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- PDB-9qzd: de novo NTF2-like protein -

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Basic information

Entry
Database: PDB / ID: 9qzd
Titlede novo NTF2-like protein
ComponentsdNTH0-H1
KeywordsDE NOVO PROTEIN / NTF2
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsNadal, M. / Marcos, E. / Castellvi, A.
Funding support Spain, 1items
OrganizationGrant numberCountry
Spanish National Research Council 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 22, 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: dNTH0-H1
B: dNTH0-H1
C: dNTH0-H1


Theoretical massNumber of molelcules
Total (without water)43,3423
Polymers43,3423
Non-polymers00
Water362
1
A: dNTH0-H1


Theoretical massNumber of molelcules
Total (without water)14,4471
Polymers14,4471
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: dNTH0-H1


Theoretical massNumber of molelcules
Total (without water)14,4471
Polymers14,4471
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: dNTH0-H1


Theoretical massNumber of molelcules
Total (without water)14,4471
Polymers14,4471
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)36.829, 62.021, 80.443
Angle α, β, γ (deg.)90.00, 102.50, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein dNTH0-H1


Mass: 14447.486 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Production host: Escherichia coli (E. coli)
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: H2O
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: 2.12 Å3/Da / Density % sol: 41.95 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 27% PEG 3350, 0.1M Bis-Tris pH 5.4

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.98 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Oct 1, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.4→78.54 Å / Num. obs: 12468 / % possible obs: 93.6 % / Redundancy: 1.6 % / CC1/2: 0.999 / Net I/σ(I): 6.8
Reflection shellResolution: 2.4→2.462 Å / Rmerge(I) obs: 1.524 / Num. unique obs: 1023 / CC1/2: 0.664

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Processing

Software
NameVersionClassification
REFMAC5refinement
PDB_EXTRACTdata extraction
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.4→78.54 Å / SU B: 36.586 / SU ML: 0.337 / Cross valid method: THROUGHOUT / ESU R: 1.306 / ESU R Free: 0.312 / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.25607 631 4.8 %RANDOM
Rwork0.22281 ---
obs0.2245 12468 93.62 %-
Displacement parametersBiso mean: 39.483 Å2
Baniso -1Baniso -2Baniso -3
1-2.09 Å20 Å2-3.72 Å2
2--7.98 Å20 Å2
3----7.67 Å2
Refinement stepCycle: LAST / Resolution: 2.4→78.54 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2980 0 0 2 2982

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