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- PDB-1sua: SUBTILISIN BPN' -

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Basic information

Entry
Database: PDB / ID: 1sua
TitleSUBTILISIN BPN'
Components
  • SUBTILISIN BPN'
  • TETRAPEPTIDE ALA-LEU-ALA-LEU
KeywordsCOMPLEX (HYDROLASE/PEPTIDE) / COMPLEX (HYDROLASE-PEPTIDE) / HYDROLASE / SERINE PROTEINASE / COMPLEX (HYDROLASE-PEPTIDE) complex
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 / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsAlmog, O. / Gilliland, G.L.
CitationJournal: Proteins / Year: 1998
Title: Crystal structure of calcium-independent subtilisin BPN' with restored thermal stability folded without the prodomain.
Authors: Almog, O. / Gallagher, T. / Tordova, M. / Hoskins, J. / Bryan, P. / Gilliland, G.L.
History
DepositionJan 14, 1997Processing site: BNL
Revision 1.0Jan 14, 1998Provider: 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 / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.4Aug 9, 2023Group: Refinement description / Category: pdbx_initial_refinement_model
Revision 1.5May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: SUBTILISIN BPN'
C: TETRAPEPTIDE ALA-LEU-ALA-LEU


Theoretical massNumber of molelcules
Total (without water)27,0092
Polymers27,0092
Non-polymers00
Water2,504139
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area770 Å2
ΔGint-5 kcal/mol
Surface area9610 Å2
MethodPISA
Unit cell
Length a, b, c (Å)53.530, 60.330, 83.370
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein SUBTILISIN BPN'


Mass: 26622.480 Da / Num. of mol.: 1
Mutation: DEL(75-83), K43N, M50F, G73A, Q206V, Y217K, N218S, S221A, Q271E
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus amyloliquefaciens (bacteria) / Cell line: BL21 / Cellular location: EXTRACELLULAR / Plasmid: BL21 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) / References: UniProt: P00782, subtilisin
#2: Protein/peptide TETRAPEPTIDE ALA-LEU-ALA-LEU


Mass: 386.486 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 139 / Source method: isolated from a natural source / Formula: H2O
Compound detailsGLN 275 IS THE LAST RESIDUE BEFORE THE TETRA PEPTIDE ALAL. ALAL IS IN THE ACTIVE SITE.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.3 Å3/Da / Density % sol: 47 %
Crystal growpH: 7.5 / Details: 1.25M LI2SO4 0.1M HEPES/HCL PH7.5
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
16 mg/mlprotein1drop
20.055 MHEPES/HCl1drop
30.625 M1dropLi2SO4
40.1 MHEPES/HCl1reservoir
51.25 M1reservoirLi2SO4

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH2R / Wavelength: 1.5418
DetectorType: SIEMENS / Detector: AREA DETECTOR / Date: Jul 1, 1994
RadiationMonochromator: NI/FILTER / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionHighest resolution: 2.1 Å / Num. obs: 13358 / % possible obs: 82 % / Redundancy: 3 % / Rsym value: 0.123 / Net I/σ(I): 6
Reflection shellResolution: 2.1→2.19 Å / Redundancy: 0.5 % / Mean I/σ(I) obs: 1 / Rsym value: 0.37 / % possible all: 34
Reflection
*PLUS
Observed criterion σ(I): 1 / Num. measured all: 39158 / Rmerge(I) obs: 0.12
Reflection shell
*PLUS
Lowest resolution: 2.2 Å / % possible obs: 91 % / Rmerge(I) obs: 0.37

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Processing

Software
NameClassification
AMoREphasing
PROLSQrefinement
XENGENdata reduction
XENGENdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1SUC

1suc


Resolution: 2.1→8 Å / σ(F): 2
RfactorNum. reflection% reflection
Rwork0.18 --
obs-13558 82 %
Displacement parametersBiso mean: 10.36 Å2
Refinement stepCycle: LAST / Resolution: 2.1→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1852 0 126 138 2116
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.020.018
X-RAY DIFFRACTIONp_angle_d0.0320.02
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.0390.04
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it1.0151
X-RAY DIFFRACTIONp_mcangle_it1.5871.5
X-RAY DIFFRACTIONp_scbond_it1.2031
X-RAY DIFFRACTIONp_scangle_it1.8361.5
X-RAY DIFFRACTIONp_plane_restr0.020.015
X-RAY DIFFRACTIONp_chiral_restr0.420.25
X-RAY DIFFRACTIONp_singtor_nbd
X-RAY DIFFRACTIONp_multtor_nbd
X-RAY DIFFRACTIONp_xhyhbond_nbd
X-RAY DIFFRACTIONp_xyhbond_nbd
X-RAY DIFFRACTIONp_planar_tor3.63
X-RAY DIFFRACTIONp_staggered_tor20.715
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor
X-RAY DIFFRACTIONp_special_tor
Software
*PLUS
Name: PROLSQ / Classification: refinement
Refinement
*PLUS
Rfactor obs: 0.18
Solvent computation
*PLUS
Displacement parameters
*PLUS

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