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- PDB-1sgc: THE 1.8 ANGSTROMS STRUCTURE OF THE COMPLEX BETWEEN CHYMOSTATIN AN... -

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Basic information

Entry
Database: PDB / ID: 1sgc
TitleTHE 1.8 ANGSTROMS STRUCTURE OF THE COMPLEX BETWEEN CHYMOSTATIN AND STREPTOMYCES GRISEUS PROTEASE A. A MODEL FOR SERINE PROTEASE CATALYTIC TETRAHEDRAL INTERMEDIATES
Components
  • CHYMOSTATIN A
  • PROTEINASE A
KeywordsHYDROLASE/HYDROLASE INHIBITOR / HYDROLASE (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
Chymostatin A / Streptogrisin-A
Similarity search - Component
Biological speciesStreptomyces griseus (bacteria)
Streptomyces hygroscopicus (bacteria)
MC521-C8
MethodX-RAY DIFFRACTION / Resolution: 1.8 Å
AuthorsDelbaere, L.T.J. / Brayer, G.D.
Citation
Journal: J.Mol.Biol. / Year: 1985
Title: The 1.8 A structure of the complex between chymostatin and Streptomyces griseus protease A. A model for serine protease catalytic tetrahedral intermediates.
Authors: Delbaere, L.T. / Brayer, G.D.
#1: 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.
History
DepositionApr 18, 1986Processing site: BNL
Revision 1.0Jul 14, 1986Provider: repository / Type: Initial release
Revision 1.1Mar 3, 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 1.3Feb 27, 2013Group: Other
Revision 2.0Jun 5, 2024Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations / Other / Polymer sequence
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / entity_poly / pdbx_database_status / pdbx_validate_polymer_linkage / 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 / _entity_poly.pdbx_seq_one_letter_code_can / _pdbx_database_status.process_site / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _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_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details
Revision 2.1Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: PROTEINASE A
B: CHYMOSTATIN A


Theoretical massNumber of molelcules
Total (without water)18,6242
Polymers18,6242
Non-polymers00
Water3,909217
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)55.050, 55.050, 54.630
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number77
Space group name H-MP42
Atom site foot note1: RESIDUE 99A IS A CIS-PROLINE.
2: THE SIDE CHAIN ATOMS OF ARG 221 BEYOND CB WERE NOT WELL DEFINED AND, THEREFORE, ARE NOT INCLUDED IN THIS ENTRY.
Components on special symmetry positions
IDModelComponents
11A-252-

HOH

21A-281-

HOH

31A-295-

HOH

41A-357-

HOH

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Components

#1: Protein PROTEINASE A


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 CHYMOSTATIN A


Type: Oligopeptide / Class: Enzyme inhibitor / Mass: 607.701 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Streptomyces hygroscopicus, MC521-C8 / References: Chymostatin A
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 217 / Source method: isolated from a natural source / Formula: H2O
Compound detailsTHE INHIBITOR CHYMOSTATIN A HAS LAST RESIDUE PHENYLALANINAL REPRESENTED WITH ALTERNATE ...THE INHIBITOR CHYMOSTATIN A HAS LAST RESIDUE PHENYLALANINAL REPRESENTED WITH ALTERNATE CONFORMATIONS ON ITS TERMINAL OXYGEN.
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: 2.3 Å3/Da / Density % sol: 46.45 %
Crystal grow
*PLUS
Method: other / Details: Delbaere, L.T.J., (1980) J. Mol. Biol., 139, 45.

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Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
Reflection
*PLUS
Highest resolution: 1.8 Å / Num. all: 15941 / Num. obs: 15116 / Rmerge(I) obs: 0.021

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Processing

SoftwareName: PROLSQ / Classification: refinement
RefinementRfactor Rwork: 0.123 / Highest resolution: 1.8 Å
Refinement stepCycle: LAST / Highest resolution: 1.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1303 0 0 217 1520
Refinement
*PLUS
Num. reflection obs: 11755 / σ(I): 3 / Rfactor obs: 0.123
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 11.5 Å2

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