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- PDB-1tzs: Crystal Structure of an activation intermediate of Cathepsin E -

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Basic information

Entry
Database: PDB / ID: 1tzs
TitleCrystal Structure of an activation intermediate of Cathepsin E
Components
  • 23-mer peptide from PelB-IgG kappa light chain fusion protein
  • Cathepsin E
  • activation peptide from Cathepsin E
KeywordsHYDROLASE / aspartic protease / activation intermediate
Function / homology
Function and homology information


cathepsin E / protein autoprocessing / MHC class II antigen presentation / antigen processing and presentation of exogenous peptide antigen via MHC class II / peptidase activity / aspartic-type endopeptidase activity / endosome / intracellular membrane-bounded organelle / proteolysis / identical protein binding
Similarity search - Function
Aspartic peptidase, N-terminal / A1 Propeptide / Eukaryotic aspartyl protease / Aspartic peptidase A1 family / Peptidase family A1 domain / Peptidase family A1 domain profile. / Cathepsin D, subunit A; domain 1 / Acid Proteases / Aspartic peptidase, active site / Eukaryotic and viral aspartyl proteases active site. ...Aspartic peptidase, N-terminal / A1 Propeptide / Eukaryotic aspartyl protease / Aspartic peptidase A1 family / Peptidase family A1 domain / Peptidase family A1 domain profile. / Cathepsin D, subunit A; domain 1 / Acid Proteases / Aspartic peptidase, active site / Eukaryotic and viral aspartyl proteases active site. / Aspartic peptidase domain superfamily / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.35 Å
AuthorsOstermann, N. / Gerhartz, B. / Worpenberg, S. / Trappe, J. / Eder, J.
CitationJournal: J.Mol.Biol. / Year: 2004
Title: Crystal structure of an activation intermediate of cathepsin e
Authors: Ostermann, N. / Gerhartz, B. / Worpenberg, S. / Trappe, J. / Eder, J.
History
DepositionJul 12, 2004Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jul 12, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 25, 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 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.4Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Cathepsin E
P: activation peptide from Cathepsin E
X: 23-mer peptide from PelB-IgG kappa light chain fusion protein


Theoretical massNumber of molelcules
Total (without water)44,2473
Polymers44,2473
Non-polymers00
Water3,855214
1
A: Cathepsin E
P: activation peptide from Cathepsin E
X: 23-mer peptide from PelB-IgG kappa light chain fusion protein

A: Cathepsin E
P: activation peptide from Cathepsin E
X: 23-mer peptide from PelB-IgG kappa light chain fusion protein


Theoretical massNumber of molelcules
Total (without water)88,4946
Polymers88,4946
Non-polymers00
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_555-y,-x,-z+1/21
Unit cell
Length a, b, c (Å)61.321, 61.321, 207.800
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein Cathepsin E


Mass: 37663.887 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pET22b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pLysS / References: UniProt: P14091, cathepsin E
#2: Protein/peptide activation peptide from Cathepsin E


Mass: 4221.982 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pET22b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pLysS / References: UniProt: P14091, cathepsin E
#3: Protein/peptide 23-mer peptide from PelB-IgG kappa light chain fusion protein


Mass: 2360.961 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: the sequence occurs peptide synthesis / References: GenBank: 5834246
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 214 / 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: 2.29 Å3/Da / Density % sol: 45.8 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.6
Details: PEG4000, sodium citrate, ammonium sulfate, pH 5.6, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: ENRAF-NONIUS FR591 / Wavelength: 1.5418 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Aug 28, 2003 / Details: mirrors
RadiationMonochromator: Osmic mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.35→25.5 Å / Num. obs: 16976 / % possible obs: 98.5 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Biso Wilson estimate: 26.4 Å2 / Rmerge(I) obs: 0.094
Reflection shellResolution: 2.35→2.48 Å / Rmerge(I) obs: 0.371 / % possible all: 99.1

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Processing

Software
NameVersionClassification
CNX2000.1refinement
MOSFLMdata reduction
CCP4(SCALA)data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1PSN

1psn


Resolution: 2.35→25.5 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 2024942.82 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.238 1723 10.2 %RANDOM
Rwork0.198 ---
all-16964 --
obs-16964 97.5 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 37.199 Å2 / ksol: 0.344904 e/Å3
Displacement parametersBiso mean: 30.7 Å2
Baniso -1Baniso -2Baniso -3
1--1.02 Å20 Å20 Å2
2---1.02 Å20 Å2
3---2.03 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.32 Å0.26 Å
Luzzati d res low-26 Å
Luzzati sigma a0.29 Å0.21 Å
Refinement stepCycle: LAST / Resolution: 2.35→25.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2524 0 0 214 2738
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_dihedral_angle_d26.3
X-RAY DIFFRACTIONc_improper_angle_d0.81
X-RAY DIFFRACTIONc_mcbond_it1.121.5
X-RAY DIFFRACTIONc_mcangle_it1.982
X-RAY DIFFRACTIONc_scbond_it1.412
X-RAY DIFFRACTIONc_scangle_it2.132.5
LS refinement shellResolution: 2.35→2.5 Å / Rfactor Rfree error: 0.018 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.308 285 10.3 %
Rwork0.246 2486 -
obs--98.9 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2CIS_PEPTIDE.PARAM
X-RAY DIFFRACTION4WATER_REP.PARAM
X-RAY DIFFRACTION3WATER.TOP

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