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- PDB-8vfq: De novo design apixaban-binding protein: apx1049 -

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Basic information

Entry
Database: PDB / ID: 8vfq
TitleDe novo design apixaban-binding protein: apx1049
ComponentsDe novo designed apixaban-binding protein apx1049
KeywordsDE NOVO PROTEIN / protein design / deep learning / small-molecule-binding / de novo design
Function / homologyChem-GG2
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsBera, A.K. / Lee, G.R. / Baker, D.
Funding support United States, 3items
OrganizationGrant numberCountry
National Institutes of Health/National Institute on Aging (NIH/NIA) United States
Howard Hughes Medical Institute (HHMI) United States
Department of Defense (DOD, United States) United States
CitationJournal: To Be Published
Title: Small-molecule binding and sensing with a designed protein family
Authors: Lee, G.R. / Bera, A.K. / Baker, D.
History
DepositionDec 21, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 25, 2024Provider: 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 apixaban-binding protein apx1049
B: De novo designed apixaban-binding protein apx1049
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,8274
Polymers25,9082
Non-polymers9192
Water1,45981
1
A: De novo designed apixaban-binding protein apx1049
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,4142
Polymers12,9541
Non-polymers4591
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: De novo designed apixaban-binding protein apx1049
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,4142
Polymers12,9541
Non-polymers4591
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)55.470, 60.271, 63.277
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

#1: Protein De novo designed apixaban-binding protein apx1049


Mass: 12954.110 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Production host: Escherichia coli (E. coli)
#2: Chemical ChemComp-GG2 / 1-(4-METHOXYPHENYL)-7-OXO-6-[4-(2-OXOPIPERIDIN-1-YL)PHENYL]-4,5,6,7-TETRAHYDRO-1H-PYRAZOLO[3,4-C]PYRIDINE-3-CARBOXAMIDE


Mass: 459.497 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C25H25N5O4 / Feature type: SUBJECT OF INVESTIGATION / Comment: medication, anticoagulant*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 81 / 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: 1.99 Å3/Da / Density % sol: 39.75 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.1 M Potassium thiocyanate, 30% w/v Polyethylene glycol monomethyl ether 2,000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 0.99996 Å
DetectorType: DECTRIS EIGER2 S 9M / Detector: PIXEL / Date: Nov 16, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99996 Å / Relative weight: 1
ReflectionResolution: 2.1→40.82 Å / Num. obs: 12166 / % possible obs: 94.43 % / Redundancy: 13.2 % / Biso Wilson estimate: 24.65 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.157 / Rpim(I) all: 0.045 / Net I/σ(I): 10.58
Reflection shellResolution: 2.1→2.18 Å / Redundancy: 13.7 % / Rmerge(I) obs: 0.669 / Mean I/σ(I) obs: 4.1 / Num. unique obs: 1278 / CC1/2: 0.989 / Rpim(I) all: 0.186 / % possible all: 91.61

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Processing

Software
NameVersionClassification
PHENIXdev_4761refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.1→40.82 Å / SU ML: 0.3292 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 34.5243
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.3232 1193 9.81 %
Rwork0.2794 10973 -
obs0.2837 12166 94.43 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 26.19 Å2
Refinement stepCycle: LAST / Resolution: 2.1→40.82 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1770 0 68 81 1919
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00271870
X-RAY DIFFRACTIONf_angle_d0.7222520
X-RAY DIFFRACTIONf_chiral_restr0.0448287
X-RAY DIFFRACTIONf_plane_restr0.0032305
X-RAY DIFFRACTIONf_dihedral_angle_d7.001265
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1-2.180.39141260.30931152X-RAY DIFFRACTION91.61
2.18-2.280.33291290.30951203X-RAY DIFFRACTION95.48
2.28-2.40.33341350.27581247X-RAY DIFFRACTION97.39
2.4-2.550.31121430.2921220X-RAY DIFFRACTION96.67
2.55-2.750.36081310.27841268X-RAY DIFFRACTION99.01
2.75-3.030.32111350.27221265X-RAY DIFFRACTION97.83
3.03-3.470.33931430.27461212X-RAY DIFFRACTION95.29
3.47-4.370.30631110.26421213X-RAY DIFFRACTION90.93
4.37-40.820.29521400.28151193X-RAY DIFFRACTION86.56

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