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- PDB-9r0z: De novo designed homodimeric NTF2-like protein -

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Basic information

Entry
Database: PDB / ID: 9r0z
TitleDe novo designed homodimeric NTF2-like protein
ComponentsNTF0-DIM1
KeywordsDE NOVO PROTEIN / NTF2
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 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

Downloads & links

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Assembly

Deposited unit
A: NTF0-DIM1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,9062
Polymers12,8411
Non-polymers651
Water905
1
A: NTF0-DIM1
hetero molecules

A: NTF0-DIM1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,8134
Polymers25,6822
Non-polymers1312
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555x,-y,-z1
Buried area2190 Å2
ΔGint-60 kcal/mol
Surface area9770 Å2
MethodPISA
Unit cell
Length a, b, c (Å)37.321, 37.883, 68.669
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP22121

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Components

#1: Protein NTF0-DIM1


Mass: 12840.880 Da / Num. of mol.: 1
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.: 1 / Source method: obtained synthetically / Formula: Zn
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 5 / 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: 1.89 Å3/Da / Density % sol: 34.93 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 23 % peg 3350 , Zinc acetate 0.05M

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.97926 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Oct 5, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97926 Å / Relative weight: 1
ReflectionResolution: 2→37.88 Å / Num. obs: 18616 / % possible obs: 100 % / Redundancy: 6.8 % / CC1/2: 1 / Net I/σ(I): 31.7
Reflection shellResolution: 2→2.05 Å / Num. unique obs: 504 / CC1/2: 0.994

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Processing

Software
NameVersionClassification
REFMAC5refinement
autoPROCdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→37.32 Å / SU B: 4.565 / SU ML: 0.128 / Cross valid method: THROUGHOUT / ESU R: 0.226 / ESU R Free: 0.191 / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.25736 686 9.8 %RANDOM
Rwork0.21176 ---
obs0.2162 6300 99.89 %-
Displacement parametersBiso mean: 42.882 Å2
Baniso -1Baniso -2Baniso -3
1--5.03 Å2-0 Å20 Å2
2--5.33 Å2-0 Å2
3----0.29 Å2
Refinement stepCycle: LAST / Resolution: 2→37.32 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms806 0 1 5 812

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