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- PDB-1s01: LARGE INCREASES IN GENERAL STABILITY FOR SUBTILISIN BPN(PRIME) TH... -

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Entry
Database: PDB / ID: 1s01
TitleLARGE INCREASES IN GENERAL STABILITY FOR SUBTILISIN BPN(PRIME) THROUGH INCREMENTAL CHANGES IN THE FREE ENERGY OF UNFOLDING
ComponentsSubtilisin BPN'
KeywordsHYDROLASE / HYDROLASE (SERINE PROTEINASE)
Function / homology
Function and homology information


subtilisin / sporulation resulting in formation of a cellular spore / fibrinolysis / serine-type endopeptidase activity / proteolysis / extracellular region / metal ion binding
Similarity search - Function
: / 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 ...: / 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 / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ISOPROPYL ALCOHOL / Subtilisin BPN'
Similarity search - Component
Biological speciesBacillus amyloliquefaciens (bacteria)
MethodX-RAY DIFFRACTION / Resolution: 1.7 Å
AuthorsWhitlow, M. / Howard, A.J. / Wood, J.F.
Citation
Journal: Biochemistry / Year: 1989
Title: Large increases in general stability for subtilisin BPN' through incremental changes in the free energy of unfolding.
Authors: Pantoliano, M.W. / Whitlow, M. / Wood, J.F. / Dodd, S.W. / Hardman, K.D. / Rollence, M.L. / Bryan, P.N.
#1: Journal: J.Am.Chem.Soc. / Year: 1990
Title: Enzymes in Organic Synthesis. Use of Subtilisin and a Highly Stable Mutant Derived from Multiple Site-Specific Mutations
Authors: Wong, C.-H. / Chen, S.-T. / Hennen, W.J. / Bibbs, J.A. / Wang, Y.-F. / Liu, J.L.-C. / Pantoliano, M.W. / Whitlow, M. / Bryan, P.N.
#2: Journal: Biochemistry / Year: 1988
Title: The Engineering of Binding Affinity at Metal Ion Binding Sites for the Stabilization of Proteins. Subtilisin as a Test Case
Authors: Pantoliano, M.W. / Whitlow, M. / Wood, J.F. / Rollence, M.L. / Finzel, B.C. / Gilliland, G.L. / Poulos, T.L. / Bryan, P.N.
#3: Journal: Crit.Rev.Biotechnol. / Year: 1988
Title: Engineering Thermostability in Subtilisin Bpn(Prime) by in Vitro Mutagenesis
Authors: Rollence, M.L. / Filpula, D. / Pantoliano, M.W. / Bryan, P.N.
#4: Journal: Proteins / Year: 1986
Title: Proteases of Enhanced Stability. Characterization of a Thermostable Variant of Subtilisin
Authors: Bryan, P.N. / Rollence, M.L. / Pantoiano, M.W. / Wood, J. / Finzel, B.C. / Gilliland, G.L. / Howard, A.J. / Poulos, T.L.
#5: Journal: Biochem.Biophys.Res.Commun. / Year: 1971
Title: Atomic Coordinates for Subtilisin Bpn(or Novo)
Authors: Alden, R.A. / Birktoft, J.J. / Kraut, J. / Robertus, J.D. / Wright, C.S.
History
DepositionAug 21, 1989Processing site: BNL
Revision 1.0Oct 15, 1990Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 2.0Feb 14, 2018Group: Advisory / Atomic model ...Advisory / Atomic model / Database references / Derived calculations / Non-polymer description / Other / Polymer sequence / Refinement description / Source and taxonomy / Structure summary
Category: atom_site / entity ...atom_site / entity / entity_name_com / entity_poly / entity_poly_seq / entity_src_gen / pdbx_database_status / pdbx_entry_details / pdbx_struct_assembly_gen / pdbx_struct_conn_angle / pdbx_unobs_or_zero_occ_atoms / pdbx_validate_close_contact / refine_hist / refine_ls_restr / struct_conn / struct_keywords / struct_ref / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.group_PDB / _atom_site.label_alt_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.label_seq_id / _atom_site.occupancy / _atom_site.type_symbol / _chem_comp.formula / _chem_comp.id / _chem_comp.name / _chem_comp.pdbx_synonyms / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_ec / _entity.pdbx_number_of_molecules / _entity_poly.nstd_monomer / _entity_poly.pdbx_seq_one_letter_code / _entity_poly_seq.mon_id / _entity_src_gen.gene_src_common_name / _entity_src_gen.pdbx_beg_seq_num / _entity_src_gen.pdbx_end_seq_num / _entity_src_gen.pdbx_gene_src_gene / _entity_src_gen.pdbx_host_org_ncbi_taxonomy_id / _entity_src_gen.pdbx_host_org_scientific_name / _entity_src_gen.pdbx_seq_type / _pdbx_database_status.process_site / _pdbx_entry_details.compound_details / _pdbx_struct_assembly_gen.asym_id_list / _refine_hist.number_atoms_solvent / _refine_hist.number_atoms_total / _refine_hist.pdbx_number_atoms_ligand / _refine_hist.pdbx_number_atoms_protein / _refine_ls_restr.dev_ideal / _refine_ls_restr.dev_ideal_target / _struct_keywords.pdbx_keywords / _struct_keywords.text / _struct_ref.pdbx_seq_one_letter_code / _struct_ref_seq_dif.details / _struct_ref_seq_dif.mon_id
Revision 2.1Mar 26, 2025Group: 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 / struct_conn / struct_conn_type / struct_sheet
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_entry_details.has_protein_modification / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_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_conn_type.id / _struct_sheet.number_strands

