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- PDB-9dw2: Crystal structure of ABLE, 10% DMSO soak -

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Basic information

Entry
Database: PDB / ID: 9dw2
TitleCrystal structure of ABLE, 10% DMSO soak
ComponentsDe novo designed ABLE protein
KeywordsDE NOVO PROTEIN / Protein design / four-helix bundle / apixaban
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.3 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: Fragment screen against ABLE
Authors: Correy, G.J. / Fraser, J.S.
History
DepositionOct 8, 2024Deposition 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 ABLE protein


Theoretical massNumber of molelcules
Total (without water)13,8171
Polymers13,8171
Non-polymers00
Water2,378132
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)25.970, 47.126, 46.489
Angle α, β, γ (deg.)90.00, 102.92, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein De novo designed ABLE protein


Mass: 13817.490 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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 132 / Source method: isolated from a natural source / Formula: H2O
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: 2.01 Å3/Da / Density % sol: 38.71 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop / Details: 220 mM sodium malonate, 22% (w/v) PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-1 / Wavelength: 0.97946 Å
DetectorType: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Feb 22, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97946 Å / Relative weight: 1
ReflectionResolution: 1.3→45.31 Å / Num. obs: 26151 / % possible obs: 97.2 % / Redundancy: 3.4 % / CC1/2: 0.999 / Rmerge(I) obs: 0.029 / Rpim(I) all: 0.019 / Rrim(I) all: 0.034 / Χ2: 0.96 / Net I/σ(I): 17.5 / Num. measured all: 87861
Reflection shellResolution: 1.3→1.32 Å / % possible obs: 97.5 % / Redundancy: 3.4 % / Rmerge(I) obs: 0.595 / Num. measured all: 4350 / Num. unique obs: 1296 / CC1/2: 0.839 / Rpim(I) all: 0.382 / Rrim(I) all: 0.711 / Χ2: 0.73 / Net I/σ(I) obs: 1.9

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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: 1.3→45.31 Å / SU ML: 0.17 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 30.1 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2357 1313 5.04 %
Rwork0.1933 --
obs0.1954 26063 96.76 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.3→45.31 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms971 0 0 132 1103
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.007997
X-RAY DIFFRACTIONf_angle_d0.8891345
X-RAY DIFFRACTIONf_dihedral_angle_d13.128365
X-RAY DIFFRACTIONf_chiral_restr0.055153
X-RAY DIFFRACTIONf_plane_restr0.006178
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.3-1.350.36221570.31562750X-RAY DIFFRACTION98
1.35-1.410.30331580.2922751X-RAY DIFFRACTION98
1.41-1.490.28371400.24682760X-RAY DIFFRACTION97
1.49-1.580.25031230.21072751X-RAY DIFFRACTION96
1.58-1.70.19221370.20362794X-RAY DIFFRACTION98
1.7-1.880.26641280.21042783X-RAY DIFFRACTION97
1.88-2.150.22981500.19272681X-RAY DIFFRACTION94
2.15-2.70.20621760.17972688X-RAY DIFFRACTION96
2.71-45.310.23851440.17642792X-RAY DIFFRACTION96

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