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- PDB-3est: STRUCTURE OF NATIVE PORCINE PANCREATIC ELASTASE AT 1.65 ANGSTROMS... -

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Entry
Database: PDB / ID: 3est
TitleSTRUCTURE OF NATIVE PORCINE PANCREATIC ELASTASE AT 1.65 ANGSTROMS RESOLUTION
ComponentsPORCINE PANCREATIC ELASTASE
KeywordsHYDROLASE(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 / Peptidase S1A, chymotrypsin family / Serine proteases, trypsin family, histidine active site. / 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 / Peptidase S1A, chymotrypsin family / Serine proteases, trypsin family, histidine active site. / 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
Chymotrypsin-like elastase family member 1
Similarity search - Component
Biological speciesSus scrofa (pig)
MethodX-RAY DIFFRACTION / Resolution: 1.65 Å
AuthorsMeyer, E.F. / Cole, G. / Radhakrishnan, R. / Epp, O.
Citation
Journal: Acta Crystallogr.,Sect.B / Year: 1988
Title: Structure of native porcine pancreatic elastase at 1.65 A resolutions.
Authors: Meyer, E. / Cole, G. / Radhakrishnan, R. / Epp, O.
#1: Journal: J.Mol.Biol. / Year: 1987
Title: Crystal Structures of the Complex of Porcine Pancreatic Elastase with Two Valine-Derived Benzoxazinone Inhibitors
Authors: Radhakrishnan, R. / Presta, L.G. / Meyerjunior, E.F. / Wildonger, R.
#2: Journal: Biochemistry / Year: 1988
Title: Analysis of an Enzyme-Substrate Complex by X-Ray Crystallography and Transferred Nuclear Overhauser Enhancement Measurements: Porcine Pancreatic Elastase and a Hexapeptide
Authors: Meyerjunior, E.F. / Clore, G.M. / Gronenborn, A.M. / Hansen, H.A.S.
#3: Journal: J.Mol.Biol. / Year: 1986
Title: Structure of the Product Complex of Acetyl-Ala-Pro-Ala with Porcine Pancreatic Elastase at 1.65 Angstroms Resolution
Authors: Meyerjunior, E.F. / Radhakrishnan, R. / Cole, G.M. / Presta, L.G.
#4: Journal: J.Mol.Biol. / Year: 1986
Title: Stereochemistry of Binding of the Tetrapeptide Acetyl-Pro-Ala-Pro-Tyr-NH2 to Porcine Pancreatic Elastase. Combined Use of Two-Dimensional Transferred Nuclear Overhauser Enhancement ...Title: Stereochemistry of Binding of the Tetrapeptide Acetyl-Pro-Ala-Pro-Tyr-NH2 to Porcine Pancreatic Elastase. Combined Use of Two-Dimensional Transferred Nuclear Overhauser Enhancement Measurements, Restrained Molecular Dynamics, X-Ray Crystallography and Molecular Modelling
Authors: Clore, G.M. / Gronenborn, A.M. / Carlson, G. / Meyer, E.F.
#5: Journal: J.Am.Chem.Soc. / Year: 1985
Title: Stereospecific Reaction of 3-Methoxy-4-Chloro-7-Amino-Isocoumarin with Crystalline Porcine Pancreatic Elastase
Authors: Meyerjunior, E.F. / Presta, L.G. / Radhakrishnan, R.
#6: Journal: J.Mol.Biol. / Year: 1978
Title: The Atomic Structure of Crystalline Porcine Pancreatic Elastase at 2.5 Angstroms 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.
#7: Journal: Biochem.Biophys.Res.Commun. / Year: 1973
Title: Atomic Coordinates for Tosyl-Elastase
Authors: Sawyer, L. / Shotton, D.M. / Watson, H.C.
#8: 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.
#9: 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.
#10: Journal: Nature / Year: 1970
Title: Three Dimensional Structure of Tosyl-Elastase
Authors: Shotton, D.M. / Watson, H.C.
#11: Journal: Atlas of Protein Sequence and Structure,Supplement 2
Year: 1976
History
DepositionSep 17, 1987Processing site: BNL
Revision 1.0Jan 16, 1988Provider: 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.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 / Item: _pdbx_entry_details.has_protein_modification
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)26,1604
Polymers25,9281
Non-polymers2323
Water2,288127
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)52.100, 58.100, 75.200
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Atom site foot note1: THE FOLLOWING ATOMS WERE TREATED AS DUMMY ATOMS, WHICH MEANS THAT THEY CONTRIBUTED TO THE ENERGY REFINEMENT PART OF EREF BUT NOT TO THE CALCULATED STRUCTURE FACTORS -SER 36C OG, SER 37 OG, ARG 61 ...1: THE FOLLOWING ATOMS WERE TREATED AS DUMMY ATOMS, WHICH MEANS THAT THEY CONTRIBUTED TO THE ENERGY REFINEMENT PART OF EREF BUT NOT TO THE CALCULATED STRUCTURE FACTORS -SER 36C OG, SER 37 OG, ARG 61 (CZ,NH1,NH2), GLN 110 (CG,CD,OE1,NE2), ARG 125 (CG,CD,NE,CZ,NH1,NH2), SO4 290 (O1,O3).

