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- PDB-2c0y: THE CRYSTAL STRUCTURE OF A CYS25ALA MUTANT OF HUMAN PROCATHEPSIN S -

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Basic information

Entry
Database: PDB / ID: 2c0y
TitleTHE CRYSTAL STRUCTURE OF A CYS25ALA MUTANT OF HUMAN PROCATHEPSIN S
ComponentsPROCATHEPSIN S
KeywordsHYDROLASE / PROCATHEPSIN S / PROENZYME / PROTEINASE / THIOL PROTEASE / PROSEGMENT BINDING LOOP / GLYCOPROTEIN / LYSOSOME / PROTEASE / ZYMOGEN
Function / homology
Function and homology information


cathepsin S / basement membrane disassembly / positive regulation of cation channel activity / antigen processing and presentation of peptide antigen / endolysosome lumen / response to acidic pH / cellular response to thyroid hormone stimulus / Trafficking and processing of endosomal TLR / proteoglycan binding / Assembly of collagen fibrils and other multimeric structures ...cathepsin S / basement membrane disassembly / positive regulation of cation channel activity / antigen processing and presentation of peptide antigen / endolysosome lumen / response to acidic pH / cellular response to thyroid hormone stimulus / Trafficking and processing of endosomal TLR / proteoglycan binding / Assembly of collagen fibrils and other multimeric structures / toll-like receptor signaling pathway / antigen processing and presentation / cysteine-type endopeptidase activator activity involved in apoptotic process / fibronectin binding / collagen catabolic process / extracellular matrix disassembly / laminin binding / collagen binding / MHC class II antigen presentation / phagocytic vesicle / Degradation of the extracellular matrix / lysosomal lumen / proteolysis involved in protein catabolic process / Endosomal/Vacuolar pathway / positive regulation of apoptotic signaling pathway / protein processing / antigen processing and presentation of exogenous peptide antigen via MHC class II / late endosome / tertiary granule lumen / collagen-containing extracellular matrix / adaptive immune response / ficolin-1-rich granule lumen / lysosome / immune response / cysteine-type endopeptidase activity / intracellular membrane-bounded organelle / serine-type endopeptidase activity / Neutrophil degranulation / proteolysis / extracellular space / extracellular region
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
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsKaulmann, G. / Palm, G.J. / Schilling, K. / Hilgenfeld, R. / Wiederanders, B.
Citation
Journal: Protein Sci. / Year: 2006
Title: The Crystal Structure of a Cys25 -> Ala Mutant of Human Procathepsin S Elucidates Enzyme-Prosequence Interactions.
Authors: Kaulmann, G. / Palm, G.J. / Schilling, K. / Hilgenfeld, R. / Wiederanders, B.
#1: Journal: Protein Sci. / Year: 1998
Title: Crystal Structure of Human Cathepsin S
Authors: Mcgrath, M.E. / Palmer, J.T. / Bromme, D. / Somoza, J.R.
#2: Journal: Acta Crystallogr.,Sect.D / Year: 2002
Title: Structure of a Cys25 to Ser Mutant of Human Cathepsin S
Authors: Turkenburg, J.P. / Lamers, M.B. / Brzozowski, A.M. / Wright, L.M. / Hubbard, R.E. / Sturt, S.L. / Williams, D.H.
#3: Journal: Biochemistry / Year: 2003
Title: Specificity Determinants of Human Cathepsin S Revealed by Crystal Structures of Complexes
Authors: Pauly, T.A. / Sulea, T. / Ammirati, M. / Sivaraman, J. / Danley, D.E. / Griffor, M.C. / Kamath, A.V. / Wang, I.K. / Laird, E.R. / Seddon, A.P. / Menard, R. / Cygler, M. / Rath, V.L.
History
DepositionSep 8, 2005Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 8, 2006Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Apr 3, 2019Group: Data collection / Other / Source and taxonomy
Category: entity_src_gen / pdbx_database_proc / pdbx_database_status
Item: _entity_src_gen.pdbx_host_org_cell_line / _pdbx_database_status.recvd_author_approval
Revision 1.4May 29, 2019Group: Data collection / Experimental preparation / Category: exptl_crystal_grow / struct_biol / Item: _exptl_crystal_grow.method
Revision 1.5Jul 24, 2019Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.6Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf
Remark 700 SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: PROCATHEPSIN S


