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- PDB-1est: THE ATOMIC STRUCTURE OF CRYSTALLINE PORCINE PANCREATIC ELASTASE A... -

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Basic information

Entry
Database: PDB / ID: 1est
TitleTHE ATOMIC STRUCTURE OF CRYSTALLINE PORCINE PANCREATIC ELASTASE AT 2.5 ANGSTROMS RESOLUTION. COMPARISONS WITH THE STRUCTURE OF ALPHA-CHYMOTRYPSIN
ComponentsPORCINE PANCREATIC ELASTASE
KeywordsHYDROLASE / HYDROLASE (SERINE PROTEINASE)
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
PARA-TOLUENE SULFONATE / Chymotrypsin-like elastase family member 1
Similarity search - Component
Biological speciesSus scrofa (pig)
MethodX-RAY DIFFRACTION / Resolution: 2.5 Å
AuthorsSawyer, L. / Shotton, D.M. / Watson, H.C.
Citation
Journal: J.Mol.Biol. / Year: 1978
Title: The atomic structure of crystalline porcine pancreatic elastase at 2.5 A resolution: comparisons with the structure of alpha-chymotrypsin.
Authors: Sawyer, L. / Shotton, D.M. / Campbell, J.W. / Wendell, P.L. / Muirhead, H. / Watson, H.C. / Diamond, R. / Ladner, R.C.
#1: Journal: Biochem.Biophys.Res.Commun. / Year: 1973
Title: Atomic Coordinates for Tosyl-Elastase
Authors: Sawyer, L. / Shotton, D.M. / Watson, H.C.
#2: Journal: Nature / Year: 1970
Title: Amino-Acid Sequence of Porcine Pancreatic Elastase and its Homologies with Other Serine Proteinases
Authors: Shotton, D.M. / Hartley, B.S.
#3: Journal: Nature / Year: 1970
Title: Three-Dimensional Fourier Synthesis of Tosyl-Elastase at 3.5 Angstroms Resolution
Authors: Watson, H.C. / Shotton, D.M. / Cox, J.M. / Muirhead, H.
#4: Journal: Nature / Year: 1970
Title: Three Dimensional Structure of Tosyl-Elastase
Authors: Shotton, D.M. / Watson, H.C.
#5: Journal: Atlas of Macromolecular Structure on Microfiche / Year: 1976
#6: Journal: Atlas of Protein Sequence and Structure,Supplement 2
Year: 1976
History
DepositionMay 17, 1976Processing site: BNL
Revision 1.0May 27, 1976Provider: repository / Type: Initial release
Revision 1.1Mar 3, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 24, 2011Group: Non-polymer description
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_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 / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Nov 13, 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 ...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

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Assembly

Deposited unit
A: PORCINE PANCREATIC ELASTASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,1963
Polymers25,9281
Non-polymers2682
Water45025
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)51.500, 58.000, 75.500
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Atom site foot note1: RESIDUE SER 195 (THE CATALYTICALLY ACTIVE SERINE ) HAS BEEN TOSYLATED IN THIS STRUCTURE. COORDINATES FOR THE TOSYL GROUP ARE GIVEN IN THE HETATM RECORDS BELOW.

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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-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-TSU / PARA-TOLUENE SULFONATE


Mass: 172.202 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H8O3S
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 25 / 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: 2.17 Å3/Da / Density % sol: 43.42 %
Crystal grow
*PLUS
Temperature: 2 ℃ / pH: 5 / Method: unknown
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
11 Msodium sulfate11
220 mg/mlprotein11
310 mMsodium acetate11

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Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1

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Processing

RefinementHighest resolution: 2.5 Å
Details: COORDINATES FOR THE 27 WATER MOLECULES AND 1 SULPHATE ION WERE TAKEN FROM THE ARTICLE CITED AS REFERENCE 1.
Refinement stepCycle: LAST / Highest resolution: 2.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1822 0 11 25 1858

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