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- PDB-5sga: Structures of product and inhibitor complexes of Streptomyces gri... -

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Basic information

Entry
Database: PDB / ID: 5sga
TitleStructures of product and inhibitor complexes of Streptomyces griseus protease a at 1.8 Angstroms resolution. a model for serine protease catalysis
Components
  • PROTEINASE A (SGPA)
  • TETRAPEPTIDE ACE-PRO-ALA-PRO-TYR
KeywordsHYDROLASE/HYDROLASE INHIBITOR / SERINE PROTEINASE / HYDROLASE-HYDROLASE INHIBITOR complex
Function / homology
Function and homology information


streptogrisin A / serine-type endopeptidase activity / proteolysis / extracellular region
Similarity search - Function
Peptidase S1A, alpha-lytic prodomain / Alpha-lytic protease prodomain / Peptidase S1A, streptogrisin / Serine proteases, trypsin family, histidine active site. / Serine proteases, trypsin family, serine active site. / Serine proteases, trypsin domain / Trypsin / Trypsin-like serine proteases / Thrombin, subunit H / Peptidase S1, PA clan, chymotrypsin-like fold ...Peptidase S1A, alpha-lytic prodomain / Alpha-lytic protease prodomain / Peptidase S1A, streptogrisin / Serine proteases, trypsin family, histidine active site. / Serine proteases, trypsin family, serine active site. / 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
Biological speciesStreptomyces griseus (bacteria)
MethodX-RAY DIFFRACTION / Resolution: 1.8 Å
AuthorsSielecki, A.R. / James, M.N.G.
Citation
Journal: J.Mol.Biol. / Year: 1980
Title: Structures of product and inhibitor complexes of Streptomyces griseus protease A at 1.8 A resolution. A model for serine protease catalysis.
Authors: James, M.N. / Sielecki, A.R. / Brayer, G.D. / Delbaere, L.T. / Bauer, C.A.
#1: Journal: Proceedings of the Daresbury Study Weekend: Refinement of Protein Structures
Year: 1981
Title: The Importance of Refined Structures to the Understanding of Enzyme Action
Authors: Sielecki, A.R. / James, M.N.G.
#2: Journal: J.Mol.Biol. / Year: 1979
Title: Protein Structure Refinement. Streptomyces Griseus Serine Protease A at 1.8 Angstroms Resolution
Authors: Sielecki, A.R. / Hendrickson, W.A. / Broughton, C.G. / Delbaere, L.T.J. / Brayer, G.D. / James, M.N.G.
#3: Journal: J.Mol.Biol. / Year: 1985
Title: Electron Density Calculations as an Extension of Protein Structure Refinement. Streptomyces Griseus Protease at 1.5 Angstroms Resolution
Authors: Moult, J. / Sussman, F. / James, M.N.G.
#4: Journal: Proc.Natl.Acad.Sci.USA / Year: 1979
Title: Crystallographic and Kinetic Investigations of the Covalent Complex Formed by a Specific Tetrapeptide Aldehyde and the Serine Protease from Streptomyces Griseus
Authors: Brayer, G.D. / Delbaere, L.T.J. / James, M.N.G. / Bauer, C.-A. / Thompson, R.C.
#5: Journal: J.Mol.Biol. / Year: 1978
Title: Molecular Structure of Crystalline Streptomyces Griseus Protease A at 2.8 Angstroms Resolution. II. Molecular Conformation, Comparison with Alpha-Chymotrypsin and Active-Site Geometry
Authors: Brayer, G.D. / Delbaere, L.T.J. / James, M.N.G.
#6: Journal: J.Mol.Biol. / Year: 1978
Title: Molecular Structure of Crystalline Streptomyces Griseus Protease A at 2.8 Angstroms Resolution. I. Crystallization, Data Collection and Structural Analysis
Authors: Brayer, G.D. / Delbaere, L.T.J. / James, M.N.G.
#7: Journal: Can.J.Biochem. / Year: 1978
Title: Amino Acid Sequence Alignment of Bacterial and Mammalian Pancreatic Serine Proteases Based on Topological Equivalences
Authors: James, M.N.G. / Delbaere, L.T.J. / Brayer, G.D.
#8: Journal: Nature / Year: 1975
Title: Tertiary Structural Differences between Microbial Serine Proteases and Pancreatic Serine Enzymes
Authors: Delbaere, L.T.J. / Hutcheon, W.L.B. / James, M.N.G. / Thiessen, W.E.
#9: Journal: J.Mol.Biol. / Year: 1980
Title: Structure of the Complex Formed between the Bacterial-Produced Inhibitor Chymostatin and the Serine Enzyme Streptomyces Griseus Protease A
Authors: Delbaere, L.T.J. / Brayer, G.D.
#10: Journal: J.Mol.Biol. / Year: 1985
Title: Refined Structure of Alpha-Lytic Protease at 1.7 Angstroms Resolution: Analysis of Hydrogen Bonding and Solvent Structure
Authors: Fujinaga, M. / Delbaere, L.T.J. / Brayer, G.D. / James, M.N.G.
History
DepositionMay 29, 1990Processing site: BNL
Revision 1.0Oct 15, 1991Provider: repository / Type: Initial release
Revision 1.1Mar 25, 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 1.3Dec 12, 2012Group: Other
Revision 1.4Mar 13, 2013Group: Other
Revision 1.5Jun 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_ref_seq_dif
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_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_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_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details
Revision 1.6Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
E: PROTEINASE A (SGPA)
P: TETRAPEPTIDE ACE-PRO-ALA-PRO-TYR


