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- PDB-2st1: THE THREE-DIMENSIONAL STRUCTURE OF BACILLUS AMYLOLIQUEFACIENS SUB... -

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Basic information

Entry
Database: PDB / ID: 2st1
TitleTHE THREE-DIMENSIONAL STRUCTURE OF BACILLUS AMYLOLIQUEFACIENS SUBTILISIN AT 1.8 ANGSTROMS AND AN ANALYSIS OF THE STRUCTURAL CONSEQUENCES OF PEROXIDE INACTIVATION
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: 1.8 Å
AuthorsBott, R.
Citation
Journal: J.Biol.Chem. / Year: 1988
Title: The three-dimensional structure of Bacillus amyloliquefaciens subtilisin at 1.8 A and an analysis of the structural consequences of peroxide inactivation.
Authors: Bott, R. / Ultsch, M. / Kossiakoff, A. / Graycar, T. / Katz, B. / Power, S.
#1: Journal: Nucleic Acids Res. / Year: 1983
Title: Cloning, Sequencing and Secretion of Bacillus Amyloliquefaciens Subtilisin in Bacillus Subtilis
Authors: Wells, J.A. / Ferrari, E. / Henner, D.J. / Estell, D.A. / Chen, E.Y.
History
DepositionMay 11, 1990Processing site: BNL
Revision 1.0Jul 15, 1991Provider: repository / Type: Initial release
Revision 1.1Mar 25, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 21, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / 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_database_status.process_site / _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
A: SUBTILISIN BPN'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,7294
Polymers27,5531
Non-polymers1763
Water2,774154
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)39.250, 72.860, 75.200
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: 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: 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.: 154 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 1.95 Å3/Da / Density % sol: 36.93 %
Crystal grow
*PLUS
pH: 6 / Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
13-5 mg/mlprotein1drop
227 %sat1drop(NH4)2SO4
30.5 Msodium acetate1drop
410 mM1dropCaCl2
640 %sat1reservoir(NH4)2SO4
5phenylmethylsulfonyl fluoride1drop

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Data collection

Reflection
*PLUS
Highest resolution: 1.8 Å / Num. obs: 15461 / Num. measured all: 15461 / Rmerge(I) obs: 0.04

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Processing

SoftwareName: PROLSQ / Classification: refinement
RefinementResolution: 1.8→10 Å / Rfactor obs: 0.144
Refinement stepCycle: LAST / Resolution: 1.8→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1938 0 7 154 2099
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_bond_d0.015
X-RAY DIFFRACTIONp_angle_deg2.5
Refinement
*PLUS
Num. reflection obs: 15433 / Highest resolution: 1.8 Å / Lowest resolution: 10 Å / Rfactor obs: 0.144
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_angle_d
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.02

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