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- PDB-6ube: Azide-triggered subtilisin SUBT_BACAM complexed with the peptide LFRAL -

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Basic information

Entry
Database: PDB / ID: 6ube
TitleAzide-triggered subtilisin SUBT_BACAM complexed with the peptide LFRAL
Components
  • Peptide LFRAL
  • SUBTILISIN BPN'
KeywordsHYDROLASE / engineered protease
Function / homologyAZIDE ION
Function and homology information
Biological speciesBacillus amyloliquefaciens (bacteria)
synthetic construct (others)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.6 Å
AuthorsToth, E.A. / Bryan, P.N. / Orban, J. / Gallagher, D.T. / Custer, G.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Cancer Institute (NIH/NCI) United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS) United States
CitationJournal: Commun Biol / Year: 2021
Title: Engineering subtilisin proteases that specifically degrade active RAS.
Authors: Chen, Y. / Toth, E.A. / Ruan, B. / Choi, E.J. / Simmerman, R. / Chen, Y. / He, Y. / Wang, R. / Godoy-Ruiz, R. / King, H. / Custer, G. / Travis Gallagher, D. / Rozak, D.A. / Solomon, M. / ...Authors: Chen, Y. / Toth, E.A. / Ruan, B. / Choi, E.J. / Simmerman, R. / Chen, Y. / He, Y. / Wang, R. / Godoy-Ruiz, R. / King, H. / Custer, G. / Travis Gallagher, D. / Rozak, D.A. / Solomon, M. / Muro, S. / Weber, D.J. / Orban, J. / Fuerst, T.R. / Bryan, P.N.
History
DepositionSep 11, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 16, 2020Provider: repository / Type: Initial release
Revision 1.1Mar 31, 2021Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Oct 11, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.3Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
S: SUBTILISIN BPN'
B: Peptide LFRAL
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,54811
Polymers27,0572
Non-polymers4909
Water5,386299
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2690 Å2
ΔGint-27 kcal/mol
Surface area9520 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.646, 58.646, 125.670
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212

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Components

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Protein / Protein/peptide , 2 types, 2 molecules SB

#1: Protein SUBTILISIN BPN'


Mass: 26437.475 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)
#2: Protein/peptide Peptide LFRAL


Mass: 619.776 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

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Non-polymers , 4 types, 308 molecules

#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#4: Chemical
ChemComp-AZI / AZIDE ION


Mass: 42.020 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: N3
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 299 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN
Has protein modificationY

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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 Å3/Da / Density % sol: 38.4 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / Details: 0.1 M Imidazole pH 8.0, 0.2 M NaCl, 30% PEG 8K

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Jul 1, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.6→19.73 Å / Num. obs: 29454 / % possible obs: 98.9 % / Redundancy: 5.81 % / Rmerge(I) obs: 0.037 / Rrim(I) all: 0.041 / Χ2: 0.96 / Net I/σ(I): 25.2
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique obsRrim(I) allΧ2Rejects% possible all
1.6-1.663.180.1337.6847826520.1581.145091.3
1.66-1.724.960.1299.41454729070.1451.1212199.2
1.72-1.86.050.10811.51786429190.1181.0819099.9
1.8-1.96.120.08114.31811429260.0880.99213100
1.9-2.026.180.06518.11841129490.0710.94190100
2.02-2.176.240.05920.21847929410.0650.93141100
2.17-2.396.290.05124.21872729590.0560.91101100
2.39-2.736.320.04128.61898229890.0450.8777100
2.73-3.446.340.0339.91935230400.0320.8467100
3.44-19.726.120.02161.21954231720.0230.9114499

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
d*TREKdata reduction
d*TREK9.9.8.6 W9RSSIdata scaling
MOLREPphasing
REFMAC5.8.0253refinement
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3f49

3f49


Resolution: 1.6→19.73 Å / Cor.coef. Fo:Fc: 0.978 / Cor.coef. Fo:Fc free: 0.967 / SU R Cruickshank DPI: 0.0725 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.073 / ESU R Free: 0.074
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.158 1492 5.1 %RANDOM
Rwork0.1278 ---
obs0.1294 27961 98.86 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 52.47 Å2 / Biso mean: 13.16 Å2 / Biso min: 7.3 Å2
Baniso -1Baniso -2Baniso -3
1--0.04 Å20 Å20 Å2
2---0.04 Å20 Å2
3---0.07 Å2
Refinement stepCycle: final / Resolution: 1.6→19.73 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1895 0 32 299 2226
Biso mean--31.6 28.66 -
Num. residues----271
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0270.0132015
X-RAY DIFFRACTIONr_bond_other_d0.0370.0171827
X-RAY DIFFRACTIONr_angle_refined_deg2.3411.6172755
X-RAY DIFFRACTIONr_angle_other_deg2.5921.5644265
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.3925287
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.29524.53164
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.99715284
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.923153
X-RAY DIFFRACTIONr_chiral_restr0.1510.2278
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.022322
X-RAY DIFFRACTIONr_gen_planes_other0.0150.02371
LS refinement shellResolution: 1.6→1.642 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.228 83 -
Rwork0.219 1837 -
all-1920 -
obs--89.18 %

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