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- PDB-3sgb: STRUCTURE OF THE COMPLEX OF STREPTOMYCES GRISEUS PROTEASE B AND T... -

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Basic information

Entry
Database: PDB / ID: 3sgb
TitleSTRUCTURE OF THE COMPLEX OF STREPTOMYCES GRISEUS PROTEASE B AND THE THIRD DOMAIN OF THE TURKEY OVOMUCOID INHIBITOR AT 1.8 ANGSTROMS RESOLUTION
Components
  • PROTEINASE B (SGPB)
  • TURKEY OVOMUCOID INHIBITOR (OMTKY3)
KeywordsCOMPLEX(SERINE PROTEINASE-INHIBITOR)
Function / homology
Function and homology information


streptogrisin B / molecular function inhibitor activity / serine-type endopeptidase inhibitor activity / serine-type endopeptidase activity / proteolysis / extracellular region
Similarity search - Function
Proteinase inhibitor I1, Kazal-type, metazoa / Kazal serine protease inhibitors family signature. / Peptidase S1A, alpha-lytic prodomain / Alpha-lytic protease prodomain / Peptidase S1A, streptogrisin / Kazal-type serine protease inhibitor domain / Wheat Germ Agglutinin (Isolectin 2); domain 1 - #30 / Kazal type serine protease inhibitors / Kazal domain superfamily / Kazal domain ...Proteinase inhibitor I1, Kazal-type, metazoa / Kazal serine protease inhibitors family signature. / Peptidase S1A, alpha-lytic prodomain / Alpha-lytic protease prodomain / Peptidase S1A, streptogrisin / Kazal-type serine protease inhibitor domain / Wheat Germ Agglutinin (Isolectin 2); domain 1 - #30 / Kazal type serine protease inhibitors / Kazal domain superfamily / Kazal domain / Kazal domain profile. / Wheat Germ Agglutinin (Isolectin 2); domain 1 / Serine proteases, trypsin family, histidine active site / Serine proteases, trypsin family, serine active site / 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 / 2-Layer Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Streptogrisin-B / Ovomucoid
Similarity search - Component
Biological speciesStreptomyces griseus (bacteria)
MethodX-RAY DIFFRACTION / Resolution: 1.8 Å
AuthorsRead, R.J. / Fujinaga, M. / Sielecki, A.R. / James, M.N.G.
Citation
Journal: Biochemistry / Year: 1983
Title: Structure of the complex of Streptomyces griseus protease B and the third domain of the turkey ovomucoid inhibitor at 1.8-A resolution.
Authors: Read, R.J. / Fujinaga, M. / Sielecki, A.R. / James, M.N.
#1: Journal: J.Mol.Biol. / Year: 1987
Title: Crystal and Molecular Structures of the Complex of Alpha-Chymotrypsin with its Inhibitor Turkey Ovomucoid Third Domain at 1.8 Angstroms Resolution
Authors: Fujinaga, M. / Sielecki, A.R. / Read, R.J. / Ardelt, W. / Laskowskijunior, M. / James, M.N.G.
#2: Journal: Proc.Natl.Acad.Sci.USA / Year: 1982
Title: Refined Crystal Structure of the Molecular Complex of Streptomyces Griseus Protease B, a Serine Protease, with the Third Domain of the Ovomucoid Inhibitor from Turkey
Authors: Fujinaga, M. / Read, R.J. / Sielecki, A. / Ardelt, W. / Laskowski Junior, M. / James, M.N.G.
#3: Journal: J.Mol.Biol. / Year: 1980
Title: Crystal Structure Studies and Inhibition Kinetics of Tripeptide Chloromethyl Ketone Inhibitors with Streptomyces Griseus Protease B
Authors: James, M.N.G. / Brayer, G.D. / Delbaere, L.T.J. / Sielecki, A.R. / Gertler, A.
#4: Journal: Can.J.Biochem. / Year: 1979
Title: The 2.8 Angstroms Resolution Structure of Streptomyces Griseus Protease B and its Homology with Alpha-Chymotrypsin and Streptomyces Griseus Protease A
Authors: Delbaere, L.T.J. / Brayer, G.D. / James, M.M.G.
#5: 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.
#6: Journal: Miami Winter Symp. / Year: 1976
Title: Relationship between the Structures and Activities of Some Microbial Serine Proteases. II. Comparison of the Tertiary Structures of Microbial and Pancreatic Serine Proteases
Authors: James, M.N.G.
#7: 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. / Theissen, W.E.
#8: Journal: Can.J.Biochem. / Year: 1974
Title: 4.5 Angstroms Resolution Structure of a Bacterial Serine Protease from Streptomyces Griseus
Authors: Codding, P.W. / Delbaere, L.T.J. / Hayakawa, K. / Hutcheon, W.L.B. / James, M.N.G. / Jurasek, L.
History
DepositionJan 21, 1983Processing site: BNL
SupersessionJul 12, 1983ID: 2SGB
Revision 1.0Jul 12, 1983Provider: repository / Type: Initial release
Revision 1.1Mar 25, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 29, 2017Group: Derived calculations / Other
Category: pdbx_database_status / struct_conf / struct_conf_type
Item: _pdbx_database_status.process_site
Revision 1.4Oct 30, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Remark 700SHEET THE SEVEN-STRANDED SHEETS BL1 AND BL2 PRESENTED ON SHEET RECORDS BELOW ARE ACTUALLY SIX- ...SHEET THE SEVEN-STRANDED SHEETS BL1 AND BL2 PRESENTED ON SHEET RECORDS BELOW ARE ACTUALLY 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
E: PROTEINASE B (SGPB)
I: TURKEY OVOMUCOID INHIBITOR (OMTKY3)


