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- PDB-9dwa: Crystal structure of FABLE, MPD condition -

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Basic information

Entry
Database: PDB / ID: 9dwa
TitleCrystal structure of FABLE, MPD 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: 1.85 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

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Assembly

Deposited unit
A: De novo designed FABLE protein
B: De novo designed FABLE protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,94512
Polymers27,7642
Non-polymers1,18210
Water1,820101
1
A: De novo designed FABLE protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,4736
Polymers13,8821
Non-polymers5915
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: De novo designed FABLE protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,4736
Polymers13,8821
Non-polymers5915
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)49.379, 43.933, 65.268
Angle α, β, γ (deg.)90.00, 97.84, 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: Chemical
ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 101 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
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: 2.53 Å3/Da / Density % sol: 51.31 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop / pH: 8 / Details: 100 mM Tris pH 8.0, 20% (v/v) MPD

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.97946 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Sep 4, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97946 Å / Relative weight: 1
ReflectionResolution: 1.85→48.92 Å / Num. obs: 23431 / % possible obs: 98.1 % / Redundancy: 3.4 % / CC1/2: 0.998 / Rmerge(I) obs: 0.072 / Rpim(I) all: 0.046 / Rrim(I) all: 0.086 / Χ2: 0.94 / Net I/σ(I): 9.7 / Num. measured all: 80456
Reflection shellResolution: 1.85→1.89 Å / % possible obs: 98.7 % / Redundancy: 3.5 % / Rmerge(I) obs: 1.502 / Num. measured all: 4998 / Num. unique obs: 1443 / CC1/2: 0.374 / Rpim(I) all: 0.937 / Rrim(I) all: 1.777 / Χ2: 0.73 / 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: 1.85→48.92 Å / SU ML: 0.33 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 29.63 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2406 1138 4.87 %
Rwork0.1913 --
obs0.1937 23391 97.76 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.85→48.92 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1952 0 80 101 2133
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.012095
X-RAY DIFFRACTIONf_angle_d0.9732834
X-RAY DIFFRACTIONf_dihedral_angle_d13.743768
X-RAY DIFFRACTIONf_chiral_restr0.044322
X-RAY DIFFRACTIONf_plane_restr0.007356
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.85-1.930.45091300.38542760X-RAY DIFFRACTION98
1.93-2.040.32761480.27912764X-RAY DIFFRACTION99
2.04-2.160.27481680.24042723X-RAY DIFFRACTION97
2.16-2.330.28791340.19442826X-RAY DIFFRACTION99
2.33-2.570.23421360.16512794X-RAY DIFFRACTION99
2.57-2.940.25491470.18312785X-RAY DIFFRACTION98
2.94-3.70.23791320.1772767X-RAY DIFFRACTION97
3.7-48.920.19351430.17372834X-RAY DIFFRACTION97

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