Theoretical massNumber of molelcules
Total (without water)18,4892
Polymers18,4892
Non-polymers00
Water3,333185
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area950 Å2
ΔGint-7 kcal/mol
Surface area7010 Å2
MethodPISA
Unit cell
Length a, b, c (Å)55.160, 55.160, 54.780
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number77
Space group name H-MP42
Atom site foot note1: THE SIDE CHAIN OF ARG E 221 IS VERY DISORDERED. COORDINATES FOR THE ATOMS BEYOND CB HAVE BEEN OMITTED.
2: RESIDUE E 99A IS A CIS-PROLINE.
3: SOLVENT 229, ALTHOUGH REFINED AS AN OXYGEN ATOM, HAS BEEN INTERPRETED AS A NA+ ION. SEE REFERENCE 2 ABOVE FOR FURTHER DETAILS.
Components on special symmetry positions
IDModelComponents
11E-252-

HOH

21E-280-

HOH

31E-293-

HOH

41E-352-

HOH

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Components

#1: Protein PROTEINASE A (SGPA)


Mass: 18016.625 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces griseus (bacteria) / References: UniProt: P00776
#2: Protein/peptide TETRAPEPTIDE ACE-PRO-ALA-PRO-TYR


Mass: 472.534 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 185 / 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: 2.25 Å3/Da / Density % sol: 45.41 %
Crystal grow
*PLUS
pH: 4.1 / Method: equilibrium dialysis
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
11 %(w/v)protein1drop
21.3 M1dropNaH2PO4

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Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
Reflection
*PLUS
Highest resolution: 1.8 Å / Num. obs: 15254 / % possible obs: 80.7 % / Observed criterion σ(I): 3 / Num. measured all: 16136 / Rmerge(I) obs: 0.085 / Biso Wilson estimate: 12.1 Å2

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Processing

SoftwareName: PROLSQ / Classification: refinement
RefinementResolution: 1.8→10 Å / Rfactor obs: 0.116
Refinement stepCycle: LAST / Resolution: 1.8→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1294 0 0 185 1479
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0190.03
X-RAY DIFFRACTIONp_angle_d0.0360.046
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_restr0.0150.018
X-RAY DIFFRACTIONp_chiral_restr0.1480.18
X-RAY DIFFRACTIONp_singtor_nbd0.2070.4
X-RAY DIFFRACTIONp_multtor_nbd
X-RAY DIFFRACTIONp_xhyhbond_nbd0.147
X-RAY DIFFRACTIONp_xyhbond_nbd
X-RAY DIFFRACTIONp_planar_tor2.96
X-RAY DIFFRACTIONp_staggered_tor
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor
X-RAY DIFFRACTIONp_special_tor
Refinement
*PLUS
Highest resolution: 1.8 Å / Lowest resolution: 10 Å / Rfactor obs: 0.116 / Num. reflection obs: 12166
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 14.3 Å2

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