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- PDB-1arc: THE PRIMARY STRUCTURE AND STRUCTURAL CHARACTERISTICS OF ACHROMOBA... -

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Basic information

Entry
Database: PDB / ID: 1arc
TitleTHE PRIMARY STRUCTURE AND STRUCTURAL CHARACTERISTICS OF ACHROMOBACTER LYTICUS PROTEASE I, A LYSINE-SPECIFIC SERINE PROTEASE
ComponentsACHROMOBACTER PROTEASE I
KeywordsHYDROLASE/HYDROLASE INHIBITOR / SERINE PROTEASE / HYDROLASE-HYDROLASE INHIBITOR complex
Function / homology
Function and homology information


lysyl endopeptidase / serine-type endopeptidase activity / proteolysis / extracellular region
Similarity search - Function
Lysyl endopeptidase / P domain / Proprotein convertase P-domain / P/Homo B domain profile. / PKD domain / Polycystic kidney disease (PKD) domain profile. / PKD domain / PKD domain superfamily / PKD/Chitinase domain / Repeats in polycystic kidney disease 1 (PKD1) and other proteins ...Lysyl endopeptidase / P domain / Proprotein convertase P-domain / P/Homo B domain profile. / PKD domain / Polycystic kidney disease (PKD) domain profile. / PKD domain / PKD domain superfamily / PKD/Chitinase domain / Repeats in polycystic kidney disease 1 (PKD1) and other proteins / Galactose-binding-like domain superfamily / Trypsin-like serine proteases / Thrombin, subunit H / Peptidase S1, PA clan, chymotrypsin-like fold / Immunoglobulin-like fold / Peptidase S1, PA clan / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Tosyl-L-lysine chloromethyl ketone / Chem-TCK / Protease 1
Similarity search - Component
Biological speciesAchromobacter lyticus (bacteria)
MethodX-RAY DIFFRACTION / Resolution: 2 Å
AuthorsKitagawa, Y. / Katsube, Y.
CitationJournal: J.Biol.Chem. / Year: 1989
Title: The primary structure and structural characteristics of Achromobacter lyticus protease I, a lysine-specific serine protease.
Authors: Tsunasawa, S. / Masaki, T. / Hirose, M. / Soejima, M. / Sakiyama, F.
History
DepositionApr 15, 1993Processing site: BNL
Revision 1.0Oct 31, 1993Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Atomic model / Database references ...Atomic model / Database references / Derived calculations / Non-polymer description / Structure summary / Version format compliance
Revision 1.3Feb 27, 2013Group: Other
Revision 1.4Jun 5, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site / _struct_conn.pdbx_leaving_atom_flag / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Nov 20, 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: ACHROMOBACTER PROTEASE I
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,0922
Polymers27,7591
Non-polymers3331
Water1,29772
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)37.300, 42.800, 48.000
Angle α, β, γ (deg.)120.10, 112.80, 68.50
Int Tables number1
Space group name H-MP1

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Components

#1: Protein ACHROMOBACTER PROTEASE I


Mass: 27759.227 Da / Num. of mol.: 1 / Fragment: residues 206-473
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Achromobacter lyticus (bacteria) / References: UniProt: P15636, lysyl endopeptidase
#2: Chemical ChemComp-TCK / N-[(1S)-5-amino-1-(chloroacetyl)pentyl]-4-methylbenzenesulfonamide / Tos-Lys-CH2Cl


Type: peptide-like, Peptide-like / Class: Inhibitor / Mass: 332.846 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H21ClN2O3S / References: Tosyl-L-lysine chloromethyl ketone
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 72 / 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

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Sample preparation

CrystalDensity Matthews: 2.15 Å3/Da / Density % sol: 42.75 %
Crystal grow
*PLUS
Method: other

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Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1

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Processing

SoftwareName: PROLSQ / Classification: refinement
RefinementRfactor obs: 0.152 / Highest resolution: 2 Å
Refinement stepCycle: LAST / Highest resolution: 2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1924 0 20 72 2016
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_bond_d0.014
X-RAY DIFFRACTIONp_angle_d
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it
X-RAY DIFFRACTIONp_mcangle_it
X-RAY DIFFRACTIONp_scbond_it
X-RAY DIFFRACTIONp_scangle_it
X-RAY DIFFRACTIONp_plane_restr
X-RAY DIFFRACTIONp_chiral_restr
X-RAY DIFFRACTIONp_singtor_nbd
X-RAY DIFFRACTIONp_multtor_nbd
X-RAY DIFFRACTIONp_xhyhbond_nbd
X-RAY DIFFRACTIONp_xyhbond_nbd
X-RAY DIFFRACTIONp_planar_tor
X-RAY DIFFRACTIONp_staggered_tor
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor
X-RAY DIFFRACTIONp_special_tor
Refinement
*PLUS
Highest resolution: 2 Å / Rfactor obs: 0.152
Solvent computation
*PLUS
Displacement parameters
*PLUS

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