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

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Basic information

Entry
Database: PDB / ID: 7hiz
TitlePanDDA analysis group deposition -- Crystal structure of ABLE in complex with ZINC000008579298
ComponentsDe novo designed ABLE protein
KeywordsDE NOVO PROTEIN / Protein design / four-helix bundle / apixaban
Function / homologyQUINOLIN-2(1H)-ONE
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,9632
Polymers13,8171
Non-polymers1451
Water1,802100
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area350 Å2
ΔGint8 kcal/mol
Surface area7120 Å2
MethodPISA
Unit cell
Length a, b, c (Å)26.380, 47.236, 46.479
Angle α, β, γ (deg.)90.000, 103.530, 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-OCH / QUINOLIN-2(1H)-ONE / 2-OXOQUINOLINE


Mass: 145.158 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H7NO
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 100 / 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: 2.1 Å3/Da / Density % sol: 41.42 %
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: 1.3→47.24 Å / Num. obs: 26458 / % possible obs: 96.7 % / Redundancy: 3.3 % / Biso Wilson estimate: 18.41 Å2 / CC1/2: 0.994 / Rmerge(I) obs: 0.05 / Rpim(I) all: 0.033 / Rrim(I) all: 0.06 / Net I/σ(I): 10.4 / Num. measured all: 87332
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
1.3-1.323.22.331438013710.3011.5352.8060.596.2
7-47.243.30.0255991800.9880.0190.03143.492.4

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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: 1.3→25.65 Å / SU ML: 0.22 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 35.27 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2475 1325 5.07 %
Rwork0.2101 24827 -
obs0.212 26152 95.49 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 95.37 Å2 / Biso mean: 29.4564 Å2 / Biso min: 11.62 Å2
Refinement stepCycle: final / Resolution: 1.3→25.65 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms971 0 18 100 1089
Biso mean--27.62 35.36 -
Num. residues----126
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 9

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.3-1.350.43161440.45092557270190
1.35-1.410.40641600.39482799295997
1.41-1.490.35281410.33812783292497
1.49-1.580.27161260.25862758288495
1.58-1.70.26651410.23112848298999
1.7-1.880.25871370.21232845298298
1.88-2.150.22371590.19332775293497
2.15-2.70.20181750.18732714288995
2.7-25.650.24651420.1862748289093

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