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- PDB-1jqp: dipeptidyl peptidase I (cathepsin C), a tetrameric cysteine prote... -

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Basic information

Entry
Database: PDB / ID: 1jqp
Titledipeptidyl peptidase I (cathepsin C), a tetrameric cysteine protease of the papain family
Componentsdipeptidyl peptidase ICathepsin C
KeywordsHYDROLASE / cathepsin c / DPP I / papain / tetramer / chloride / cysteine protease
Function / homology
Function and homology information


dipeptidyl-peptidase I / peptidase activator activity involved in apoptotic process / positive regulation of proteolysis involved in protein catabolic process / Cargo concentration in the ER / COPII-mediated vesicle transport / : / MHC class II antigen presentation / negative regulation of myelination / positive regulation of microglial cell activation / Neutrophil degranulation ...dipeptidyl-peptidase I / peptidase activator activity involved in apoptotic process / positive regulation of proteolysis involved in protein catabolic process / Cargo concentration in the ER / COPII-mediated vesicle transport / : / MHC class II antigen presentation / negative regulation of myelination / positive regulation of microglial cell activation / Neutrophil degranulation / chloride ion binding / phosphatase binding / cysteine-type peptidase activity / positive regulation of apoptotic signaling pathway / proteolysis involved in protein catabolic process / response to organic substance / T cell mediated cytotoxicity / : / protein-folding chaperone binding / lysosome / cysteine-type endopeptidase activity / serine-type endopeptidase activity / centrosome / Golgi apparatus / endoplasmic reticulum / proteolysis / extracellular space / nucleoplasm / identical protein binding / cytoplasm
Similarity search - Function
Cathepsin C, exclusion domain / Cathepsin C exclusion / Cathepsin C, exclusion domain superfamily / Cathepsin C / Cathepsin C exclusion domain / 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 C, exclusion domain / Cathepsin C exclusion / Cathepsin C, exclusion domain superfamily / Cathepsin C / Cathepsin C exclusion domain / 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 / Lipocalin / Papain-like cysteine peptidase superfamily / Alpha-Beta Complex / Beta Barrel / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Dipeptidyl peptidase 1
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.4 Å
AuthorsOlsen, J.G. / Kadziola, A. / Lauritzen, C. / Pedersen, J. / Larsen, S. / Dahl, S.W.
CitationJournal: FEBS LETT. / Year: 2001
Title: Tetrameric dipeptidyl peptidase I directs substrate specificity by use of the residual pro-part domain
Authors: Olsen, J.G. / Kadziola, A. / Lauritzen, C. / Pedersen, J. / Larsen, S. / Dahl, S.W.
History
DepositionAug 8, 2001Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Oct 18, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Feb 14, 2018Group: Data collection / Experimental preparation / Category: diffrn_source / exptl_crystal_grow
Item: _diffrn_source.pdbx_synchrotron_site / _exptl_crystal_grow.pdbx_details / _exptl_crystal_grow.temp
Revision 1.4Jul 29, 2020Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_conn / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: dipeptidyl peptidase I
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,4405
Polymers49,8661
Non-polymers5744
Water1,49583
1
A: dipeptidyl peptidase I
hetero molecules

A: dipeptidyl peptidase I
hetero molecules

A: dipeptidyl peptidase I
hetero molecules

A: dipeptidyl peptidase I
hetero molecules


Theoretical massNumber of molelcules
Total (without water)201,76120
Polymers199,4654
Non-polymers2,29616
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_665-x+1,-y+1,z1
crystal symmetry operation7_556y,x,-z+4/31
crystal symmetry operation10_666-y+1,-x+1,-z+4/31
MethodPQS
2
A: dipeptidyl peptidase I
hetero molecules

A: dipeptidyl peptidase I
hetero molecules


Theoretical massNumber of molelcules
Total (without water)100,88010
Polymers99,7332
Non-polymers1,1488
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_556y,x,-z+4/31
Buried area4030 Å2
ΔGint-30 kcal/mol
Surface area28380 Å2
MethodPISA
3
A: dipeptidyl peptidase I
hetero molecules

A: dipeptidyl peptidase I
hetero molecules


Theoretical massNumber of molelcules
Total (without water)100,88010
Polymers99,7332
Non-polymers1,1488
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation11_556-x+y,y,-z+11
Buried area2810 Å2
ΔGint-25 kcal/mol
Surface area29470 Å2
MethodPISA
Unit cell
Length a, b, c (Å)166.240, 166.240, 80.480
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number181
Space group name H-MP6422
Components on special symmetry positions
IDModelComponents
11A-503-

CL

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Components

#1: Protein dipeptidyl peptidase I / Cathepsin C / cathepsin C


Mass: 49866.277 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P80067, dipeptidyl-peptidase I
#2: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-Acetylglucosamine


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#3: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


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


Mass: 18.015 Da / Num. of mol.: 83 / 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: 3.22 Å3/Da / Density % sol: 61.77 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: bis-tris, NaCl, dithiothreitol, EDTA, bis-tris propane, ammonium sulfate, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal grow
*PLUS
pH: 7
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formulaDetails
110 mg/mlprotein1drop
220 mMBis-Tris1drop
3150 mM1dropNaCl
42 mMdithiothreitol1drop
52 mMEDTA1droppH7.0
60.1 MBis-Tris propane1reservoirpH7.5
71.4 Mammonium sulfate1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: MAX II / Beamline: I711 / Wavelength: 1 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Apr 20, 1998
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.4→30 Å / Num. obs: 26061 / % possible obs: 99.2 % / Redundancy: 13 % / Rmerge(I) obs: 0.071
Reflection shellHighest resolution: 2.4 Å / Rmerge(I) obs: 0.322

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
CNSphasing
RefinementResolution: 2.4→30 Å
RfactorNum. reflection% reflection
Rfree0.274 1303 4.9998 %
Rwork0.245 --
obs-26061 94.2 %
Refinement stepCycle: LAST / Resolution: 2.4→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2781 0 34 83 2898
Refinement
*PLUS
Rfactor all: 5
Solvent computation
*PLUS
Displacement parameters
*PLUS

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