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- PDB-1elg: NATURE OF THE INACTIVATION OF ELASTASE BY N-PEPTIDYL-O-AROYL HYDR... -

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Basic information

Entry
Database: PDB / ID: 1elg
TitleNATURE OF THE INACTIVATION OF ELASTASE BY N-PEPTIDYL-O-AROYL HYDROXYLAMINE AS A FUNCTION OF PH
ComponentsPORCINE PANCREATIC ELASTASE
KeywordsCOMPLEX (HYDROLASE/INHIBITOR) / COMPLEX (HYDROLASE-INHIBITOR) / COMPLEX (HYDROLASE-INHIBITOR) complex
Function / homology
Function and homology information


pancreatic elastase / serine-type endopeptidase activity / proteolysis / extracellular space / metal ion binding
Similarity search - Function
: / Serine proteases, trypsin family, histidine active site / Serine proteases, trypsin family, serine active site / Serine proteases, trypsin family, histidine active site. / Peptidase S1A, chymotrypsin family / Serine proteases, trypsin family, serine active site. / Serine proteases, trypsin domain profile. / Trypsin-like serine protease / Serine proteases, trypsin domain / Trypsin ...: / Serine proteases, trypsin family, histidine active site / Serine proteases, trypsin family, serine active site / Serine proteases, trypsin family, histidine active site. / Peptidase S1A, chymotrypsin family / Serine proteases, trypsin family, serine active site. / Serine proteases, trypsin domain profile. / Trypsin-like serine protease / Serine proteases, trypsin domain / Trypsin / Trypsin-like serine proteases / Thrombin, subunit H / Peptidase S1, PA clan, chymotrypsin-like fold / Peptidase S1, PA clan / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
(TERT-BUTYLOXYCARBONYL)-ALANYL-ALANYL-AMINE / Chymotrypsin-like elastase family member 1
Similarity search - Component
Biological speciesSus scrofa (pig)
MethodX-RAY DIFFRACTION / Resolution: 1.65 Å
AuthorsDing, X. / Rasmussen, B. / Demuth, H.-U. / Ringe, D. / Steinmetz, A.C.U.
Citation
Journal: Biochemistry / Year: 1995
Title: Nature of the inactivation of elastase by N-peptidyl-O-aroyl hydroxylamine as a function of pH.
Authors: Ding, X. / Rasmussen, B.F. / Demuth, H.U. / Ringe, D. / Steinmetz, A.C.
#1: Journal: Biochemistry / Year: 1994
Title: Direct Structural Observation of an Acyl-Enzyme Intermediate in the Hydrolysis of an Ester Substrate by Elastase
Authors: Ding, X. / Rasmussen, B.F. / Petsko, G.A. / Ringe, D.
#2: Journal: J.Enzyme Inhib. / Year: 1991
Title: Inhibition of Proteases with Enkephalin-Analogue Inhibitors
Authors: Demuth, H.-U. / Silberring, J. / Nyberg, F.
#3: Journal: J.Am.Chem.Soc. / Year: 1991
Title: Competing Redox and Inactivation Processes in the Inhibition of Cysteine Proteinases by Peptidyl O-Acylhydroxamates. 13C and 15N NMR Evidence for a Novel Sulfenamide Enzyme Adduct
Authors: Robinson, V.J. / Coles, P.J. / Smith, R.A. / Krantz, A.
#4: Journal: J.Org.Chem. / Year: 1989
Title: N-O Bond Fission as the Rate-Determining Step in the Aqueous Conversion of N-Peptiyl-O-(P-Nitrobenzoyl)Hydroxylamines to P-Nitrobenzoic Acid and Peptidylhydroxamic Acids
Authors: Demuth, H.-U. / Fischer, G. / Barth, A. / Schowen, R.L.
#5: Journal: J.Am.Chem.Soc. / Year: 1989
Title: Crystal Structure of the Covalent Complex Formed by a Peptidyl Difluoro Keto Amide with Porcine Pancreatic Elastase at 1.78 Angstroms Resolution
Authors: Takahashi, L.H. / Radhakrishnan, R. / Rosenfield Junior, R.E. / Meyer Junior, E.F. / Trainor, D.A.
History
DepositionMar 13, 1995Processing site: BNL
Revision 1.0Jul 10, 1995Provider: repository / Type: Initial release
Revision 1.1Mar 3, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jun 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 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / 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 / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_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.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_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.pdbx_leaving_atom_flag / _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_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature
Remark 700SHEET THE TWO SEVEN STRANDED SHEETS IN THIS STRUCTURE ARE REALLY SIX STRANDED BETA BARRELS. THIS IS ...SHEET THE TWO SEVEN STRANDED SHEETS IN THIS STRUCTURE ARE REALLY SIX STRANDED BETA BARRELS. THIS IS DENOTED BY THE FIRST STRAND RECURRING AS THE LAST STRAND.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: PORCINE PANCREATIC ELASTASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,2273
Polymers25,9281
Non-polymers2992
Water3,405189
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)51.080, 58.040, 75.180
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein PORCINE PANCREATIC ELASTASE


Mass: 25928.031 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sus scrofa (pig) / References: UniProt: P00772, pancreatic elastase
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-BAA / (TERT-BUTYLOXYCARBONYL)-ALANYL-ALANYL-AMINE


Mass: 259.302 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H21N3O4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 189 / 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
pH: 5 / Method: vapor diffusion, sitting drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
16.8-8.3 mg/mlprotein1drop
20.52 mMinactivator1drop
3100 mMsodium acetate1drop
4100 mMsodium sulphate1reservoir
5100 mMacetate1reservoir

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Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 1.65→10 Å / Num. obs: 23730 / % possible obs: 85 % / Observed criterion σ(I): 2
Reflection
*PLUS
Lowest resolution: 44 Å / Num. obs: 27890 / % possible obs: 100 % / Observed criterion σ(I): 0

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Processing

Software
NameClassification
X-PLORmodel building
X-PLORrefinement
X-PLORphasing
RefinementRfactor Rwork: 0.17 / Rfactor obs: 0.17 / Highest resolution: 1.65 Å
Refinement stepCycle: LAST / Highest resolution: 1.65 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1822 0 19 189 2030
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.013
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg2.6
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Refinement
*PLUS
Lowest resolution: 10 Å / Num. reflection all: 23730 / σ(I): 2
Solvent computation
*PLUS
Displacement parameters
*PLUS

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