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

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Basic information

Entry
Database: PDB / ID: 1elf
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 / Peptidase S1A, chymotrypsin family / Serine proteases, trypsin family, histidine active site. / Serine proteases, trypsin domain profile. / Serine proteases, trypsin family, serine active site. / Trypsin-like serine protease / Serine proteases, trypsin domain / Trypsin / Trypsin-like serine proteases ...Serine proteases, trypsin family, histidine active site / Serine proteases, trypsin family, serine active site / Peptidase S1A, chymotrypsin family / Serine proteases, trypsin family, histidine active site. / Serine proteases, trypsin domain profile. / Serine proteases, trypsin family, serine active site. / 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
Chem-BAF / Chymotrypsin-like elastase family member 1
Similarity search - Component
Biological speciesSus scrofa (pig)
MethodX-RAY DIFFRACTION / Resolution: 1.7 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-Peptidyl-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, 1995-
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
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)26,4205
Polymers25,9281
Non-polymers4924
Water2,882160
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)52.270, 58.090, 75.330
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-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-BAF / (TERT-BUTYLOXYCARBONYL)-ALANYL-AMINO ETHYL-FORMAMIDE


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


Mass: 18.015 Da / Num. of mol.: 160 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.2 Å3/Da / Density % sol: 44.21 %
Crystal grow
*PLUS
pH: 5 / Method: vapor diffusion, sitting drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
16.0-7.4 mg/mlprotein1drop
25-11 mMsodium sulfate1drop
310 mMsodium acetate1drop
420 mMsodium sulphate1reservoir
510 mMacetate1reservoir

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Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 1.7→10 Å / Num. obs: 21705 / % possible obs: 84 % / Observed criterion σ(I): 1
Reflection
*PLUS
Highest resolution: 1.68 Å / Lowest resolution: 22.36 Å / Num. obs: 23713 / % possible obs: 91 % / Observed criterion σ(I): 0 / Rmerge(I) obs: 0.1

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Processing

Software
NameClassification
X-PLORmodel building
X-PLORrefinement
X-PLORphasing
RefinementRfactor Rwork: 0.18 / Rfactor obs: 0.18 / Highest resolution: 1.7 Å
Refinement stepCycle: LAST / Highest resolution: 1.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1822 0 29 160 2011
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.014
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_deg3.9
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: 21705 / σ(I): 1
Solvent computation
*PLUS
Displacement parameters
*PLUS

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