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- PDB-3ssi: PROTEINASE INHIBITOR SSI (STREPTOMYCES SUBTILISIN, INHIBITOR) FRO... -

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Basic information

Entry
Database: PDB / ID: 3ssi
TitlePROTEINASE INHIBITOR SSI (STREPTOMYCES SUBTILISIN, INHIBITOR) FROM STREPTOMYCES ALBOGRISEOLUS
ComponentsSTREPTOMYCES SUBTILISIN INHIBITOR
KeywordsSERINE PROTEASE INHIBITOR / SSI / SUBTILISIN BPN
Function / homology
Function and homology information


serine-type endopeptidase inhibitor activity / extracellular region
Similarity search - Function
Proteinase inhibitor I16, Streptomyces subtilisin-type inhibitor, conserved site / Streptomyces subtilisin-type inhibitors signature. / Subtilisin Inhibitor / Subtilisin inhibitor-like / Proteinase inhibitor I16, Streptomyces subtilisin-type inhibitor / Subtilisin inhibitor / Subtilisin inhibitor-like superfamily / Subtilisin inhibitor-like / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Subtilisin inhibitor
Similarity search - Component
Biological speciesStreptomyces albogriseolus (bacteria)
MethodX-RAY DIFFRACTION / Resolution: 2.3 Å
AuthorsSuzuki, T. / Nonaka, T. / Mitsui, Y.
Citation
Journal: To be Published
Title: Structural Modulation of the Protein Proteinase Inhibitor Ssi (Streptomyces Subtilisin Inhibitor)
Authors: Suzuki, T.
#1: 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.
#2: Journal: J.Mol.Biol. / Year: 1991
Title: Refined Crystal Structure of the Complex of Subtilisin Bpn' and Streptomyces Subtilisin Inhibitor at 1.8 A Resolution
Authors: Takeuchi, Y. / Satow, Y. / Nakamura, K.T. / Mitsui, Y.
#3: Journal: Protein Eng. / Year: 1991
Title: Molecular Recognition at the Active Site of Subtilisin Bpn': Crystallographic Studies Using Genetically Engineered Proteinaceous Inhibitor Ssi (Streptomyces Subtilisin Inhibitor)
Authors: Takeuchi, Y. / Noguchi, S. / Satow, Y. / Kojima, S. / Kumagai, I. / Miura, K. / Nakamura, K.T. / Mitsui, Y.
#4: Journal: J.Biochem.(Tokyo) / Year: 1985
Title: Interactions of Streptomyces Subtilisin Inhibitor with Streptomyces Griseus Proteases a and B. Enzyme Kinetic and Computer Simulation Studies
Authors: Christensen, U. / Ishida, S. / Ishii, S. / Mitsui, Y. / Iitaka, Y. / Mcclarin, J. / Langridge, R.
#6: Journal: J.Mol.Biol. / Year: 1984
Title: Crystal Structure at 2.6 A Resolution of the Complex of Subtilisin Bpn' with Streptomyces Subtilisin Inhibitor
Authors: Hirono, S. / Akagawa, H. / Mitsui, Y. / Iitaka, Y.
#7: Journal: J.Biochem.(Tokyo) / Year: 1980
Title: Solvent Accessibility and Microenvironment in a Bacterial Protein Proteinase Inhibitor Ssi (Streptomyces Subtilisin Inhibitor)
Authors: Satow, Y. / Watanabe, Y. / Mitsui, Y.
#8: Journal: J.Mol.Biol. / Year: 1979
Title: Crystal Structure of the Complex of Subtilisin Bpn' with its Protein Inhibitor Streptomyces Subtilisin Inhibitor. The Structure at 4.3 Angstroms Resolution
Authors: Hirono, S. / Nakamura, K.T. / Iitaka, Y. / Mitsui, Y.
#9: Journal: J.Mol.Biol. / Year: 1979
Title: Crystal Structure of a Bacterial Protein Proteinase Inhibitor (Streptomyces Subtilisin Inhibitor) at 2.6 A Resolution
Authors: Mitsui, Y. / Satow, Y. / Watanabe, Y. / Iitaka, Y.
#10: Journal: Nature / Year: 1979
Title: Crystal Structures of Streptomyces Subtilisin Inhibitor and its Complex with Subtilisin Bpn
Authors: Mitsui, Y. / Satow, Y. / Watanabe, Y. / Hirono, S. / Iitaka, Y.
#11: Journal: J.Biochem.(Tokyo) / Year: 1978
Title: Crystal Structure of a Protein Proteinase Inhibitor, Ssi (Streptomyces Subtilisin Inhibitor), at 4 A Resolution
Authors: Satow, Y. / Mitsui, Y. / Iitaka, Y.
#12: Journal: J.Biochem.(Tokyo) / Year: 1977
Title: Crystal Structure of a Protein Proteinase Inhibitor, Streptomyces Subtilisin Inhibitor, at 2.3 Angstrom Resolution
Authors: Mitsui, Y. / Satow, Y. / Sakamaki, T. / Iitaka, Y.
#13: Journal: J.Mol.Biol. / Year: 1973
Title: Crystallization and Preliminary X-Ray Investigation of a New Alkaline Protease Inhibitor and its Complex with Subtilisin Bpn
Authors: Satow, Y. / Mitsui, Y. / Iitaka, Y. / Murao, S. / Sato, S.
#5: Journal: Protein Protease Inhibitor: The Case of Streptomyces Subtilisin Inhibitor (Ssi)
Year: 1985
History
DepositionMar 1, 1996Processing site: BNL
SupersessionAug 17, 1996ID: 2SSI
Revision 1.0Aug 17, 1996Provider: repository / Type: Initial release
Revision 1.1Mar 25, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jun 5, 2024Group: Data collection / Database references / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site
Revision 1.4Nov 20, 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
A: STREPTOMYCES SUBTILISIN INHIBITOR


