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- PDB-7hj0: PanDDA analysis group deposition -- Crystal structure of ABLE in ... -

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Basic information

Entry
Database: PDB / ID: 7hj0
TitlePanDDA analysis group deposition -- Crystal structure of ABLE in complex with ZINC000006657973
ComponentsDe novo designed ABLE protein
KeywordsDE NOVO PROTEIN / Protein design / four-helix bundle / apixaban
Function / homologyChem-5GT
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.39 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,0342
Polymers13,8171
Non-polymers2161
Water1,63991
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area7040 Å2
MethodPISA
Unit cell
Length a, b, c (Å)26.150, 47.198, 46.387
Angle α, β, γ (deg.)90.000, 103.240, 90.000
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
Details: HIS6 purification tag (MHHHHHHENLYFQ) cleaved with TEV protease
Source: (gene. exp.) synthetic construct (others) / Plasmid: pET11a / Production host: Escherichia coli BL21(DE3) (bacteria)
#2: Chemical ChemComp-5GT / 7-(trifluoromethyl)-3,4-dihydroquinoxalin-2(1H)-one


Mass: 216.160 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H7F3N2O
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 91 / 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: 2.07 Å3/Da / Density % sol: 40.74 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 5 / Details: 220 mM sodium malonate, 22% PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.97946 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Mar 5, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97946 Å / Relative weight: 1
ReflectionResolution: 1.39→45.15 Å / Num. obs: 21369 / % possible obs: 96.4 % / Redundancy: 3.3 % / Biso Wilson estimate: 18.39 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.072 / Rpim(I) all: 0.047 / Rrim(I) all: 0.087 / Net I/σ(I): 8.1 / Num. measured all: 71235
Reflection shell

Diffraction-ID: 1 / Redundancy: 3.3 %

Resolution (Å)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
1.39-1.412.189342810260.3361.4022.6110.795.9
7.61-45.150.0464921480.9990.0280.05526.198.8

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
PHENIX1.20.1_4487refinement
Aimless0.8.2data scaling
PDB_EXTRACT3.28data extraction
XDSJun 30, 2023data reduction
PHASER2.8.3phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.39→25.46 Å / SU ML: 0.26 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 37.49 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.255 1053 4.95 %
Rwork0.2085 20232 -
obs0.2108 21285 95.9 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 120.68 Å2 / Biso mean: 29.9461 Å2 / Biso min: 11.05 Å2
Refinement stepCycle: final / Resolution: 1.39→25.46 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms971 0 22 91 1084
Biso mean--31.74 37.02 -
Num. residues----126
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 8

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.39-1.450.48131240.44022490261495
1.45-1.530.42071130.36922502261594
1.53-1.630.37461090.3152482259194
1.63-1.750.26521270.24982572269998
1.75-1.930.24891420.1992576271898
1.93-2.210.22451370.18522549268697
2.21-2.780.2031700.18442498266896
2.78-25.460.2591310.18432563269495

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