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- PDB-9dwc: Crystal structure of FABLE, PEG 600 condition -

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Basic information

Entry
Database: PDB / ID: 9dwc
TitleCrystal structure of FABLE, PEG 600 condition
ComponentsDe novo designed FABLE protein
KeywordsDE NOVO PROTEIN / Protein design / four-helix bundle / apixaban
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.46 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 9, 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

Downloads & links

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Assembly

Deposited unit
A: De novo designed FABLE protein
B: De novo designed FABLE protein
C: De novo designed FABLE protein
D: De novo designed FABLE protein


Theoretical massNumber of molelcules
Total (without water)55,5284
Polymers55,5284
Non-polymers00
Water3,081171
1
A: De novo designed FABLE protein


Theoretical massNumber of molelcules
Total (without water)13,8821
Polymers13,8821
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: De novo designed FABLE protein


Theoretical massNumber of molelcules
Total (without water)13,8821
Polymers13,8821
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: De novo designed FABLE protein


Theoretical massNumber of molelcules
Total (without water)13,8821
Polymers13,8821
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: De novo designed FABLE protein


Theoretical massNumber of molelcules
Total (without water)13,8821
Polymers13,8821
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)62.469, 42.760, 96.624
Angle α, β, γ (deg.)90.00, 97.87, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
De novo designed FABLE protein


Mass: 13881.878 Da / Num. of mol.: 4
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.: 171 / 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: 2.3 Å3/Da / Density % sol: 46.57 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop / pH: 9.5 / Details: 100 mM CHES pH 9.5 , 30% (v/v) PEG 600

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.11585 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 10, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.11585 Å / Relative weight: 1
ReflectionResolution: 1.46→47.86 Å / Num. obs: 86345 / % possible obs: 97.8 % / Redundancy: 3.3 % / CC1/2: 0.998 / Rmerge(I) obs: 0.071 / Rpim(I) all: 0.046 / Rrim(I) all: 0.085 / Χ2: 0.94 / Net I/σ(I): 7.9 / Num. measured all: 283829
Reflection shellResolution: 1.46→1.48 Å / % possible obs: 95.3 % / Redundancy: 3.2 % / Rmerge(I) obs: 1.591 / Num. measured all: 13347 / Num. unique obs: 4175 / CC1/2: 0.383 / Rpim(I) all: 1.034 / Rrim(I) all: 1.904 / Χ2: 0.8 / Net I/σ(I) obs: 0.7

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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: 1.46→40.65 Å / SU ML: 0.24 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 30.32 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2289 4241 4.92 %
Rwork0.2057 --
obs0.2069 86203 97.69 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.46→40.65 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3904 0 0 171 4075
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0084219
X-RAY DIFFRACTIONf_angle_d0.8835722
X-RAY DIFFRACTIONf_dihedral_angle_d13.9061550
X-RAY DIFFRACTIONf_chiral_restr0.057650
X-RAY DIFFRACTIONf_plane_restr0.008754
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.46-1.480.47641390.4562580X-RAY DIFFRACTION93
1.48-1.490.4381490.40472665X-RAY DIFFRACTION97
1.49-1.510.3951500.39862678X-RAY DIFFRACTION96
1.51-1.530.42131490.38282661X-RAY DIFFRACTION96
1.53-1.550.44071440.36252690X-RAY DIFFRACTION98
1.55-1.570.32421390.33672698X-RAY DIFFRACTION96
1.57-1.60.35691470.32522685X-RAY DIFFRACTION98
1.6-1.620.35971320.30912718X-RAY DIFFRACTION98
1.62-1.640.34551530.29842690X-RAY DIFFRACTION96
1.64-1.670.30831480.27312710X-RAY DIFFRACTION99
1.67-1.70.32541320.27592741X-RAY DIFFRACTION97
1.7-1.730.28551520.26732707X-RAY DIFFRACTION98
1.73-1.760.31751320.25842753X-RAY DIFFRACTION98
1.76-1.80.23831280.24082711X-RAY DIFFRACTION98
1.8-1.840.26231330.21692748X-RAY DIFFRACTION99
1.84-1.880.28171330.20752745X-RAY DIFFRACTION98
1.88-1.930.21291250.19532788X-RAY DIFFRACTION99
1.93-1.980.24311570.18522689X-RAY DIFFRACTION98
1.98-2.040.23191460.17112774X-RAY DIFFRACTION98
2.04-2.110.20691510.16642759X-RAY DIFFRACTION99
2.11-2.180.19721400.17252708X-RAY DIFFRACTION98
2.18-2.270.19011490.15932778X-RAY DIFFRACTION99
2.27-2.370.18241350.15362787X-RAY DIFFRACTION99
2.37-2.50.19621470.14652762X-RAY DIFFRACTION99
2.5-2.650.16011360.16132748X-RAY DIFFRACTION98
2.65-2.860.22941280.17322797X-RAY DIFFRACTION98
2.86-3.150.20271380.1882763X-RAY DIFFRACTION98
3.15-3.60.20891330.19462799X-RAY DIFFRACTION99
3.6-4.530.19211370.1772762X-RAY DIFFRACTION97
4.54-40.650.21281590.22952868X-RAY DIFFRACTION98

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