[English] 日本語
Yorodumi
- PDB-3sga: STRUCTURES OF PRODUCT AND INHIBITOR COMPLEXES OF STREPTOMYCES GRI... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3sga
TitleSTRUCTURES OF PRODUCT AND INHIBITOR COMPLEXES OF STREPTOMYCES GRISEUS PROTEASE A AT 1.8 ANGSTROMS RESOLUTION. A MODEL FOR SERINE PROTEASE CATALYSIS
Components
  • ACE-PRO-ALA-PRO-PHE-ALDEHYDE
  • PROTEINASE A (SGPA)
KeywordsHYDROLASE/HYDROLASE INHIBITOR / HYDROLASE-HYDROLASE INHIBITOR COMPLEX / SERINE PROTEINASE
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
ACE-PRO-ALA-PRO-PHE-ALDEHYDE, BOUND FORM / Streptogrisin-A
Similarity search - Component
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 1.3Sep 19, 2012Group: Structure summary
Revision 1.4Dec 12, 2012Group: Other
Revision 1.5Jun 5, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / struct_conn / struct_ref_seq / struct_ref_seq_dif
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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_asym_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.db_align_beg / _struct_ref_seq.db_align_end / _struct_ref_seq_dif.details

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
E: PROTEINASE A (SGPA)
P: ACE-PRO-ALA-PRO-PHE-ALDEHYDE


Theoretical massNumber of molelcules
Total (without water)18,4592
Polymers18,4592
Non-polymers00
Water3,441191
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1180 Å2
ΔGint-9 kcal/mol
Surface area6920 Å2
MethodPISA
Unit cell
Length a, b, c (Å)55.180, 55.180, 54.660
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-310-

HOH

21E-338-

HOH

31E-351-

HOH

41E-409-

HOH

-
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) / Gene: sprA / References: UniProt: P00776
#2: Protein/peptide ACE-PRO-ALA-PRO-PHE-ALDEHYDE


Type: Peptide-like / Class: Inhibitor / Mass: 442.551 Da / Num. of mol.: 1 / Source method: obtained synthetically / References: ACE-PRO-ALA-PRO-PHE-ALDEHYDE, BOUND FORM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 191 / Source method: isolated from a natural source / Formula: H2O
Compound detailsTHE C-TERMINUS OF THE INHIBITOR IS A MODIFIED PHENYLALANINE IN WHICH THE CARBOXYLATE GOURD HAS BEEN ...THE C-TERMINUS OF THE INHIBITOR IS A MODIFIED PHENYLALANINE IN WHICH THE CARBOXYLATE GOURD HAS BEEN REDUCED TO AN ALDEHYDE.

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION

-
Sample preparation

CrystalDensity Matthews: 2.25 Å3/Da / Density % sol: 45.42 %
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

-
Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
Reflection
*PLUS
Highest resolution: 1.8 Å / Lowest resolution: 10 Å / Num. obs: 15228 / % possible obs: 71.7 % / Num. measured all: 16005 / Rmerge(I) obs: 0.034 / Biso Wilson estimate: 10.2 Å2

-
Processing

SoftwareName: PROLSQ / Classification: refinement
RefinementResolution: 1.8→10 Å / Rfactor obs: 0.12
Refinement stepCycle: LAST / Resolution: 1.8→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1292 0 0 191 1483
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.030.03
X-RAY DIFFRACTIONp_angle_d0.040.046
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_restr0.010.018
X-RAY DIFFRACTIONp_chiral_restr0.180.18
X-RAY DIFFRACTIONp_singtor_nbd0.40.4
X-RAY DIFFRACTIONp_multtor_nbd
X-RAY DIFFRACTIONp_xhyhbond_nbd0.162
X-RAY DIFFRACTIONp_xyhbond_nbd
X-RAY DIFFRACTIONp_planar_tor2.46
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 all: 0.12
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 13.3 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_bond_d0.017
X-RAY DIFFRACTIONp_angle_d0.036
X-RAY DIFFRACTIONp_plane_restr0.012
X-RAY DIFFRACTIONp_chiral_restr0.124

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more