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

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Basic information

Entry
Database: PDB / ID: 7hiy
TitlePanDDA analysis group deposition -- Crystal structure of ABLE in complex with ZINC000000058111
ComponentsDe novo designed ABLE protein
KeywordsDE NOVO PROTEIN / Protein design / four-helix bundle / apixaban
Function / homology7-hydroxy-2H-chromen-2-one
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.43 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)13,9802
Polymers13,8171
Non-polymers1621
Water1,76598
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area7170 Å2
MethodPISA
Unit cell
Length a, b, c (Å)26.277, 47.527, 46.452
Angle α, β, γ (deg.)90.000, 103.100, 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-07L / 7-hydroxy-2H-chromen-2-one / 7-hydroxycoumarin


Mass: 162.142 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H6O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 98 / 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: 41.52 %
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: BL12-1 / Wavelength: 0.97946 Å
DetectorType: DECTRIS EIGER X 16M / 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: 1.43→47.53 Å / Num. obs: 20123 / % possible obs: 97.3 % / Redundancy: 3.3 % / Biso Wilson estimate: 20.83 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.052 / Rpim(I) all: 0.034 / Rrim(I) all: 0.063 / Net I/σ(I): 9.2 / Num. measured all: 67203
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
1.43-1.462.71.41226229640.3181.0281.760.690.9
7.7-47.533.20.02246414310.0150.02727.597.2

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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: 1.43→45.24 Å / SU ML: 0.22 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 35.06 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2464 1002 5.01 %
Rwork0.2022 19011 -
obs0.2045 20013 96.71 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 106.46 Å2 / Biso mean: 32.8074 Å2 / Biso min: 13.71 Å2
Refinement stepCycle: final / Resolution: 1.43→45.24 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms971 0 18 98 1087
Biso mean--35.4 40.36 -
Num. residues----126
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 7

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.43-1.510.41781290.40592620274993
1.51-1.60.34991250.3132748287398
1.6-1.720.29481360.25372748288498
1.72-1.90.28651340.19692750288498
1.9-2.170.21541610.18912755291698
2.17-2.740.20871750.18582647282296
2.74-45.240.24741420.18622743288596

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