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- PDB-1sbt: ATOMIC COORDINATES FOR SUBTILISIN BPN (OR NOVO) -

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Entry
Database: PDB / ID: 1sbt
TitleATOMIC COORDINATES FOR SUBTILISIN BPN (OR NOVO)
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: 2.5 Å
AuthorsAlden, R.A. / Birktoft, J.J. / Kraut, J. / Robertus, J.D. / Wright, C.S.
Citation
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.
#1: Journal: J.Biol.Chem. / Year: 1976
Title: Polypeptide Halomethyl Ketones Bind to Serine Proteases as Analogs of the Tetrahedral Intermediate,X-Ray Crystallographic Comparison of Lysine-and Phenylalanine-Polypeptide Chloromethyl Ketone-Inhibited Subtilisin
Authors: Poulos, T.L. / Alden, R.A. / Freer, S.T. / Birktoft, J.J. / Kraut, J.
#2: Journal: J.Biol.Chem. / Year: 1975
Title: X-Ray Crystallographic Study of Boronic Acid Adducts with Subtilisin Bpn(Novo),A Model for the Catalytic Transition State
Authors: Matthews, D.A. / Alden, R.A. / Birktoft, J.J. / Freer, S.T. / Kraut, J.
#3: Journal: Biochemistry / Year: 1972
Title: Subtilisin,A Stereochemical Mechanism Involving Transition-State Stabilization
Authors: Robertus, J.D. / Kraut, J. / Alden, R.A. / Birktoft, J.J.
#4: Journal: Biochemistry / Year: 1972
Title: An X-Ray Crystallographic Study of the Binding of Peptide Chloromethyl Ketone Inhibitors to Subtilisin Bpn
Authors: Robertus, J.D. / Alden, R.A. / Birktoft, J.J. / Kraut, J. / Powers, J.C. / Wilcox, P.E.
#5: Journal: Cold Spring Harbor Symp.Quant.Biol. / Year: 1972
Title: The Aromatic Substrate Binding Site in Subtilisin Bpnand its Resemblance to Chymotrypsin
Authors: Kraut, J. / Robertus, J.D. / Birktoft, J.J. / Alden, R.A. / Wilcox, P.E. / Powers, J.C.
#6: Journal: Biochem.Biophys.Res.Commun. / Year: 1971
Title: On the Identity of Subtilisins Bpnand Novo
Authors: Robertus, J.D. / Alden, R.A. / Kraut, J.
#7: Journal: Philos.Trans.R.Soc.London,Ser.B / Year: 1970
Title: A Hydrogen-Bond Network at the Active Site of Subtilisin Bpn
Authors: Alden, R.A. / Wright, C.S. / Kraut, J.
#8: Journal: Nature / Year: 1969
Title: Structure of Subtilisin Bpnat 2.5 Angstroms Resolution
Authors: Wright, C.S. / Alden, R.A. / Kraut, J.
#9: Journal: Atlas of Macromolecular Structure on Microfiche / Year: 1976
#10: Journal: Atlas of Protein Sequence and Structure (Data Section)
Year: 1972
History
DepositionAug 11, 1972Processing site: BNL
Revision 1.0Jan 6, 1977Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 2.0Sep 27, 2023Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Other
Category: atom_site / atom_sites ...atom_site / atom_sites / chem_comp_atom / chem_comp_bond / database_2 / database_PDB_matrix / pdbx_database_remark / pdbx_database_status / pdbx_validate_close_contact / pdbx_validate_symm_contact / struct_ref_seq_dif
Item: _atom_site.Cartn_x / _atom_site.Cartn_y ..._atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_sites.fract_transf_matrix[1][1] / _atom_sites.fract_transf_matrix[1][3] / _atom_sites.fract_transf_matrix[2][2] / _atom_sites.fract_transf_matrix[3][1] / _atom_sites.fract_transf_matrix[3][3] / _atom_sites.fract_transf_vector[1] / _atom_sites.fract_transf_vector[2] / _atom_sites.fract_transf_vector[3] / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _database_PDB_matrix.origx_vector[1] / _database_PDB_matrix.origx_vector[2] / _database_PDB_matrix.origx_vector[3] / _pdbx_database_status.process_site / _pdbx_validate_close_contact.dist / _struct_ref_seq_dif.details
Details: Coordinates and associated ncs operations (if present) transformed into standard crystal frame
Provider: repository / Type: Remediation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: SUBTILISIN BPN'


Theoretical massNumber of molelcules
Total (without water)27,5531
Polymers27,5531
Non-polymers00
Water30617
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)66.700, 54.400, 62.900
Angle α, β, γ (deg.)90.00, 91.90, 90.00
Int Tables number5
Space group name H-MC121
Atom site foot note1: THE FO-FC MAP INDICATES COORDINATE ERRORS OF MORE THAN 1 ANGSTROM.
2: THESE COORDINATES ARE THE OUTPUT OF A REFINEMENT BY DIAMOND'S MODEL-BUILDING PROGRAM.

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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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 17 / 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: 2.07 Å3/Da / Density % sol: 40.54 %
Crystal grow
*PLUS
Method: other / Details: Wright, C.S., (1969) Nature, 221, 235.

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Processing

RefinementHighest resolution: 2.5 Å
Details: THE FO-FC MAP INDICATES COORDINATE ERRORS OF MORE THAN 1 ANGSTROM. THESE COORDINATES ARE THE OUTPUT OF A REFINEMENT BY DIAMOND'S MODEL-BUILDING PROGRAM
Refinement stepCycle: LAST / Highest resolution: 2.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1938 0 0 17 1955

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