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- PDB-9zio: Crystal Structure of RASProtease(II), a Designed RAS-specific Sub... -

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Basic information

Entry
Database: PDB / ID: 9zio
TitleCrystal Structure of RASProtease(II), a Designed RAS-specific Subtilisin
ComponentsSUBTILISIN BPN'
KeywordsHYDROLASE / Engineered protease
Function / homologyFORMIC ACID / DI(HYDROXYETHYL)ETHER
Function and homology information
Biological speciesBacillus amyloliquefaciens (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.49 Å
AuthorsChu, B. / Toth, E.A. / Orban, J.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS) United States
CitationJournal: Biorxiv / Year: 2026
Title: Substrate specificity in a designed RAS-targeting protease is coupled to active site and distal motions.
Authors: Chu, B. / He, Y. / Chen, Y. / Toth, E.A. / Orban, J.
History
DepositionDec 4, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 22, 2026Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
S: SUBTILISIN BPN'
A: SUBTILISIN BPN'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,24819
Polymers53,1092
Non-polymers1,13917
Water8,179454
1
S: SUBTILISIN BPN'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,14810
Polymers26,5551
Non-polymers5949
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: SUBTILISIN BPN'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,1009
Polymers26,5551
Non-polymers5468
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)49.130, 60.580, 70.160
Angle α, β, γ (deg.)90.00, 93.75, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 2 molecules SA

#1: Protein SUBTILISIN BPN'


Mass: 26554.619 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus amyloliquefaciens (bacteria) / Production host: Escherichia coli (E. coli)

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Non-polymers , 6 types, 471 molecules

#2: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#5: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3
#6: Chemical ChemComp-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CH2O2
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 454 / 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: 1.96 Å3/Da / Density % sol: 37.3 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / Details: 200 mM sodium formate, 20% PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Feb 19, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.49→45.81 Å / Num. obs: 65293 / % possible obs: 97.9 % / Redundancy: 6.5 % / CC1/2: 0.998 / Rmerge(I) obs: 0.07 / Rpim(I) all: 0.029 / Rrim(I) all: 0.076 / Χ2: 0.8 / Net I/σ(I): 15.8 / Num. measured all: 426425
Reflection shellResolution: 1.49→1.52 Å / % possible obs: 91.8 % / Redundancy: 6.2 % / Rmerge(I) obs: 0.467 / Num. measured all: 18722 / Num. unique obs: 3024 / CC1/2: 0.901 / Rpim(I) all: 0.2 / Rrim(I) all: 0.51 / Χ2: 0.33 / Net I/σ(I) obs: 2.4

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Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
Aimlessdata scaling
PDB_EXTRACTdata extraction
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.49→41.45 Å / SU ML: 0.12 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 14.1 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1585 3172 4.86 %
Rwork0.1221 --
obs0.1239 65240 97.71 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.49→41.45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3685 0 73 454 4212
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0084081
X-RAY DIFFRACTIONf_angle_d1.0585587
X-RAY DIFFRACTIONf_dihedral_angle_d7.2658
X-RAY DIFFRACTIONf_chiral_restr0.092656
X-RAY DIFFRACTIONf_plane_restr0.009730
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.49-1.520.18121230.12382500X-RAY DIFFRACTION91
1.52-1.540.2051330.11882707X-RAY DIFFRACTION98
1.54-1.560.20531380.11212707X-RAY DIFFRACTION99
1.56-1.590.16811240.10892750X-RAY DIFFRACTION99
1.59-1.620.18431400.10952661X-RAY DIFFRACTION99
1.62-1.650.18961210.10912760X-RAY DIFFRACTION99
1.65-1.680.16161370.10742715X-RAY DIFFRACTION99
1.68-1.720.17481290.12532699X-RAY DIFFRACTION99
1.72-1.760.2011220.12492710X-RAY DIFFRACTION98
1.76-1.810.15271300.11762662X-RAY DIFFRACTION96
1.81-1.850.211340.11322590X-RAY DIFFRACTION94
1.85-1.910.14421800.10632684X-RAY DIFFRACTION99
1.91-1.970.15481410.10962758X-RAY DIFFRACTION100
1.97-2.040.17081440.11282720X-RAY DIFFRACTION100
2.04-2.120.15821520.11722729X-RAY DIFFRACTION99
2.12-2.220.16171590.11342709X-RAY DIFFRACTION99
2.22-2.340.15621550.11162731X-RAY DIFFRACTION99
2.34-2.480.14021630.12222661X-RAY DIFFRACTION98
2.48-2.670.15211510.12452570X-RAY DIFFRACTION93
2.67-2.940.16311200.12792781X-RAY DIFFRACTION99
2.94-3.370.14231330.12862768X-RAY DIFFRACTION99
3.37-4.240.14221130.12092806X-RAY DIFFRACTION99

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