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- PDB-1sue: SUBTILISIN BPN' FROM BACILLUS AMYLOLIQUEFACIENS, MUTANT -

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Basic information

Entry
Database: PDB / ID: 1sue
TitleSUBTILISIN BPN' FROM BACILLUS AMYLOLIQUEFACIENS, MUTANT
ComponentsSUBTILISIN BPN'
KeywordsSERINE PROTEASE / HYDROLASE
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
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. ...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 / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
DIISOPROPYL PHOSPHONATE / Subtilisin BPN'
Similarity search - Component
Biological speciesBacillus amyloliquefaciens (bacteria)
MethodX-RAY DIFFRACTION / molecular replacement / Resolution: 1.8 Å
AuthorsGallagher, D.T. / Bryan, P. / Pan, Q. / Gilliland, G.L.
CitationJournal: J.Cryst.Growth / Year: 1998
Title: Mechanism of ionic strength dependence of crystal growth rates in a subtilisin variant.
Authors: Gallagher, D.T. / Pan, Q.W. / Gilliland, G.L.
History
DepositionFeb 17, 1998Processing site: BNL
Revision 1.0Oct 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 / Derived calculations
Category: database_2 / struct_conn ...database_2 / 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 / _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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Apr 3, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: SUBTILISIN BPN'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,8393
Polymers26,6501
Non-polymers1892
Water1,946108
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)45.590, 58.090, 86.580
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: 26649.570 Da / Num. of mol.: 1
Mutation: Q2K, S3C, P5S, K43N, M50F, A73L, Q206C, Y217K, N218S, DEL (75-83)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus amyloliquefaciens (bacteria) / Cellular location: SECRETEDSecretion / Plasmid: PUB110-BASED / Cellular location (production host): SECRETED / Production host: Bacillus amyloliquefaciens (bacteria) / References: UniProt: P00782, subtilisin
#2: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#3: Chemical ChemComp-DFP / DIISOPROPYL PHOSPHONATE


Mass: 166.155 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H15O3P
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 108 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 2

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Sample preparation

CrystalDensity Matthews: 2.24 Å3/Da / Density % sol: 44 %
Crystal growpH: 4.6
Details: 22% PEG 4K, 100 MM SODIUM ACETATE PH 4.6, 100 MM AMMONIUM SULFATE
Crystal grow
*PLUS
Temperature: 24 ℃ / pH: 7 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
18 mg/mlprotein1drop
210 mMHEPES1drop
320-24 %PEG40001reservoir
4100 mMsodium acetate1reservoir
50-500 mMsalt1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-D / Wavelength: 1.5418
DetectorType: SIEMENS / Detector: AREA DETECTOR / Date: Jun 1, 1997
RadiationMonochromator: GRAPHITE(002) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.8→16 Å / Num. obs: 19675 / % possible obs: 88 % / Observed criterion σ(I): 1 / Redundancy: 2 % / Rmerge(I) obs: 0.06 / Rsym value: 0.06 / Net I/σ(I): 5
Reflection shellResolution: 1.8→1.9 Å / Redundancy: 1.1 % / Rmerge(I) obs: 0.11 / Mean I/σ(I) obs: 2 / Rsym value: 0.11 / % possible all: 60
Reflection shell
*PLUS
% possible obs: 60 %

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Processing

Software
NameVersionClassification
XENGENdata collection
XENGENdata reduction
AMoREphasing
TNT5Erefinement
XENGENdata scaling
RefinementMethod to determine structure: molecular replacement
Starting model: REFINED SAME MUTANT IN OTHER CRYSTAL FORM

Resolution: 1.8→16 Å / Isotropic thermal model: TNT BCORREL V1.0 / σ(F): 0 / Stereochemistry target values: TNT PROTGEO
Details: CRYSTAL MORPHOLOGY VARIES DRAMATICALLY AS A FUNCTION OF IONIC STRENGTH (ADDED SALTS IN 0-500 MM RANGE). OMITTING RESIDUE NUMBERS 75-83 REFLECTS THE ENGINEERED DELETION AND PRESERVES WILD ...Details: CRYSTAL MORPHOLOGY VARIES DRAMATICALLY AS A FUNCTION OF IONIC STRENGTH (ADDED SALTS IN 0-500 MM RANGE). OMITTING RESIDUE NUMBERS 75-83 REFLECTS THE ENGINEERED DELETION AND PRESERVES WILD TYPE NUMBERING OF RESIDUES 84-275. THE ACTIVE SITE IS THE CATALYTIC TRIAD ASP 32, HIS 64, CYS 221 DESCRIBED IN THE SITE RECORD BELOW. SECONDARY STRUCTURE STRUCTURE ASSIGNMENT IS ACCORDING TO KABSCH AND SANDER (BIOPOLYMERS 22, 2577-2637, 1983). RESIDUE SER 221 IS COVALENTLY LINKED TO THE INHIBITOR DIISOPROPYL FLUOROPHOSPHATE (HET GROUP DFP). ONLY ONE OF THE TWO ISOPROPYL GROUPS IS VISIBLE AND INCLUDED IN THE MODEL. SEE HETATM RECORDS DFP, RESIDUE NUMBER 288. CONECT RECORDS SPECIFY BONDING. THE CALCIUM 'A' SITE HAS BEEN DELETED. RESIDUE NA 297 IS IN THE 'B' CATION-BINDING SITE, MONOVALENT SUBSITE. STABILIZING DISULFIDE 3-206 INTRODUCED BY MUTAGENESIS.
RfactorNum. reflection% reflection
Rwork0.17 --
all0.17 19675 -
obs0.17 19675 88 %
Solvent computationSolvent model: TNT / Bsol: 140 Å2 / ksol: 0.74 e/Å3
Refinement stepCycle: LAST / Resolution: 1.8→16 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1873 0 8 108 1989
Refine LS restraints
Refine-IDTypeDev idealNumberWeight
X-RAY DIFFRACTIONt_bond_d0.0219060.8
X-RAY DIFFRACTIONt_angle_deg2.9425881.3
X-RAY DIFFRACTIONt_dihedral_angle_d24.811260
X-RAY DIFFRACTIONt_incorr_chiral_ct0
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes0.025382
X-RAY DIFFRACTIONt_gen_planes0.0172885
X-RAY DIFFRACTIONt_it9.0518990.5
X-RAY DIFFRACTIONt_nbd
Software
*PLUS
Name: TNT / Version: 5E / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev idealWeight
X-RAY DIFFRACTIONt_dihedral_angle_d
X-RAY DIFFRACTIONt_dihedral_angle_deg24.80
X-RAY DIFFRACTIONt_plane_restr0.0175

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