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- PDB-5sic: MOLECULAR RECOGNITION AT THE ACTIVE SITE OF SUBTILISIN BPN': CRYS... -

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Basic information

Entry
Database: PDB / ID: 5sic
TitleMOLECULAR RECOGNITION AT THE ACTIVE SITE OF SUBTILISIN BPN': CRYSTALLOGRAPHIC STUDIES USING GENETICALLY ENGINEERED PROTEINACEOUS INHIBITOR SSI (STREPTOMYCES SUBTILISIN INHIBITOR)
Components
  • SUBTILISIN BPN'
  • SUBTILISIN INHIBITOR (SSI)
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: 2.2 Å
AuthorsMitsui, Y. / Takeuchi, Y. / Nakamura, K.T.
Citation
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.
#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.
#2: Journal: J.Mol.Biol. / Year: 1984
Title: Crystal Structure at 2.6 Angstroms Resolution of the Complex of Subtilisin/Bpn' with Streptomyces Subtilisin Inhibitor
Authors: Hirono, S. / Akagawa, H. / 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.
#4: Journal: J.Mol.Biol. / Year: 1979
Title: Crystal Structures 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.
History
DepositionNov 18, 1991Processing site: BNL
Revision 1.0Jan 31, 1994Provider: 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 13, 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_ref_seq_dif / 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_ref_seq_dif.details / _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: SUBTILISIN INHIBITOR (SSI)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,4974
Polymers38,4172
Non-polymers802
Water5,188288
1
E: SUBTILISIN BPN'
I: SUBTILISIN INHIBITOR (SSI)
hetero molecules

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


Theoretical massNumber of molelcules
Total (without water)76,9948
Polymers76,8334
Non-polymers1604
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
Unit cell
Length a, b, c (Å)77.200, 185.900, 69.500
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222
Atom site foot note1: CIS PROLINE - PRO E 168 / 2: CIS PROLINE - PRO I 37
DetailsSSI IS A DIMERIC MOLECULE(I2) CONSISTING OF TWO IDENTICAL SUBUNITS. IT BINDS TWO SUBTILISIN BPN' MOLECULES (2E) TO FORM A DIMERIC COMPLEX E2I2. HOWEVER, THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT CORRESPONDS TO HALF THE COMPLEX MOLECULE (EI). IN THIS ENTRY, COORDINATES FOR ALL NON-HYDROGEN ATOMS ARE PROVIDED FOR ONE CHAIN OF SUBTILISIN USING CHAIN IDENTIFIER *E* AND FOR ONE CHAIN OF SSI USING CHAIN IDENTIFIER *I*. COORDINATES FOR THE OTHER EI COMPLEX CAN BE GENERATED BY TRANSFORMING (X,Y,Z) TO (-X,-Y,Z).

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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, subtilisin
#2: Protein SUBTILISIN INHIBITOR (SSI)


Mass: 10864.174 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.: 288 / 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: 62.08 %
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: 19948 / Num. measured all: 62627 / Rmerge(I) obs: 0.0857

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Processing

SoftwareName: PROLSQ / Classification: refinement
RefinementRfactor obs: 0.176 / Highest resolution: 2.2 Å
Refinement stepCycle: LAST / Highest resolution: 2.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2699 0 2 288 2989
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_bond_d0.017
X-RAY DIFFRACTIONp_angle_d
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_restr
X-RAY DIFFRACTIONp_chiral_restr
X-RAY DIFFRACTIONp_singtor_nbd
X-RAY DIFFRACTIONp_multtor_nbd
X-RAY DIFFRACTIONp_xhyhbond_nbd
X-RAY DIFFRACTIONp_xyhbond_nbd
X-RAY DIFFRACTIONp_planar_tor
X-RAY DIFFRACTIONp_staggered_tor
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor
X-RAY DIFFRACTIONp_special_tor
Software
*PLUS
Name: PROLSQ / Classification: refinement
Refinement
*PLUS
Lowest resolution: 6 Å / Num. reflection obs: 15087 / Rfactor obs: 0.176
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_angle_d0.039
X-RAY DIFFRACTIONp_planar_d0.05

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