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- PDB-1spb: SUBTILISIN BPN' PROSEGMENT (77 RESIDUES) COMPLEXED WITH A MUTANT ... -

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Entry
Database: PDB / ID: 1spb
TitleSUBTILISIN BPN' PROSEGMENT (77 RESIDUES) COMPLEXED WITH A MUTANT SUBTILISIN BPN' (266 RESIDUES). CRYSTAL PH 4.6. CRYSTALLIZATION TEMPERATURE 20 C DIFFRACTION TEMPERATURE-160 C
Components
  • SUBTILISIN BPN'
  • SUBTILISIN BPN' PROSEGMENT
KeywordsCOMPLEX (SERINE PROTEINASE/PROSEGMENT) / PROPEPTIDE / FOLDASE / FOLDING CATALYST / ACTIVATION DOMAIN / COMPLEX (SERINE PROTEINASE-PROSEGMENT) 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
Peptidase S8 propeptide/proteinase inhibitor I9 / Subtilisin Carlsberg-like catalytic domain / Peptidase S8/S53 domain / Peptidase S8 propeptide/proteinase inhibitor I9 / Peptidase inhibitor I9 / 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 ...Peptidase S8 propeptide/proteinase inhibitor I9 / Subtilisin Carlsberg-like catalytic domain / Peptidase S8/S53 domain / Peptidase S8 propeptide/proteinase inhibitor I9 / Peptidase inhibitor I9 / 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 / Serine proteases, subtilase domain profile. / Peptidase S8, subtilisin-related / Peptidase S8/S53 domain superfamily / Subtilase family / Peptidase S8/S53 domain / Alpha-Beta Plaits / Rossmann fold / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesBacillus amyloliquefaciens (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2 Å
AuthorsGallagher, D.T. / Gilliland, G.L. / Wang, L. / Bryan, P.N.
CitationJournal: Structure / Year: 1995
Title: The prosegment-subtilisin BPN' complex: crystal structure of a specific 'foldase'.
Authors: Gallagher, T. / Gilliland, G. / Wang, L. / Bryan, P.
History
DepositionJun 21, 1995Processing site: BNL
Revision 1.0Oct 15, 1995Provider: 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 / 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_database_status.process_site / _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
Revision 1.4Feb 14, 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
P: SUBTILISIN BPN' PROSEGMENT
S: SUBTILISIN BPN'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,1673
Polymers35,1442
Non-polymers231
Water4,504250
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2360 Å2
ΔGint-24 kcal/mol
Surface area12980 Å2
MethodPISA
Unit cell
Length a, b, c (Å)74.100, 77.850, 57.650
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Atom site foot note1: CIS PROLINE - PRO S 168
Components on special symmetry positions
IDModelComponents
11S-387-

HOH

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Components

#1: Protein SUBTILISIN BPN' PROSEGMENT / SUBTILISIN BPN' PROPEPTIDE


Mass: 8523.699 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus amyloliquefaciens (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: P00782
#2: Protein SUBTILISIN BPN'


Mass: 26620.510 Da / Num. of mol.: 1
Mutation: D32N, K43N, M50F, A73L, DEL(75-83), Q206V, Y217K, N218S, S221A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus amyloliquefaciens (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: P00782, subtilisin
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 250 / 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: 2.36 Å3/Da / Density % sol: 47.98 %
Crystal growpH: 4.6 / Details: pH 4.6
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
12.0 Mammonium sulphate1reservoir
20.1 Msodium acetate1reservoir

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Data collection

DiffractionMean temperature: 113 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X8C / Wavelength: 1
DetectorDetector: CCD / Date: Jun 21, 1994
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionNum. obs: 17956 / % possible obs: 84 % / Redundancy: 4.25 % / Rmerge(I) obs: 0.08
Reflection
*PLUS
Highest resolution: 2 Å / Rmerge(I) obs: 0.08

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Processing

Software
NameClassification
PROLSQrefinement
XENGENdata reduction
RefinementResolution: 2→8 Å / σ(F): 2 /
RfactorNum. reflection
obs0.204 17179
Displacement parametersBiso mean: 11.3 Å2
Refinement stepCycle: LAST / Resolution: 2→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2417 0 1 250 2668
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0220.021
X-RAY DIFFRACTIONp_angle_d0.0460.03
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.0480.04
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it0.9591
X-RAY DIFFRACTIONp_mcangle_it1.481.5
X-RAY DIFFRACTIONp_scbond_it1.051
X-RAY DIFFRACTIONp_scangle_it1.5251.5
X-RAY DIFFRACTIONp_plane_restr0.0350.03
X-RAY DIFFRACTIONp_chiral_restr0.430.25
X-RAY DIFFRACTIONp_singtor_nbd0.3470.2
X-RAY DIFFRACTIONp_multtor_nbd0.1790.2
X-RAY DIFFRACTIONp_xhyhbond_nbd0.2150.2
X-RAY DIFFRACTIONp_xyhbond_nbd
X-RAY DIFFRACTIONp_planar_tor5.53
X-RAY DIFFRACTIONp_staggered_tor21.615
X-RAY DIFFRACTIONp_orthonormal_tor33.620
X-RAY DIFFRACTIONp_transverse_tor
X-RAY DIFFRACTIONp_special_tor
Software
*PLUS
Name: PROLSQ / Classification: refinement
Refinement
*PLUS
Rfactor obs: 0.26
Solvent computation
*PLUS
Displacement parameters
*PLUS

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