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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


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 127 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Nonpolymer detailsSEVEN GROUPS OF WATER MOLECULES ARE REPORTED. THESE TEND TO BE CONSERVED IN THE FAMILY OF SERINE ...SEVEN GROUPS OF WATER MOLECULES ARE REPORTED. THESE TEND TO BE CONSERVED IN THE FAMILY OF SERINE PROTEASES. FUNCTIONAL IMPORTANCE IS PROPOSED FOR CLUSTERS WT1 (301-302-303-304-326-328-SURFACE) AND WT7 (313-314-315), WHICH ARE CHANNELS LINKING THE P1, THE PRIMARY SPECIFICITY SITE, WITH THE REMOTE, SOLVATED SURFACES OF THE ENZYME. CLUSTER WT4 (319-320-321) ESTABLISHES AN H-BONDING LINKAGE BETWEEN THE CATALYTIC TETRAD AND THE REMOTE SURFACE OF THE ENZYME, SUGGESTING A MECHANISM FOR A BASE TO EXTRACT A PROTON THAT, BY MEANS OF "FLIP-FLOP" H-BONDS, CAN BE PROPAGATED TO THE ACTIVE SITE SERINE 195. THIS H-BONDING LINKAGE IS NOW FOUND TO BE CONSERVED IN ALL SERINE PROTEASES.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.19 Å3/Da / Density % sol: 43.94 %
Crystal grow
*PLUS
Method: microdialysis
Details: took Meyer, Radhakrishman et al., (1986) from original paper
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
15 %(w/v)protein1buttom
20.1 Msodium acetate1buttom
30.02 %(w/v)sodium azide1buttom
40.1 Msodium sulfate1reservoir

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Data collection

Reflection
*PLUS
Highest resolution: 1.65 Å / Num. obs: 19232 / % possible obs: 66 % / Rmerge(I) obs: 0.093

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Processing

SoftwareName: EREF / Classification: refinement
RefinementRfactor Rwork: 0.169 / Highest resolution: 1.65 Å
Details: THE FOLLOWING ATOMS WERE TREATED AS DUMMY ATOMS, WHICH MEANS THAT THEY CONTRIBUTED TO THE ENERGY REFINEMENT PART OF EREF BUT NOT TO THE CALCULATED STRUCTURE FACTORS -SER 36C OG, SER 37 OG, ...Details: THE FOLLOWING ATOMS WERE TREATED AS DUMMY ATOMS, WHICH MEANS THAT THEY CONTRIBUTED TO THE ENERGY REFINEMENT PART OF EREF BUT NOT TO THE CALCULATED STRUCTURE FACTORS -SER 36C OG, SER 37 OG, ARG 61 (CZ,NH1,NH2), GLN 110 (CG,CD,OE1,NE2), ARG 125 (CG,CD,NE,CZ,NH1,NH2), SO4 290 (O1,O3).
Refinement stepCycle: LAST / Highest resolution: 1.65 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1822 0 11 127 1960
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONo_bond_d0.018
X-RAY DIFFRACTIONo_bond_d_na
X-RAY DIFFRACTIONo_bond_d_prot
X-RAY DIFFRACTIONo_angle_d
X-RAY DIFFRACTIONo_angle_d_na
X-RAY DIFFRACTIONo_angle_d_prot
X-RAY DIFFRACTIONo_angle_deg2.5
X-RAY DIFFRACTIONo_angle_deg_na
X-RAY DIFFRACTIONo_angle_deg_prot
X-RAY DIFFRACTIONo_dihedral_angle_d
X-RAY DIFFRACTIONo_dihedral_angle_d_na
X-RAY DIFFRACTIONo_dihedral_angle_d_prot
X-RAY DIFFRACTIONo_improper_angle_d
X-RAY DIFFRACTIONo_improper_angle_d_na
X-RAY DIFFRACTIONo_improper_angle_d_prot
X-RAY DIFFRACTIONo_mcbond_it
X-RAY DIFFRACTIONo_mcangle_it
X-RAY DIFFRACTIONo_scbond_it
X-RAY DIFFRACTIONo_scangle_it
Software
*PLUS
Name: X-PLOR / Classification: refinement
Refinement
*PLUS
Lowest resolution: 7 Å / Rfactor all: 0.169
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 14.1 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d
X-RAY DIFFRACTIONx_angle_d2.5
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scangle_it

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