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- PDB-3bgo: Azide complex of Engineered Subtilisin SUBT_BACAM -

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Basic information

Entry
Database: PDB / ID: 3bgo
TitleAzide complex of Engineered Subtilisin SUBT_BACAM
Components(Subtilisin BPN') x 2
KeywordsHYDROLASE / azide switch / anion sensor / Metal-binding / Protease / Secreted / Serine protease / Sporulation / 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
Peptidase S8 propeptide/proteinase inhibitor I9 / : / 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 propeptide/proteinase inhibitor I9 / : / 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 / Alpha-Beta Plaits / Rossmann fold / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
AZIDE ION / Subtilisin BPN'
Similarity search - Component
Biological speciesBacillus amyloliquefaciens (bacteria)
MethodX-RAY DIFFRACTION / Resolution: 1.8 Å
AuthorsGallagher, D.T. / Bryan, P.N.
CitationJournal: Biochemistry / Year: 2009
Title: Structure of a switchable subtilisin complexed with a substrate and with the activator azide.
Authors: Gallagher, T. / Ruan, B. / London, M. / Bryan, M.A. / Bryan, P.N.
History
DepositionNov 27, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 3, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 2, 2016Group: Database references
Revision 1.3Oct 20, 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_dist_value / _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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Oct 9, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature
Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
P: Subtilisin BPN'
S: Subtilisin BPN'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,5107
Polymers35,2072
Non-polymers3045
Water5,278293
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2950 Å2
ΔGint-127.3 kcal/mol
Surface area12850 Å2
MethodPISA
2
P: Subtilisin BPN'

S: Subtilisin BPN'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,5107
Polymers35,2072
Non-polymers3045
Water362
TypeNameSymmetry operationNumber
crystal symmetry operation4_445x-1/2,-y-1/2,-z1
identity operation1_555x,y,z1
Buried area1160 Å2
ΔGint-135.1 kcal/mol
Surface area14640 Å2
MethodPISA
Unit cell
Length a, b, c (Å)44.290, 72.840, 95.020
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Subtilisin BPN' / Subtilisin Novo / Subtilisin DFE / Alkaline protease


Mass: 8786.066 Da / Num. of mol.: 1 / Fragment: Prodomain
Mutation: K27E, V37L, Q40C, K57E, H72K, V73L, A74Y, H75R, Y77L
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus amyloliquefaciens (bacteria) / Gene: apr / Production host: Escherichia coli (E. coli) / References: UniProt: P00782
#2: Protein Subtilisin BPN' / Subtilisin Novo / Subtilisin DFE / Alkaline protease


Mass: 26420.447 Da / Num. of mol.: 1 / Fragment: Enzyme domain
Mutation: Q2K, S3C, P5S, S9A, I31L, D32A, K43N, M50F, A73L, Y104A, G128S, E156S, G166S, G169A, S188P, Q206C, N212G, K217L, N218S, S221A, T254A, Q271E
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus amyloliquefaciens (bacteria) / Gene: apr / Production host: Escherichia coli (E. coli) / References: UniProt: P00782, subtilisin
#3: Chemical ChemComp-AZI / AZIDE ION


Mass: 42.020 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: N3
#4: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 293 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsAUTHOR STATES THAT RESIDUES 17-23 TMSTMSA WAS REPLACED WITH GFKSC

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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: 2.18 Å3/Da / Density % sol: 43.49 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: l8% PEG 8K, 0.2 M ZnAc, 0.1 M Na Cacodylate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: May 13, 2007 / Details: mirrors
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.8→15.87 Å / Num. obs: 29142 / % possible obs: 99.8 % / Redundancy: 5.59 % / Rmerge(I) obs: 0.034 / Χ2: 0.98 / Net I/σ(I): 26.6 / Scaling rejects: 1233
Reflection shellResolution: 1.8→1.86 Å / Redundancy: 4.31 % / Rmerge(I) obs: 0.152 / Mean I/σ(I) obs: 7 / Num. measured all: 12275 / Num. unique all: 2836 / Χ2: 0.94 / % possible all: 98.3

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Processing

Software
NameVersionClassificationNB
d*TREK9.4SSIdata scaling
d*TREK9.4SSIdata reduction
REFMAC5.2.0019refinement
PDB_EXTRACT3.004data extraction
RefinementResolution: 1.8→8 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.924 / SU B: 3.159 / SU ML: 0.101 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.152 / ESU R Free: 0.151 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.262 1463 5.1 %RANDOM
Rwork0.205 ---
obs0.208 28807 99.82 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 24.423 Å2
Baniso -1Baniso -2Baniso -3
1-1.45 Å20 Å20 Å2
2---1.14 Å20 Å2
3----0.31 Å2
Refinement stepCycle: LAST / Resolution: 1.8→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2394 0 7 293 2694
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0222440
X-RAY DIFFRACTIONr_angle_refined_deg1.7091.9563312
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5655331
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.38725.85482
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.0515379
X-RAY DIFFRACTIONr_dihedral_angle_4_deg5.472153
X-RAY DIFFRACTIONr_chiral_restr0.1350.2383
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.021814
X-RAY DIFFRACTIONr_nbd_refined0.2170.21277
X-RAY DIFFRACTIONr_nbtor_refined0.2990.21672
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1970.2196
X-RAY DIFFRACTIONr_metal_ion_refined0.020.21
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.4520.238
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.3340.224
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined0.1040.21
X-RAY DIFFRACTIONr_mcbond_it1.1921.51678
X-RAY DIFFRACTIONr_mcangle_it1.80822621
X-RAY DIFFRACTIONr_scbond_it2.9363859
X-RAY DIFFRACTIONr_scangle_it4.1274.5691
LS refinement shellResolution: 1.8→1.844 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.397 109 -
Rwork0.303 1900 -
all-2009 -
obs--97.71 %

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