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- PDB-6jd0: Structure of mutant human cathepsin L, engineered for GAG binding -

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Basic information

Entry
Database: PDB / ID: 6jd0
TitleStructure of mutant human cathepsin L, engineered for GAG binding
ComponentsCathepsin L1
KeywordsHYDROLASE / cathepsin L / collagenase / GAG
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 / protein autoprocessing / Collagen degradation / fibronectin binding / collagen catabolic process / antigen processing and presentation / serpin family protein binding / Attachment and Entry / cysteine-type peptidase activity / positive regulation of apoptotic signaling pathway / endocytic vesicle lumen / collagen binding / MHC class II antigen presentation / Degradation of the extracellular matrix / multivesicular body / proteolysis involved in protein catabolic process / lysosomal lumen / Endosomal/Vacuolar pathway / antigen processing and presentation of exogenous peptide antigen via MHC class II / histone binding / collagen-containing extracellular matrix / receptor-mediated endocytosis of virus by host cell / Attachment and Entry / adaptive immune response / lysosome / immune response / symbiont entry into host cell / apical plasma membrane / fusion of virus membrane with host plasma membrane / cysteine-type endopeptidase activity / 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 / TRIETHYLENE GLYCOL / PHOSPHATE ION / N-PROPANOL / Procathepsin L
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.805 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 30, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 5, 2020Provider: repository / Type: Initial release
Revision 1.1Oct 19, 2022Group: Database references / Derived calculations
Category: citation / database_2 ...citation / database_2 / pdbx_struct_conn_angle / struct_conn
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 / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_symmetry
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

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Assembly

Deposited unit
A: Cathepsin L1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,00852
Polymers40,9741
Non-polymers4,03551
Water2,810156
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9410 Å2
ΔGint-48 kcal/mol
Surface area15850 Å2
MethodPISA
Unit cell
Length a, b, c (Å)63.835, 64.172, 92.857
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: 40973.535 Da / Num. of mol.: 1
Mutation: E105K, C121S, L165Y, M257L, G260A, M291N, G292K, A310L
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 , 9 types, 207 molecules

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


Mass: 92.094 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#4: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Na
#5: Chemical
ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: PO4
#6: Chemical
ChemComp-POL / N-PROPANOL / 1-PROPONOL / Propan-1-ol


Mass: 60.095 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C3H8O
#7: Chemical
ChemComp-PGE / TRIETHYLENE GLYCOL / Polyethylene glycol


Mass: 150.173 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C6H14O4
#8: Chemical ChemComp-EOH / ETHANOL / Ethanol


Mass: 46.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O
#9: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#10: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 156 / 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: 2.32 Å3/Da / Density % sol: 47 %
Crystal growTemperature: 293 K / Method: vapor diffusion / Details: PEG 4000, 2-propanol etc

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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 130 mm / Detector: CCD / Date: Apr 20, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.8→50 Å / Num. obs: 34526 / % possible obs: 96.8 % / Redundancy: 4.7 % / Biso Wilson estimate: 24.78 Å2 / Rmerge(I) obs: 0.056 / Rpim(I) all: 0.028 / Rrim(I) all: 0.063 / Χ2: 0.905 / Net I/σ(I): 10.9
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.8-1.834.30.63114910.7810.3190.7090.71285.4
1.83-1.864.40.54415550.8660.2730.6110.71788.6
1.86-1.94.40.52416030.8530.2640.5890.74991.4
1.9-1.944.40.42416250.8650.2160.4770.88991.9
1.94-1.984.50.33916650.940.1720.3810.74295
1.98-2.034.50.27816810.9390.1420.3130.73696.6
2.03-2.084.60.24717120.9510.1280.2790.86596.7
2.08-2.134.60.20117300.9660.1050.2280.77598.1
2.13-2.24.70.17617580.9750.0910.1990.79199.1
2.2-2.274.70.17317420.9740.090.1960.98899.1
2.27-2.354.80.11817470.9910.060.1330.82898.9
2.35-2.444.80.10517630.9910.0540.1180.80999.2
2.44-2.554.90.09417430.9940.0480.1060.87998.9
2.55-2.694.90.08117640.9940.0410.0910.94499.1
2.69-2.864.90.06317700.9970.0320.070.98199.6
2.86-3.084.90.05117940.9970.0260.0581.0499.4
3.08-3.394.90.04118010.9980.020.0461.18799.6
3.39-3.884.80.03218060.9990.0160.0361.20199.7
3.88-4.884.80.02718430.9990.0130.031.13199.8
4.88-504.50.02319330.9990.0120.0260.92999.3

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
PHENIX1.12_2829refinement
PDB_EXTRACT3.24data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1CS8

1cs8


Resolution: 1.805→32.408 Å / SU ML: 0.21 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 24.46
RfactorNum. reflection% reflection
Rfree0.2148 2016 5.85 %
Rwork0.1713 --
obs0.1739 34468 96.4 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 125.63 Å2 / Biso mean: 37.8924 Å2 / Biso min: 15.11 Å2
Refinement stepCycle: final / Resolution: 1.805→32.408 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2515 0 554 156 3225
Biso mean--61.72 37.63 -
Num. residues----314
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.012809
X-RAY DIFFRACTIONf_angle_d1.0033722
X-RAY DIFFRACTIONf_chiral_restr0.053345
X-RAY DIFFRACTIONf_plane_restr0.007464
X-RAY DIFFRACTIONf_dihedral_angle_d16.8641627
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 (%)
1.8054-1.85050.33971260.30411954208082
1.8505-1.90050.34341340.27092096223089
1.9005-1.95650.31261360.25212186232293
1.9565-2.01960.25771350.21692272240795
2.0196-2.09180.23611400.20262300244097
2.0918-2.17550.24441450.18982335248099
2.1755-2.27450.23371450.18322368251399
2.2745-2.39440.21061470.16522364251199
2.3944-2.54430.24821470.16912373252099
2.5443-2.74070.23341450.16142374251999
2.7407-3.01630.21231540.15792397255199
3.0163-3.45230.1971460.15224102556100
3.4523-4.34790.15891550.140824622617100
4.3479-32.41290.20751610.170125612722100

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