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- PDB-9dwb: Crystal structure of FABLE, PEG 400 condition -

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Basic information

Entry
Database: PDB / ID: 9dwb
TitleCrystal structure of FABLE, PEG 400 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: 1.68 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


Theoretical massNumber of molelcules
Total (without water)27,7642
Polymers27,7642
Non-polymers00
Water1,33374
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
Unit cell
Length a, b, c (Å)54.218, 43.177, 60.864
Angle α, β, γ (deg.)90.00, 114.27, 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.: 2
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.: 74 / 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: 2.34 Å3/Da / Density % sol: 47.42 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop / pH: 9.5
Details: 200 mM sodium chloride, 100 mM CHES pH 9.5, 50% (v/v) PEG 400

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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: 1.68→47.98 Å / Num. obs: 29306 / % possible obs: 99.3 % / Redundancy: 3.3 % / CC1/2: 0.998 / Rmerge(I) obs: 0.066 / Rpim(I) all: 0.042 / Rrim(I) all: 0.078 / Χ2: 0.91 / Net I/σ(I): 8.7 / Num. measured all: 95881
Reflection shellResolution: 1.68→1.71 Å / % possible obs: 96.4 % / Redundancy: 3.2 % / Rmerge(I) obs: 1.452 / Num. measured all: 4591 / Num. unique obs: 1438 / CC1/2: 0.33 / Rpim(I) all: 0.945 / Rrim(I) all: 1.739 / Χ2: 0.63 / Net I/σ(I) obs: 0.6

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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: 1.68→47.98 Å / SU ML: 0.24 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 26.82 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2268 1395 4.77 %
Rwork0.1979 --
obs0.1994 29243 98.98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.68→47.98 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1952 0 0 74 2026
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0092004
X-RAY DIFFRACTIONf_angle_d0.9492701
X-RAY DIFFRACTIONf_dihedral_angle_d12.905729
X-RAY DIFFRACTIONf_chiral_restr0.045309
X-RAY DIFFRACTIONf_plane_restr0.009349
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.68-1.740.38551420.35062737X-RAY DIFFRACTION97
1.74-1.810.37551110.33552794X-RAY DIFFRACTION100
1.81-1.890.30381170.27912804X-RAY DIFFRACTION100
1.89-1.990.28461480.22992746X-RAY DIFFRACTION100
1.99-2.120.22651360.19962804X-RAY DIFFRACTION100
2.12-2.280.25661350.1912794X-RAY DIFFRACTION100
2.28-2.510.21091360.16562783X-RAY DIFFRACTION99
2.51-2.870.20951550.18382801X-RAY DIFFRACTION99
2.87-3.620.23431530.20482760X-RAY DIFFRACTION99
3.62-47.980.19941620.17852825X-RAY DIFFRACTION98

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