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

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Basic information

Entry
Database: PDB / ID: 9ziq
TitleCrystal Structure of RASProtease(II), a Designed RAS-specific Subtilisin, in Complex with the Non-cognate Peptide QEEISAM
Components
  • Peptide QEEISAM
  • SUBTILISIN BPN'
KeywordsHYDROLASE / Engineered protease
Function / homology:
Function and homology information
Biological speciesBacillus amyloliquefaciens (bacteria)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.2 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'
B: Peptide QEEISAM
C: Peptide QEEISAM
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,26427
Polymers54,7234
Non-polymers1,54123
Water8,161453
1
S: SUBTILISIN BPN'
B: Peptide QEEISAM
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,03912
Polymers27,3622
Non-polymers67710
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2420 Å2
ΔGint-39 kcal/mol
Surface area10170 Å2
MethodPISA
2
A: SUBTILISIN BPN'
C: Peptide QEEISAM
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,22515
Polymers27,3622
Non-polymers86313
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2870 Å2
ΔGint-34 kcal/mol
Surface area10310 Å2
MethodPISA
Unit cell
Length a, b, c (Å)44.243, 58.242, 82.598
Angle α, β, γ (deg.)90.00, 97.73, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein / Protein/peptide , 2 types, 4 molecules SABC

#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)
#2: Protein/peptide Peptide QEEISAM


Mass: 806.881 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

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Non-polymers , 6 types, 476 molecules

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


Mass: 62.068 Da / Num. of mol.: 13 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#6: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: K
#7: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 453 / 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: 1.93 Å3/Da / Density % sol: 36.17 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / Details: 50 mM zinc acetate, 15% PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSLS-II / Beamline: 17-ID-2 / Wavelength: 0.9793 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Oct 3, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 1.2→58.24 Å / Num. obs: 127620 / % possible obs: 98.3 % / Redundancy: 5.5 % / CC1/2: 0.996 / Rmerge(I) obs: 0.097 / Rpim(I) all: 0.044 / Rrim(I) all: 0.107 / Χ2: 0.79 / Net I/σ(I): 7.7 / Num. measured all: 704252
Reflection shellResolution: 1.2→1.22 Å / % possible obs: 94.8 % / Redundancy: 4.7 % / Rmerge(I) obs: 0.832 / Num. measured all: 28489 / Num. unique obs: 6054 / CC1/2: 0.731 / Rpim(I) all: 0.42 / Rrim(I) all: 0.936 / Χ2: 0.57 / Net I/σ(I) obs: 1.6

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Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
Aimlessdata scaling
PDB_EXTRACTdata extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.2→40.92 Å / SU ML: 0.12 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 18.49 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1596 6351 4.98 %
Rwork0.1354 --
obs0.1367 127548 98.3 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.2→40.92 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3795 0 88 453 4336
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0134126
X-RAY DIFFRACTIONf_angle_d1.3735624
X-RAY DIFFRACTIONf_dihedral_angle_d8.744656
X-RAY DIFFRACTIONf_chiral_restr0.106666
X-RAY DIFFRACTIONf_plane_restr0.015726
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.2-1.210.26371970.2293794X-RAY DIFFRACTION94
1.21-1.230.23582020.21193966X-RAY DIFFRACTION96
1.23-1.240.23281990.19783961X-RAY DIFFRACTION96
1.24-1.260.25881910.19624002X-RAY DIFFRACTION97
1.26-1.280.24051830.18393990X-RAY DIFFRACTION97
1.28-1.290.19662200.17253962X-RAY DIFFRACTION97
1.29-1.310.22562250.16593967X-RAY DIFFRACTION98
1.31-1.330.1842170.16523990X-RAY DIFFRACTION97
1.33-1.350.2122180.15873973X-RAY DIFFRACTION98
1.35-1.370.19912080.15784049X-RAY DIFFRACTION98
1.37-1.40.20092050.14633990X-RAY DIFFRACTION98
1.4-1.420.18822080.13754026X-RAY DIFFRACTION98
1.42-1.450.1551810.12954060X-RAY DIFFRACTION98
1.45-1.480.15512230.12814017X-RAY DIFFRACTION99
1.48-1.510.16861920.12784072X-RAY DIFFRACTION99
1.51-1.550.16442010.12374012X-RAY DIFFRACTION98
1.55-1.590.1572430.11974037X-RAY DIFFRACTION99
1.59-1.630.17212240.12144072X-RAY DIFFRACTION99
1.63-1.680.1512060.12164018X-RAY DIFFRACTION99
1.68-1.730.16432110.12394078X-RAY DIFFRACTION99
1.73-1.790.16952170.12634104X-RAY DIFFRACTION99
1.79-1.860.16651990.11674088X-RAY DIFFRACTION99
1.86-1.950.14732080.12264073X-RAY DIFFRACTION99
1.95-2.050.16062190.12164083X-RAY DIFFRACTION100
2.05-2.180.14152310.11624082X-RAY DIFFRACTION99
2.18-2.350.14562250.1234153X-RAY DIFFRACTION100
2.35-2.590.1582270.12894115X-RAY DIFFRACTION100
2.59-2.960.13022410.13354108X-RAY DIFFRACTION100
2.96-3.730.14062010.12554165X-RAY DIFFRACTION100

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