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- PDB-9n0j: Crystal structure of KABLE double mutant (Lys14Pro, Leu20Trp) in ... -

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Basic information

Entry
Database: PDB / ID: 9n0j
TitleCrystal structure of KABLE double mutant (Lys14Pro, Leu20Trp) in complex with 6-nitrobenzotriazole
ComponentsDe novo designed KABLE protein
KeywordsDE NOVO PROTEIN / Protein design / four-helix bundle / apixaban / Kemp elimination
Function / homology5-nitro-1H-benzotriazole / CACODYLATE ION
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.54 Å
AuthorsCorrey, G.J. / Fraser, J.S.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM145238 United States
CitationJournal: To Be Published
Title: De novo designed KABLE protein
Authors: Correy, G.J. / Fraser, J.S.
History
DepositionJan 24, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 20, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: De novo designed KABLE protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,6159
Polymers13,7241
Non-polymers8918
Water90150
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)44.601, 44.601, 128.033
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein De novo designed KABLE protein


Mass: 13723.826 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Production host: Escherichia coli BL21(DE3) (bacteria)
#2: Chemical ChemComp-3NY / 5-nitro-1H-benzotriazole


Mass: 164.122 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C6H4N4O2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-CAC / CACODYLATE ION / dimethylarsinate


Mass: 136.989 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6AsO2
#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.: 50 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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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: 2.32 Å3/Da / Density % sol: 46.98 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.2 M zinc acetate, 0.1 M sodium cacodylate pH 6.5, 18% PEG 8000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.11583 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 18, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.11583 Å / Relative weight: 1
ReflectionResolution: 1.54→44.6 Å / Num. obs: 20037 / % possible obs: 99.8 % / Redundancy: 11.8 % / CC1/2: 1 / Rmerge(I) obs: 0.06 / Rpim(I) all: 0.018 / Rrim(I) all: 0.062 / Χ2: 0.89 / Net I/σ(I): 22.2 / Num. measured all: 236844
Reflection shellResolution: 1.54→1.57 Å / % possible obs: 96.9 % / Redundancy: 10.9 % / Rmerge(I) obs: 1.229 / Num. measured all: 9984 / Num. unique obs: 912 / CC1/2: 0.849 / Rpim(I) all: 0.382 / Rrim(I) all: 1.289 / Χ2: 0.41 / Net I/σ(I) obs: 1.3

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Processing

Software
NameVersionClassification
PHENIX1.21.1_5286refinement
XDSJun 30, 2023data scaling
XDSJun 30, 2023data reduction
PHASER2.8.3phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.54→42.12 Å / SU ML: 0.24 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 31.97 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2779 972 5.06 %
Rwork0.2423 --
obs0.2442 19194 95.99 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.54→42.12 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms960 0 45 50 1055
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0131013
X-RAY DIFFRACTIONf_angle_d1.2081365
X-RAY DIFFRACTIONf_dihedral_angle_d14.884362
X-RAY DIFFRACTIONf_chiral_restr0.052150
X-RAY DIFFRACTIONf_plane_restr0.01178
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.54-1.620.37721370.33182594X-RAY DIFFRACTION99
1.62-1.720.28361530.26742637X-RAY DIFFRACTION100
1.72-1.860.32211300.24772687X-RAY DIFFRACTION100
1.86-2.040.41071280.39522178X-RAY DIFFRACTION82
2.04-2.340.30311310.29352471X-RAY DIFFRACTION91
2.34-2.950.27621240.23352757X-RAY DIFFRACTION100
2.95-42.120.24281690.20432898X-RAY DIFFRACTION100

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