Theoretical massNumber of molelcules
Total (without water)24,6922
Polymers24,6922
Non-polymers00
Water3,279182
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1270 Å2
ΔGint-8 kcal/mol
Surface area9690 Å2
MethodPISA
Unit cell
Length a, b, c (Å)45.350, 54.520, 45.650
Angle α, β, γ (deg.)90.00, 119.20, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein PROTEINASE B (SGPB)


Mass: 18665.285 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces griseus (bacteria) / Organ: PANCREATIC / References: UniProt: P00777
#2: Protein TURKEY OVOMUCOID INHIBITOR (OMTKY3)


Mass: 6026.811 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
References: UniProt: P68390
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 182 / 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: 1.99 Å3/Da / Density % sol: 38.33 %
Crystal grow
*PLUS
pH: 6 / Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formulaDetails
110 mM1dropMgCl2
210-15 mg/mlenzyme1drop
31.0 M1reservoirLi2SO4precipitant
40.7-1.0 M1reservoirKH2PO4precipitant

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Data collection

Reflection
*PLUS
Highest resolution: 1.8 Å / Num. all: 20227 / Num. obs: 18082 / Num. measured all: 13937 / Rmerge(I) obs: 2 / Biso Wilson estimate: 13.1 Å2

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Processing

RefinementResolution: 1.8→6 Å / Rfactor Rwork: 0.125
Refine analyzeLuzzati coordinate error obs: 0.14 Å
Refinement stepCycle: LAST / Resolution: 1.8→6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1690 0 0 182 1872
Refinement
*PLUS
Num. reflection obs: 13457 / σ(I): 2 / Highest resolution: 1.8 Å / Lowest resolution: 6 Å / Rfactor obs: 0.125
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONo_bond_d0.0170.008
X-RAY DIFFRACTIONo_angle_d0.0370.016
X-RAY DIFFRACTIONo_planar_d0.0420.016
X-RAY DIFFRACTIONo_plane_restr0.0210.012
X-RAY DIFFRACTIONo_chiral_restr0.1920.08

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