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Subtilisin BPN'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,7044
Polymers27,5441
Non-polymers1603
Water3,873215
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)41.640, 79.450, 37.260
Angle α, β, γ (deg.)90.00, 114.53, 90.00
Int Tables number4
Space group name H-MP1211
Atom site foot note1: RESIDUE PRO 168 IS A CIS PROLINE.
2: RESIDUE 206 APPEARS TO BE CYSTEINE PERSULFIDE. ELECTRON DENSITY FOUND BEYOND THE PERSULFIDE HAS BEEN MODELLED AS A PARTIALLY OCCUPIED CARBON ATOM. THE ADDITIONAL SULFUR AND CARBON ARE PRESENTED ON ...2: RESIDUE 206 APPEARS TO BE CYSTEINE PERSULFIDE. ELECTRON DENSITY FOUND BEYOND THE PERSULFIDE HAS BEEN MODELLED AS A PARTIALLY OCCUPIED CARBON ATOM. THE ADDITIONAL SULFUR AND CARBON ARE PRESENTED ON *HETATM* RECORDS AS HET GROUP * CS*. THE EXACT CHEMICAL IDENTITY OF THIS GROUP IS, HOWEVER, UNKNOWN. SEE THE PAPER CITED ON THE *JRNL* RECORDS ABOVE.

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Components

#1: Protein Subtilisin BPN' / Alkaline protease / Subtilisin DFE / Subtilisin Novo


Mass: 27543.602 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus amyloliquefaciens (bacteria) / Gene: apr / Production host: Bacillus amyloliquefaciens (bacteria) / References: UniProt: P00782, subtilisin
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-IPA / ISOPROPYL ALCOHOL / 2-PROPANOL


Mass: 60.095 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 215 / Source method: isolated from a natural source / Formula: H2O
Compound detailsRESIDUE 206 APPEARS TO BE CYSTEINE PERSULFIDE. ELECTRON DENSITY FOUND BEYOND THE PERSULFIDE HAS ...RESIDUE 206 APPEARS TO BE CYSTEINE PERSULFIDE. ELECTRON DENSITY FOUND BEYOND THE PERSULFIDE HAS BEEN MODELLED AS A PARTIALLY OCCUPIED CARBON AND SULFUR ATOM AND ANNOTATED AS S-METHYL-THIO-CYSTEINE (SCH). THE EXACT CHEMICAL IDENTITY OF THIS GROUP IS, HOWEVER, UNKNOWN.
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: 2.04 Å3/Da / Density % sol: 39.65 %
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
Conc.: 55 % / Common name: acetone

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Processing

SoftwareName: PROFFT / Classification: refinement
RefinementResolution: 1.7→10 Å /
RfactorNum. reflection
obs0.152 17421
Refinement stepCycle: LAST / Resolution: 1.7→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1934 0 11 215 2160
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0170.03
X-RAY DIFFRACTIONp_angle_d0.0270.04
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.0340.05
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it0.5621
X-RAY DIFFRACTIONp_mcangle_it0.9152
X-RAY DIFFRACTIONp_scbond_it1.2131.5
X-RAY DIFFRACTIONp_scangle_it1.8273
X-RAY DIFFRACTIONp_plane_restr0.0180.03
X-RAY DIFFRACTIONp_chiral_restr0.1890.3
X-RAY DIFFRACTIONp_singtor_nbd0.1570.2
X-RAY DIFFRACTIONp_multtor_nbd0.1330.2
X-RAY DIFFRACTIONp_xhyhbond_nbd0.1540.2
X-RAY DIFFRACTIONp_xyhbond_nbd
X-RAY DIFFRACTIONp_planar_tor3.17.5
X-RAY DIFFRACTIONp_staggered_tor11.610
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor
X-RAY DIFFRACTIONp_special_tor
Refinement
*PLUS
Highest resolution: 1.7 Å / Lowest resolution: 10 Å / Num. reflection obs: 17421 / Rfactor obs: 0.152
Solvent computation
*PLUS
Displacement parameters
*PLUS

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