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- PDB-9r17: De novo designed homodimeric NTF2-like protein with a hydrophobic... -

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Basic information

Entry
Database: PDB / ID: 9r17
TitleDe novo designed homodimeric NTF2-like protein with a hydrophobic pocket
ComponentsNTF0-DIM1-CAV2
KeywordsDE NOVO PROTEIN / NTF2
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 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 25, 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-CAV2


Theoretical massNumber of molelcules
Total (without water)12,5101
Polymers12,5101
Non-polymers00
Water34219
1
A: NTF0-DIM1-CAV2

A: NTF0-DIM1-CAV2


Theoretical massNumber of molelcules
Total (without water)25,0192
Polymers25,0192
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_664-y+1,-x+1,-z-1/61
Buried area2050 Å2
ΔGint-23 kcal/mol
Surface area10560 Å2
MethodPISA
Unit cell
Length a, b, c (Å)56.280, 56.280, 118.590
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122

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Components

#1: Protein NTF0-DIM1-CAV2


Mass: 12509.642 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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 19 / 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: 2.17 Å3/Da / Density % sol: 43.24 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 2.5 M ammonium sulfate, 0.01 M magnesium acetate, MES 0.05 M pH 5.6

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.976 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jul 18, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976 Å / Relative weight: 1
ReflectionResolution: 1.5→39.53 Å / Num. obs: 18616 / % possible obs: 100 % / Redundancy: 25.6 % / CC1/2: 1 / Net I/σ(I): 24.4
Reflection shellResolution: 1.5→1.53 Å / Num. unique obs: 913 / CC1/2: 0.701

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Processing

Software
NameVersionClassification
REFMAC5.8.0430refinement
AUTOMARdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.5→37.68 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.945 / Cross valid method: THROUGHOUT / ESU R: 0.082 / ESU R Free: 0.072 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.21643 887 4.8 %RANDOM
Rwork0.18432 ---
obs0.18576 17664 99.97 %-
Solvent computationIon probe radii: 0.7 Å / Shrinkage radii: 0.7 Å / VDW probe radii: 1 Å / Solvent model: MASK
Displacement parametersBiso mean: 32.319 Å2
Baniso -1Baniso -2Baniso -3
1--0.02 Å2-0.01 Å2-0 Å2
2---0.02 Å20 Å2
3---0.07 Å2
Refinement stepCycle: 1 / Resolution: 1.5→37.68 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms822 0 0 19 841
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.017837
X-RAY DIFFRACTIONr_bond_other_d00.016878
X-RAY DIFFRACTIONr_angle_refined_deg1.7061.8631125
X-RAY DIFFRACTIONr_angle_other_deg0.5841.5672022
X-RAY DIFFRACTIONr_dihedral_angle_1_deg12.2385.268112
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.57410176
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.1010.2133
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.02958
X-RAY DIFFRACTIONr_gen_planes_other0.0090.02170
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it7.4832.711421
X-RAY DIFFRACTIONr_mcangle_it10.2954.879525
X-RAY DIFFRACTIONr_mcangle_other10.335.512526
X-RAY DIFFRACTIONr_scbond_it11.4813.447416
X-RAY DIFFRACTIONr_scbond_other11.509417
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other16.7416.006600
X-RAY DIFFRACTIONr_long_range_B_refined19.22328.31878
X-RAY DIFFRACTIONr_long_range_B_other19.21128.3878
X-RAY DIFFRACTIONr_rigid_bond_restr5.3053837
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.5→1.539 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.205 65 -
Rwork0.169 1262 -
obs--100 %

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