Theoretical massNumber of molelcules
Total (without water)35,8391
Polymers35,8391
Non-polymers00
Water4,360242
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)59.860, 140.540, 78.610
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-2053-

HOH

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Components

#1: Protein PROCATHEPSIN S


Mass: 35839.477 Da / Num. of mol.: 1 / Fragment: PROENZYME, RESIDUES 17-331 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Organ: TESTIS / Cell line (production host): High Five / Production host: TRICHOPLUSIA NI (cabbage looper) / References: UniProt: P25774, cathepsin S
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 242 / Source method: isolated from a natural source / Formula: H2O
Compound detailsPROTEASE RESPONSIBLE FOR THE REMOVAL OF THE INVARIANT CHAIN FROM MHC CLASS II MOLECULES ENGINEERED ...PROTEASE RESPONSIBLE FOR THE REMOVAL OF THE INVARIANT CHAIN FROM MHC CLASS II MOLECULES ENGINEERED RESIDUE IN CHAIN A, CYS 139 TO ALA
Sequence detailsCLONED WITHOUT SIGNAL PEPTIDE

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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: 2.31 Å3/Da / Density % sol: 47 %
Crystal growMethod: vapor diffusion, hanging drop / pH: 7.5
Details: CRYSTALLISATION WAS PERFORMED BY THE HANGING-DROP VAPOUR DIFFUSION METHOD. EQUAL VOLUMES PROCATHEPSIN S (CYS25ALA) AT 7.0 MG/ML AND WELL SOLUTION WERE COMBINED AND PLACED OVER A WELL ...Details: CRYSTALLISATION WAS PERFORMED BY THE HANGING-DROP VAPOUR DIFFUSION METHOD. EQUAL VOLUMES PROCATHEPSIN S (CYS25ALA) AT 7.0 MG/ML AND WELL SOLUTION WERE COMBINED AND PLACED OVER A WELL CONTAINING 0.1M TRIS/HCL, 0.2M MAGNESIUM ACETATE AND 20% PEG 8000, PH 7.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X13 / Wavelength: 0.803
DetectorType: MARRESEARCH / Detector: CCD / Date: Jun 18, 2001
Details: TRIANGULAR SI (111) MONOCHROMATOR AND A CONTINUOUS BENT RH-COATED MIRROR
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.803 Å / Relative weight: 1
ReflectionResolution: 2.1→30 Å / Num. obs: 19350 / % possible obs: 97.9 % / Observed criterion σ(I): -3 / Redundancy: 6.4 % / Biso Wilson estimate: 24.7 Å2 / Rmerge(I) obs: 0.09 / Net I/σ(I): 13.4
Reflection shellResolution: 2.1→2.14 Å / Redundancy: 4.1 % / Rmerge(I) obs: 0.47 / Mean I/σ(I) obs: 3 / % possible all: 88.5

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Processing

Software
NameVersionClassification
CNS1.1refinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1BY8

1by8


Resolution: 2.1→19.76 Å / Rfactor Rfree error: 0.008 / Data cutoff high absF: 1874964.9 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.242 972 5 %RANDOM
Rwork0.198 ---
obs0.198 19350 97.9 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 62.2678 Å2 / ksol: 0.406382 e/Å3
Displacement parametersBiso mean: 28.7 Å2
Baniso -1Baniso -2Baniso -3
1--0.02 Å20 Å20 Å2
2---0.48 Å20 Å2
3---0.5 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.31 Å0.23 Å
Luzzati d res low-5 Å
Luzzati sigma a0.23 Å0.17 Å
Refinement stepCycle: LAST / Resolution: 2.1→19.76 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2459 0 0 242 2701
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.01
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d22.9
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.85
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.771.5
X-RAY DIFFRACTIONc_mcangle_it2.532
X-RAY DIFFRACTIONc_scbond_it2.92
X-RAY DIFFRACTIONc_scangle_it3.922.5
LS refinement shellResolution: 2.1→2.14 Å / Rfactor Rfree error: 0.031 / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.285 87 4.9 %
Rwork0.247 1691 -
obs--93 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP

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