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- PDB-2tld: CRYSTAL STRUCTURE OF AN ENGINEERED SUBTILISIN INHIBITOR COMPLEXED... -

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Basic information

Entry
Database: PDB / ID: 2tld
TitleCRYSTAL STRUCTURE OF AN ENGINEERED SUBTILISIN INHIBITOR COMPLEXED WITH BOVINE TRYPSIN
Components
  • STREPTOMYCES SUBTILISIN INHIBITOR (SSI)
  • TRYPSIN
KeywordsHYDROLASE/HYDROLASE INHIBITOR / PROTEINASE / HYDROLASE-HYDROLASE INHIBITOR COMPLEX / TRYPSIN)
Function / homology
Function and homology information


trypsin / serpin family protein binding / serine protease inhibitor complex / digestion / serine-type endopeptidase inhibitor activity / endopeptidase activity / serine-type endopeptidase activity / proteolysis / extracellular space / extracellular region / metal ion binding
Similarity search - Function
Proteinase inhibitor I16, Streptomyces subtilisin-type inhibitor, conserved site / Streptomyces subtilisin-type inhibitors signature. / Proteinase inhibitor I16, Streptomyces subtilisin-type inhibitor / Subtilisin inhibitor / Subtilisin inhibitor-like superfamily / Subtilisin inhibitor-like / : / Serine proteases, trypsin family, histidine active site / Serine proteases, trypsin family, serine active site / Serine proteases, trypsin family, histidine active site. ...Proteinase inhibitor I16, Streptomyces subtilisin-type inhibitor, conserved site / Streptomyces subtilisin-type inhibitors signature. / Proteinase inhibitor I16, Streptomyces subtilisin-type inhibitor / Subtilisin inhibitor / Subtilisin inhibitor-like superfamily / Subtilisin inhibitor-like / : / Serine proteases, trypsin family, histidine active site / Serine proteases, trypsin family, serine active site / Serine proteases, trypsin family, histidine active site. / Peptidase S1A, chymotrypsin family / Serine proteases, trypsin family, serine active site. / Serine proteases, trypsin domain profile. / Trypsin-like serine protease / Serine proteases, trypsin domain / Trypsin / Peptidase S1, PA clan, chymotrypsin-like fold / Peptidase S1, PA clan
Similarity search - Domain/homology
Serine protease 1 / Subtilisin inhibitor
Similarity search - Component
Biological speciesBos taurus (domestic cattle)
MethodX-RAY DIFFRACTION / Resolution: 2.6 Å
AuthorsMitsui, Y. / Takeuchi, Y. / Nonaka, T. / Nakamura, K.T.
Citation
Journal: Proc.Natl.Acad.Sci.USA / Year: 1992
Title: Crystal structure of an engineered subtilisin inhibitor complexed with bovine trypsin.
Authors: Takeuchi, Y. / Nonaka, T. / Nakamura, K.T. / Kojima, S. / Miura, K. / Mitsui, Y.
#1: Journal: J.Mol.Biol. / Year: 1991
Title: Refined Crystal Structure of the Complex of Subtilisin Bpn' and Streptomyces Subtilisin Inhibitor at 1.8 Angstroms Resolution
Authors: Takeuchi, Y. / Satow, Y. / Nakamura, K.T. / Mitsui, Y.
History
DepositionSep 16, 1991Processing site: BNL
Revision 1.0Jul 15, 1992Provider: repository / Type: Initial release
Revision 1.1Mar 3, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 21, 2024Group: Data collection / Database references / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / 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_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
E: TRYPSIN
I: STREPTOMYCES SUBTILISIN INHIBITOR (SSI)


Theoretical massNumber of molelcules
Total (without water)34,0392
Polymers34,0392
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)110.900, 116.800, 64.300
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222
Atom site foot note1: PRO I 37 IS A CIS PROLINE.
DetailsSSI IS A DIMERIC MOLECULE (I2) CONSISTING OF TWO IDENTICAL SUBUNITS. IT BINDS TWO TRYPSIN MOLECULES (2E) TO FORM A DIMERIC COMPLEX E2I2. THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT CORRESPONDS TO HALF THE COMPLEX MOLECULE (EI). IN THIS ENTRY COORDINATES FOR ALPHA-CARBON ATOMS ARE PROVIDED FOR ONE CHAIN OF TRYPSIN USING THE CHAIN IDENTIFIER *E* AND FOR ONE CHAIN OF MODIFIED SSI USING THE CHAIN IDENTIFIER *I*. COORDINATES FOR THE OTHER EI COMPLEX CAN BE GENERATED FROM THE COORDINATES IN THIS ENTRY USING THE FOLLOWING TRANSFORMATION: -1.0 0.0 0.0 0.0 -1.0 0.0 0.0 0.0 1.0

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Components

#1: Protein TRYPSIN / Coordinate model: Cα atoms only


Mass: 22903.805 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bos taurus (domestic cattle) / References: UniProt: P00760, trypsin
#2: Protein STREPTOMYCES SUBTILISIN INHIBITOR (SSI) / Coordinate model: Cα atoms only


Mass: 11135.486 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
References: UniProt: P01006

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 3.06 Å3/Da / Density % sol: 59.77 %
Crystal grow
*PLUS
pH: 7 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
10.05 MTris-HCl1drop
240 %sat1dropMgSO4
30.05 MTris-HCl1reservoir
480 %sat1reservoirMgSO4

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Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
Reflection
*PLUS
Highest resolution: 2.6 Å / Num. obs: 7579 / Observed criterion σ(I): 2 / Num. measured all: 23106 / Rmerge(I) obs: 0.063

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Processing

SoftwareName: X-PLOR / Classification: refinement
RefinementResolution: 2.6→8 Å /
RfactorNum. reflection
Rwork0.173 -
obs-6166
Refinement stepCycle: LAST / Resolution: 2.6→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms330 0 0 0 330
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.02
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg4.3
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Software
*PLUS
Name: X-PLOR / Classification: refinement
Refinement
*PLUS
Highest resolution: 2.6 Å / Lowest resolution: 8 Å / Num. reflection all: 6166 / Rfactor obs: 0.173
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_angle_d4.3
X-RAY DIFFRACTIONx_dihedral_angle_d28.7
X-RAY DIFFRACTIONx_dihedral_angle_deg

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