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- PDB-1s02: EFFECTS OF ENGINEERED SALT BRIDGES ON THE STABILITY OF SUBTILISIN BPN' -

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Basic information

Entry
Database: PDB / ID: 1s02
TitleEFFECTS OF ENGINEERED SALT BRIDGES ON THE STABILITY OF SUBTILISIN BPN'
ComponentsSUBTILISIN BPN'
KeywordsHYDROLASE (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
Biological speciesBacillus amyloliquefaciens (bacteria)
MethodX-RAY DIFFRACTION / Resolution: 1.9 Å
AuthorsErwin, C.R. / Barnett, B.L. / Oliver, J.D. / Sullivan, J.F.
CitationJournal: Protein Eng. / Year: 1990
Title: Effects of engineered salt bridges on the stability of subtilisin BPN'.
Authors: Erwin, C.R. / Barnett, B.L. / Oliver, J.D. / Sullivan, J.F.
History
DepositionFeb 20, 1991Processing site: BNL
Revision 1.0Jan 15, 1992Provider: 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 1.4Feb 14, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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

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Assembly

Deposited unit
A: SUBTILISIN BPN'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,7314
Polymers27,5541
Non-polymers1763
Water2,126118
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)39.300, 72.900, 75.400
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Atom site foot note1: RESIDUE 168 IS A CIS PROLINE.

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Components

#1: Protein SUBTILISIN BPN'


Mass: 27554.494 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: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 118 / Source method: isolated from a natural source / Formula: H2O
Nonpolymer detailsTHE SULFATE ION HAS AN INTRAMOLECULAR INTERACTION WITH ND1 HIS 238 AND HAS INTERMOLECULAR ...THE SULFATE ION HAS AN INTRAMOLECULAR INTERACTION WITH ND1 HIS 238 AND HAS INTERMOLECULAR INTERACTIONS WITH BACKBONE N TYR 104 AND N SER 105.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 1.96 Å3/Da / Density % sol: 37.21 %
Crystal grow
*PLUS
pH: 7 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
17 mg/mlPMSF-inhibited enzyme1drop
220 mMMES1drop
335-40 %satammonium sulfate1reservoir
40.5 %PEG80001reservoir
51 %beta-octylglucoside1reservoir
62 %MPD1reservoir
750 mMMES1reservoir

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Data collection

Reflection
*PLUS
Highest resolution: 1.8 Å / Num. obs: 9999 / % possible obs: 56.3 % / Num. measured all: 59579 / Rmerge(I) obs: 0.085

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Processing

SoftwareName: PROLSQ / Classification: refinement
RefinementRfactor obs: 0.169 / Highest resolution: 1.9 Å
Refinement stepCycle: LAST / Highest resolution: 1.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1938 0 7 118 2063
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.020.03
X-RAY DIFFRACTIONp_angle_d0.0310.04
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.0350.05
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it0.6121
X-RAY DIFFRACTIONp_mcangle_it0.9691.5
X-RAY DIFFRACTIONp_scbond_it0.7631
X-RAY DIFFRACTIONp_scangle_it1.2131.5
X-RAY DIFFRACTIONp_plane_restr0.0090.02
X-RAY DIFFRACTIONp_chiral_restr0.1240.15
X-RAY DIFFRACTIONp_singtor_nbd0.1750.5
X-RAY DIFFRACTIONp_multtor_nbd0.1880.5
X-RAY DIFFRACTIONp_xhyhbond_nbd0.2280.5
X-RAY DIFFRACTIONp_xyhbond_nbd
X-RAY DIFFRACTIONp_planar_tor1.53
X-RAY DIFFRACTIONp_staggered_tor14.615
X-RAY DIFFRACTIONp_orthonormal_tor39.120
X-RAY DIFFRACTIONp_transverse_tor
X-RAY DIFFRACTIONp_special_tor
Refinement
*PLUS
Highest resolution: 1.9 Å / Rfactor obs: 0.169
Solvent computation
*PLUS
Displacement parameters
*PLUS

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