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- PDB-9r00: De novo NTF2-like protein with a 2-helix C-terminal extension. -

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Basic information

Entry
Database: PDB / ID: 9r00
TitleDe novo NTF2-like protein with a 2-helix C-terminal extension.
ComponentsNTF2_HH
KeywordsDE NOVO PROTEIN / NTF2
Function / homology:
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsNadal, M. / Marcos, E. / Castellvi, A.
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: NTF2_HH
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,36012
Polymers16,4311
Non-polymers92911
Water1267
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1100 Å2
ΔGint-61 kcal/mol
Surface area7180 Å2
MethodPISA
Unit cell
Length a, b, c (Å)40.397, 61.043, 96.117
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222
Components on special symmetry positions
IDModelComponents
11A-202-

CD

21A-207-

CD

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Components

#1: Protein NTF2_HH


Mass: 16430.895 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-CD / CADMIUM ION


Mass: 112.411 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: Cd
#3: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 7 / 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: 1.8 Å3/Da / Density % sol: 31.79 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 27% peg 400, cadmiun chloride 0.1M Sodium acetate 100 mM pH 4.6

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.97918 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Apr 7, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 2→48.1 Å / Num. obs: 8367 / % possible obs: 100 % / Redundancy: 7.1 % / CC1/2: 0.999 / Net I/σ(I): 23.3
Reflection shellResolution: 2→2.05 Å / Num. unique obs: 599 / CC1/2: 0.987

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Processing

Software
NameVersionClassification
REFMAC5refinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→48.1 Å / SU B: 9.964 / SU ML: 0.157 / Cross valid method: THROUGHOUT / ESU R: 0.256 / ESU R Free: 0.206 / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.26391 786 9.4 %RANDOM
Rwork0.21575 ---
obs0.22026 7581 99.93 %-
Displacement parametersBiso mean: 46.005 Å2
Baniso -1Baniso -2Baniso -3
1--0.13 Å20 Å2-0 Å2
2--0.29 Å2-0 Å2
3----0.16 Å2
Refinement stepCycle: LAST / Resolution: 2→48.1 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1083 0 11 7 1101

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