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- PDB-1yja: SUBTILISIN BPN' 8397+1 (E.C. 3.4.21.14) (MUTANT WITH MET 50 REPLA... -

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Basic information

Entry
Database: PDB / ID: 1yja
TitleSUBTILISIN BPN' 8397+1 (E.C. 3.4.21.14) (MUTANT WITH MET 50 REPLACED BY PHE, ASN 76 REPLACED BY ASP, GLY 169 REPLACED BY ALA, GLN 206 REPLACED BY CYS, ASN 218 REPLACED BY SER AND LYS 256 REPLACED BY TYR) (M50F, N76D, G169A, Q206C, N218S, AND K256Y) IN 20% DIMETHYLFORMAMIDE
ComponentsSUBTILISIN 8397+1
KeywordsHYDROLASE (SERINE PROTEASE) / HYDROLASE / SPORULATION / SERINE PROTEASE / ZYMOGEN
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/S53 domain / : / Peptidase S8 propeptide/proteinase inhibitor I9 superfamily / 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/S53 domain / : / Peptidase S8 propeptide/proteinase inhibitor I9 superfamily / 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 / Peptidase S8/S53 domain / Subtilase family / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesBacillus amyloliquefaciens (bacteria)
MethodX-RAY DIFFRACTION / Resolution: 1.8 Å
AuthorsKidd, R.D. / Farber, G.K.
CitationJournal: Protein Sci. / Year: 1999
Title: Breaking the low barrier hydrogen bond in a serine protease.
Authors: Kidd, R.D. / Sears, P. / Huang, D.H. / Witte, K. / Wong, C.H. / Farber, G.K.
History
DepositionJan 16, 1996Processing site: BNL
Revision 1.0Jul 11, 1996Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 3, 2021Group: Database references / Derived calculations / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_struct_conn_angle / struct_conn / struct_conn_type / 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_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_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_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.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_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_conn_type.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
A: SUBTILISIN 8397+1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,6623
Polymers27,5811
Non-polymers802
Water1,17165
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)41.570, 79.670, 37.220
Angle α, β, γ (deg.)90.00, 114.13, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein SUBTILISIN 8397+1 / SUBTILISIN


Mass: 27581.498 Da / Num. of mol.: 1 / Mutation: M50F, N76D, G169A, Q206C, N218S, K256Y
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus amyloliquefaciens (bacteria) / Gene: 8397+1 / Plasmid: PGX5097 / Gene (production host): 8397+1 / Production host: Bacillus subtilis (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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 65 / 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: 2.04 Å3/Da / Density % sol: 39.9 %
Crystal
*PLUS
Crystal grow
*PLUS
pH: 5.6 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
15-10 mg/mlprotein1drop
25 mMsodium cacodylate1drop
38.5 %(w/v)PEG34001drop
48.5 %(v/v)2-propanol1drop
550 mMsodium citrate1drop
617 %(w/v)PEG34001reservoir
717 %(v/v)2-propanol1reservoir
8100 mMsodium citrate1reservoir

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Data collection

Diffraction sourceWavelength: 1.5418
DetectorType: RIGAKU AFC-6R / Detector: DIFFRACTOMETER / Date: Sep 20, 1994
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.8→17 Å / Num. obs: 21228 / % possible obs: 100 % / Observed criterion σ(I): 0 / Redundancy: 1 % / Rmerge(I) obs: 0.062
Reflection
*PLUS
Num. obs: 15425 / Num. measured all: 21228

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Processing

Software
NameVersionClassification
X-PLOR3.1model building
X-PLOR3.1refinement
TEXSANdata reduction
X-PLOR3.1phasing
RefinementResolution: 1.8→17 Å / σ(F): 2
RfactorNum. reflection% reflection
Rwork0.215 --
obs0.215 15245 71.8 %
Displacement parametersBiso mean: 14.7 Å2
Refinement stepCycle: LAST / Resolution: 1.8→17 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1941 0 2 65 2008
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.01
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.664
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Software
*PLUS
Name: X-PLOR / Version: 3.1 / Classification: refinement
Refinement
*PLUS
Num. reflection obs: 15425
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 14.74 Å2
Refine LS restraints
*PLUS
Type: x_angle_deg / Dev ideal: 1.663

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