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- PDB-9r0t: De novo designed homodimeric NTF2-like protein with a hydrophobic... -

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Basic information

Entry
Database: PDB / ID: 9r0t
TitleDe novo designed homodimeric NTF2-like protein with a hydrophobic pocket
ComponentsNTF0-DIM1_CAV3
KeywordsDE NOVO PROTEIN / NTF2
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsNadal, M. / Marcos, E.
Funding support Spain, 3items
OrganizationGrant numberCountry
Spanish Ministry of Science, Innovation, and UniversitiesRYC2018-025295-I Spain
Spanish Ministry of Science, Innovation, and UniversitiesEUR2020-112164 Spain
Spanish Ministry of Science, Innovation, and UniversitiesCNS2023-144990 Spain
CitationJournal: Protein Sci. / Year: 2025
Title: Buttressing ligand-binding pockets in de novo designed NTF2-like domains.
Authors: Nadal, M. / Albi-Puig, J. / Castellvi, A. / Garcia-Franco, P.M. / Vega, S. / Velazquez-Campoy, A. / Marcos, E.
History
DepositionApr 24, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 22, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: NTF0-DIM1_CAV3
B: NTF0-DIM1_CAV3
C: NTF0-DIM1_CAV3
D: NTF0-DIM1_CAV3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,66111
Polymers50,2034
Non-polymers4587
Water1,74797
1
A: NTF0-DIM1_CAV3
B: NTF0-DIM1_CAV3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,4948
Polymers25,1022
Non-polymers3926
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2380 Å2
ΔGint-112 kcal/mol
Surface area11000 Å2
2
C: NTF0-DIM1_CAV3
D: NTF0-DIM1_CAV3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,1673
Polymers25,1022
Non-polymers651
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2280 Å2
ΔGint-90 kcal/mol
Surface area10830 Å2
Unit cell
Length a, b, c (Å)149.680, 39.262, 95.261
Angle α, β, γ (deg.)90.00, 120.61, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein
NTF0-DIM1_CAV3


Mass: 12550.779 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Production host: Escherichia coli (E. coli)
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: Zn
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 97 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
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: 2.4 Å3/Da / Density % sol: 48.74 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 23 % peg 3350 0.05M Zinc Acetate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.979 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jun 14, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.9→81.98 Å / Num. obs: 38057 / % possible obs: 99.9 % / Redundancy: 6.1 % / CC1/2: 0.99 / Net I/σ(I): 14.1
Reflection shellResolution: 1.9→1.94 Å / Num. unique obs: 2444 / CC1/2: 0.825

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Processing

Software
NameVersionClassification
REFMAC5refinement
autoPROCdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.9→71.36 Å / SU B: 6.76 / SU ML: 0.101 / Cross valid method: THROUGHOUT / ESU R: 0.149 / ESU R Free: 0.14 / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.23876 1835 4.8 %RANDOM
Rwork0.20151 ---
obs0.2033 36217 99.83 %-
Displacement parametersBiso mean: 43.889 Å2
Baniso -1Baniso -2Baniso -3
1--0.09 Å20 Å2-0.36 Å2
2--0.59 Å20 Å2
3----0.04 Å2
Refinement stepCycle: LAST / Resolution: 1.9→71.36 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3227 0 7 97 3331

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