Theoretical massNumber of molelcules
Total (without water)11,4951
Polymers11,4951
Non-polymers00
Water55831
1
A: STREPTOMYCES SUBTILISIN INHIBITOR

A: STREPTOMYCES SUBTILISIN INHIBITOR


Theoretical massNumber of molelcules
Total (without water)22,9902
Polymers22,9902
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_556y,x,-z+11
Unit cell
Length a, b, c (Å)40.740, 40.740, 115.280
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

#1: Protein STREPTOMYCES SUBTILISIN INHIBITOR / SSI


Mass: 11494.929 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Streptomyces albogriseolus (bacteria) / Strain: S-3253 / References: UniProt: P01006
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 31 / 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 / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.4 Å3/Da / Density % sol: 49 %
Crystal growpH: 7 / Details: pH 7.0

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH2R / Wavelength: 1.5418
DetectorType: RIGAKU / Detector: IMAGE PLATE / Date: Feb 26, 1993 / Details: SUPPER DOUBLE FOCUSING
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.03→38.3 Å / Num. obs: 4866 / % possible obs: 63.7 % / Observed criterion σ(I): 1 / Redundancy: 2.6 % / Rmerge(I) obs: 0.048
Reflection shellResolution: 2.3→2.34 Å / % possible all: 48.8

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Processing

Software
NameVersionClassification
PROCESSdata collection
PROCESSdata reduction
X-PLOR3.1model building
X-PLOR3.1refinement
PROCESSdata scaling
X-PLOR3.1phasing
RefinementResolution: 2.3→6 Å / σ(F): 2
RfactorNum. reflection% reflection
Rwork0.185 --
obs0.185 3756 75.1 %
Displacement parametersBiso mean: 31.8 Å2
Refine analyzeLuzzati coordinate error obs: 0.15 Å
Refinement stepCycle: LAST / Resolution: 2.3→6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms722 0 0 31 753
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.011
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_deg1.595
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d27.51
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.423
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

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