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- PDB-2sic: REFINED CRYSTAL STRUCTURE OF THE COMPLEX OF SUBTILISIN BPN' AND S... -

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Basic information

Entry
Database: PDB / ID: 2sic
TitleREFINED CRYSTAL STRUCTURE OF THE COMPLEX OF SUBTILISIN BPN' AND STREPTOMYCES SUBTILISIN INHIBITOR AT 1.8 ANGSTROMS RESOLUTION
Components
  • STREPTOMYCES SUBTILISIN INHIBITOR (SSI)
  • SUBTILISIN BPN'
KeywordsCOMPLEX (PROTEINASE/INHIBITOR) / COMPLEX (PROTEINASE-INHIBITOR) / COMPLEX (PROTEINASE-INHIBITOR) complex
Function / homology
Function and homology information


subtilisin / sporulation resulting in formation of a cellular spore / fibrinolysis / serine-type endopeptidase inhibitor activity / serine-type endopeptidase activity / proteolysis / extracellular region / metal ion binding
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 / : / Fervidolysin N-terminal prodomain ...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 / : / Fervidolysin N-terminal prodomain / Subtilisin Carlsberg-like catalytic domain / Peptidase S8 propeptide/proteinase inhibitor I9 superfamily / Peptidase S8/S53 domain / : / Peptidase S8, subtilisin, His-active site / Serine proteases, subtilase family, histidine active site. / Serine proteases, subtilase family, aspartic acid active site. / Peptidase S8, subtilisin, Asp-active site / Serine proteases, subtilase family, serine active site. / Peptidase S8, subtilisin, Ser-active site / Peptidase S8, subtilisin-related / Serine proteases, subtilase domain profile. / Peptidase S8/S53 domain superfamily / Subtilase family / Peptidase S8/S53 domain / Rossmann fold / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Subtilisin BPN' / Subtilisin inhibitor
Similarity search - Component
Biological speciesBacillus amyloliquefaciens (bacteria)
MethodX-RAY DIFFRACTION / Resolution: 1.8 Å
AuthorsMitsui, Y. / Takeuchi, Y. / Hirono, S. / Akagawa, H. / Nakamura, K.T.
Citation
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.
#1: Journal: J.Mol.Biol. / Year: 1984
Title: Crystal Structure at 2.6 Angstroms Resolution of the Complex of Subtilisin with Bpn' with Streptomyces Subtilisin Inhibitor
Authors: Hirono, S. / Akagawa, H. / Mitsui, Y. / Iitaka, Y.
#2: Journal: J.Mol.Biol. / Year: 1979
Title: Crystal Structure of the Complex of Subtilisin Bpn' with its Protein Inhibitor Streptomyces Subtilisin Inhibitor
Authors: Hirono, S. / Nakamura, K.T. / Iitaka, Y. / Mitsui, Y.
#3: 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.
History
DepositionApr 1, 1991Processing site: BNL
SupersessionApr 15, 1993ID: 1SIC
Revision 1.0Apr 15, 1993Provider: repository / Type: Initial release
Revision 1.1Mar 3, 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 1.4Nov 6, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
E: SUBTILISIN BPN'
I: STREPTOMYCES SUBTILISIN INHIBITOR (SSI)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,5734
Polymers38,4932
Non-polymers802
Water4,648258
1
E: SUBTILISIN BPN'
I: STREPTOMYCES SUBTILISIN INHIBITOR (SSI)
hetero molecules

E: SUBTILISIN BPN'
I: STREPTOMYCES SUBTILISIN INHIBITOR (SSI)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)77,1468
Polymers76,9864
Non-polymers1604
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
Buried area4880 Å2
ΔGint-37.2 kcal/mol
Surface area26730 Å2
MethodPISA
Unit cell
Length a, b, c (Å)77.230, 185.900, 69.510
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222
Atom site foot note1: RESIDUES PRO E 168 AND PRO I 37 ARE CIS PROLINES.

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Components

#1: Protein SUBTILISIN BPN'


Mass: 27552.525 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus amyloliquefaciens (bacteria) / References: UniProt: P00782, 3.4.21.14
#2: Protein STREPTOMYCES SUBTILISIN INHIBITOR (SSI)


Mass: 10940.334 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
References: UniProt: P01006
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 258 / 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: 3.24 Å3/Da / Density % sol: 62.02 %
Crystal grow
*PLUS
pH: 7.5 / Method: unknown
Details: used seeding, Hirono, S., (1979) J.Mol.Biol., 131, 855.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
1BPN1150mg
2SSI1117.5mg
30.05 MTris-HCl11

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Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
Reflection
*PLUS
Highest resolution: 1.8 Å / Num. obs: 28118 / Observed criterion σ(F): 2 / Num. measured all: 97766 / Rmerge(I) obs: 0.0472

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Processing

SoftwareName: PROLSQ / Classification: refinement
RefinementResolution: 1.8→6 Å /
RfactorNum. reflection
obs0.177 26760
Refinement stepCycle: LAST / Resolution: 1.8→6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2702 0 2 258 2962
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0140.017
X-RAY DIFFRACTIONp_angle_d0.0340.027
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.0430.037
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_restr0.0110.02
X-RAY DIFFRACTIONp_chiral_restr0.110.1
X-RAY DIFFRACTIONp_singtor_nbd
X-RAY DIFFRACTIONp_multtor_nbd
X-RAY DIFFRACTIONp_xhyhbond_nbd
X-RAY DIFFRACTIONp_xyhbond_nbd
X-RAY DIFFRACTIONp_planar_tor4.82.5
X-RAY DIFFRACTIONp_staggered_tor
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor
X-RAY DIFFRACTIONp_special_tor

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