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- PDB-8ek4: De novo designed ice-binding proteins from twist-constrained helices -

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Basic information

Entry
Database: PDB / ID: 8ek4
TitleDe novo designed ice-binding proteins from twist-constrained helices
ComponentsIce-binding protein TIP-99a
KeywordsDE NOVO PROTEIN / De novo designed / ice-binding proteins
Function / homologyApolipoprotein / Four Helix Bundle (Hemerythrin (Met), subunit A) / Up-down Bundle / Mainly Alpha
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.35 Å
AuthorsBera, A.K. / De Haas, R.J.
Funding supportEuropean Union, 1items
OrganizationGrant numberCountry
European Research Council (ERC)European Union
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2023
Title: De novo designed ice-binding proteins from twist-constrained helices.
Authors: de Haas, R.J. / Tas, R.P. / van den Broek, D. / Zheng, C. / Nguyen, H. / Kang, A. / Bera, A.K. / King, N.P. / Voets, I.K. / de Vries, R.
History
DepositionSep 19, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 12, 2023Provider: repository / Type: Initial release
Revision 1.1Apr 3, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Ice-binding protein TIP-99a
B: Ice-binding protein TIP-99a


Theoretical massNumber of molelcules
Total (without water)33,1922
Polymers33,1922
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2190 Å2
ΔGint-16 kcal/mol
Surface area15750 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.582, 67.427, 74.326
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 Ice-binding protein TIP-99a


Mass: 16595.877 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)

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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: 2.06 Å3/Da / Density % sol: 40.3 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.02M 1,6-hexanediol, 0.02M 1-butanol, 0.02M 1,2-propanediol, 0.02M 2-propanol, 0.02M 2-propanol, 0.02M 1,4-butanediol, 0.02M 1,3-propanediol, 0.0466M pH 8.5 Tris (base), 0.0534M pH 8.5 ...Details: 0.02M 1,6-hexanediol, 0.02M 1-butanol, 0.02M 1,2-propanediol, 0.02M 2-propanol, 0.02M 2-propanol, 0.02M 1,4-butanediol, 0.02M 1,3-propanediol, 0.0466M pH 8.5 Tris (base), 0.0534M pH 8.5 Bicine, 20% v/v PEG 500 MME, and 10% w/v PEG 20,000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.97918 Å
DetectorType: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Mar 14, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 2.35→59.94 Å / Num. obs: 11928 / % possible obs: 99.62 % / Redundancy: 13.2 % / Biso Wilson estimate: 60.27 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.114 / Rpim(I) all: 0.033 / Rrim(I) all: 0.119 / Net I/σ(I): 13.8
Reflection shellResolution: 2.35→2.43 Å / Rmerge(I) obs: 1.379 / Mean I/σ(I) obs: 1.55 / Num. unique obs: 1172 / CC1/2: 0.753 / Rpim(I) all: 0.381

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Designed model

Resolution: 2.35→49.94 Å / SU ML: 0.31 / Cross valid method: FREE R-VALUE / σ(F): 0.31 / Phase error: 35.9447
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.3137 553 4.65 %
Rwork0.2589 11335 -
obs0.2614 11888 99.62 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 83.35 Å2
Refinement stepCycle: LAST / Resolution: 2.35→49.94 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2165 0 0 0 2165
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00212171
X-RAY DIFFRACTIONf_angle_d0.36572882
X-RAY DIFFRACTIONf_chiral_restr0.0279351
X-RAY DIFFRACTIONf_plane_restr0.0016352
X-RAY DIFFRACTIONf_dihedral_angle_d12.4956910
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.35-2.590.34591200.27382810X-RAY DIFFRACTION100
2.59-2.960.37641440.28782778X-RAY DIFFRACTION99.8
2.96-3.730.38911470.30122819X-RAY DIFFRACTION99.93
3.73-49.940.2661420.2332928X-RAY DIFFRACTION98.81

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