic process / chromaffin granule / elastin catabolic process / antigen processing and presentation of peptide antigen / RUNX1 regulates transcription of genes involved in differentiation of keratinocytes / endolysosome lumen / cellular response to thyroid hormone stimulus / zymogen activation / Trafficking and processing of endosomal TLR / proteoglycan binding / Assembly of collagen fibrils and other multimeric structures / cysteine-type endopeptidase activator activity involved in apoptotic process / antigen processing and presentation / protein autoprocessing / Collagen degradation / fibronectin binding / collagen catabolic process / serpin family protein binding / cysteine-type peptidase activity / endocytic vesicle lumen / Attachment and Entry / collagen binding / MHC class II antigen presentation / Degradation of the extracellular matrix / multivesicular body / lysosomal lumen / proteolysis involved in protein catabolic process / Endosomal/Vacuolar pathway / positive regulation of apoptotic signaling pathway / antigen processing and presentation of exogenous peptide antigen via MHC class II / histone binding / collagen-containing extracellular matrix / adaptive immune response / receptor-mediated endocytosis of virus by host cell / lysosome / Attachment and Entry / immune response / symbiont entry into host cell / apical plasma membrane / cysteine-type endopeptidase activity / fusion of virus membrane with host plasma membrane / intracellular membrane-bounded organelle / fusion of virus membrane with host endosome membrane / Golgi apparatus / proteolysis / extracellular space / extracellular exosome / extracellular region / nucleus / plasma membrane
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
ETHANOL / DI(HYDROXYETHYL)ETHER / TRIETHYLENE GLYCOL / Procathepsin L
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.457 Å
AuthorsChoudhury, D. / Biswas, S.
Funding support India, 1items
OrganizationGrant numberCountry
Department of Science & Technology (India) India
CitationJournal: Protein Eng.Des.Sel. / Year: 2021
Title: Structure-guided protein engineering of human cathepsin L for efficient collagenolytic activity.
Authors: Choudhury, D. / Biswas, S.
History
DepositionJan 31, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 5, 2020Provider: repository / Type: Initial release
Revision 1.1Oct 19, 2022Group: Database references / Category: citation / database_2
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Cathepsin L1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,88217
Polymers40,9181
Non-polymers96316
Water4,053225
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area160 Å2
ΔGint0 kcal/mol
Surface area14740 Å2
MethodPISA
Unit cell
Length a, b, c (Å)42.220, 67.584, 103.239
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Cathepsin L1 / Cathepsin L / Major excreted protein / MEP


Mass: 40918.434 Da / Num. of mol.: 1 / Mutation: C138S,L182Y,M274L,G277A,A327L
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CTSL, CTSL1 / Production host: Escherichia coli (E. coli) / References: UniProt: P07711, cathepsin L

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Non-polymers , 6 types, 241 molecules

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


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical
ChemComp-EOH / ETHANOL


Mass: 46.068 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C2H6O
#4: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#5: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#6: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O4
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 225 / 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: 1.8 Å3/Da / Density % sol: 31.66 %
Crystal growTemperature: 293 K / Method: vapor diffusion / Details: PEG 4000, 2-propanol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 1 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Apr 21, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.457→50 Å / Num. obs: 49550 / % possible obs: 94.4 % / Redundancy: 6.3 % / Biso Wilson estimate: 17.22 Å2 / Rmerge(I) obs: 0.084 / Rpim(I) all: 0.035 / Rrim(I) all: 0.092 / Χ2: 3.988 / Net I/σ(I): 14.3
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.46-1.494.70.38616410.910.180.4271.19863.6
1.49-1.514.90.36318860.9370.1630.3990.97372.3
1.51-1.545.10.34120490.9480.1520.3741.03680
1.54-1.575.20.31822630.9540.1420.351.04987.4
1.57-1.615.50.28323550.9720.1240.311.16492
1.61-1.645.80.2825340.980.1210.3051.26797.1
1.64-1.696.20.26325830.9810.1120.2861.20899.3
1.69-1.736.50.23625840.9850.10.2571.39599.9
1.73-1.786.70.20525880.9870.0850.2221.455100
1.78-1.846.70.18826330.990.0780.2041.849100
1.84-1.916.80.15925920.9910.0660.1722.104100
1.91-1.986.80.13325930.9930.0550.1442.48100
1.98-2.076.90.11626290.9940.0480.1253.082100
2.07-2.186.90.10126170.9940.0420.1093.613100
2.18-2.3270.09726140.9950.040.1054.413100
2.32-2.56.90.09226630.9940.0380.15.244100
2.5-2.756.80.09626350.9920.040.1057.642100
2.75-3.156.70.08726610.9930.0370.0959.316100
3.15-3.966.80.06827170.9950.0280.07410.52799.7
3.96-506.20.06227130.9960.0270.06811.30695.1

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Processing

Software
NameVersionClassification
HKL-2000data reduction
HKL-2000data scaling
PHENIX(1.12_2829: ???)refinement
PDB_EXTRACT3.24data extraction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1CS8

1cs8


Resolution: 1.457→25.561 Å / SU ML: 0.16 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 30.27
RfactorNum. reflection% reflection
Rfree0.2369 1996 4.04 %
Rwork0.1916 --
obs0.1934 49436 94.31 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 107.07 Å2 / Biso mean: 31.3457 Å2 / Biso min: 11.49 Å2
Refinement stepCycle: final / Resolution: 1.457→25.561 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2508 0 171 230 2909
Biso mean--51.83 33.28 -
Num. residues----314
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0082721
X-RAY DIFFRACTIONf_angle_d1.123665
X-RAY DIFFRACTIONf_chiral_restr0.184358
X-RAY DIFFRACTIONf_plane_restr0.006478
X-RAY DIFFRACTIONf_dihedral_angle_d17.9731036
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 (%)
1.4572-1.49370.3467950.27112282237765
1.4937-1.5340.28781150.27252735285077
1.534-1.57920.30591310.26173090322188
1.5792-1.63010.30151430.24383387353095
1.6301-1.68840.3161490.23673546369599
1.6884-1.7560.2581490.215535283677100
1.756-1.83590.23491510.207935613712100
1.8359-1.93260.23291480.208535523700100
1.9326-2.05370.26631500.203335683718100
2.0537-2.21210.23071520.196236003752100
2.2121-2.43460.23231490.189935893738100
2.4346-2.78650.23641530.194236263779100
2.7865-3.50930.2011550.177836723827100
3.5093-25.56480.22711560.16493704386097

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