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

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Basic information

Entry
Database: PDB / ID: 7hjb
TitlePanDDA analysis group deposition -- Crystal structure of ABLE in complex with ZINC000000154564
ComponentsDe novo designed ABLE protein
KeywordsDE NOVO PROTEIN / Protein design / four-helix bundle / apixaban
Function / homologyHYDROCINNAMIC ACID
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.58 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)14,1183
Polymers13,8171
Non-polymers3002
Water2,306128
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area810 Å2
ΔGint12 kcal/mol
Surface area7020 Å2
MethodPISA
Unit cell
Length a, b, c (Å)26.105, 47.159, 46.384
Angle α, β, γ (deg.)90.000, 103.060, 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-HCI / HYDROCINNAMIC ACID / 3PP / 3-PHENYLPROPIONIC ACID


Mass: 150.174 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C9H10O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 128 / 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: 40.56 %
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: ALS / Beamline: 8.3.1 / Wavelength: 1.11583 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Mar 8, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.11583 Å / Relative weight: 1
ReflectionResolution: 1.58→47.16 Å / Num. obs: 14853 / % possible obs: 98.1 % / Redundancy: 3.3 % / Biso Wilson estimate: 18.69 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.026 / Rpim(I) all: 0.017 / Rrim(I) all: 0.032 / Net I/σ(I): 23.5 / Num. measured all: 48354
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
1.58-1.6130.18120867020.9740.1240.224.995.2
8.65-47.163.30.01133810210.0070.01454.299.4

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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: 1.58→45.18 Å / SU ML: 0.19 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 29.76 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2377 753 5.09 %
Rwork0.1851 14038 -
obs0.1877 14791 97.68 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 96.81 Å2 / Biso mean: 27.4035 Å2 / Biso min: 10.55 Å2
Refinement stepCycle: final / Resolution: 1.58→45.18 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms971 0 40 128 1139
Biso mean--23.79 32.27 -
Num. residues----126
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 5

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.58-1.70.28471380.22512768290697
1.7-1.870.26061330.19792846297998
1.87-2.140.27571560.20092774293098
2.14-2.70.21611810.18592774295598
2.7-45.180.22751450.17332876302198

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