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- PDB-9h4a: Ribonuclease-three Like 4 crystallization and structure determina... -

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Basic information

Entry
Database: PDB / ID: 9h4a
TitleRibonuclease-three Like 4 crystallization and structure determination at room temperature in the CrystalChip
ComponentsProtein NUCLEAR FUSION DEFECTIVE 2
KeywordsRNA BINDING PROTEIN / Ribonuclease-three like / microfluidics / room temperature / RTL4
Function / homology
Function and homology information


polar nucleus fusion / karyogamy / ribonuclease III activity / plant-type vacuole / RNA processing / peroxisome
Similarity search - Function
Ribonuclease-III-like / Ribonuclease III family domain profile. / Ribonuclease III family / Ribonuclease III domain / Ribonuclease III, endonuclease domain superfamily
Similarity search - Domain/homology
Protein NUCLEAR FUSION DEFECTIVE 2
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsEngilberge, S. / Vincent, R. / Coudray, L. / Nilles, L. / Scheer, H. / Ritzenthaler, C. / Sauter, C.
Funding support France, 2items
OrganizationGrant numberCountry
Centre National de la Recherche Scientifique (CNRS) France
Agence Nationale de la Recherche (ANR)ANR-10-LABX-0036_NETRNA France
Citation
Journal: Febs Open Bio / Year: 2025
Title: Protein crystallization and structure determination at room temperature in the CrystalChip.
Authors: Pachl, P. / Coudray, L. / Vincent, R. / Nilles, L. / Scheer, H. / Ritzenthaler, C. / Fejfarova, A. / Rezacova, P. / Engilberge, S. / Sauter, C.
#1: Journal: Acta Crystallogr D Struct Biol / Year: 2019
Title: Macromolecular structure determination using X-rays, neutrons and electrons: recent developments in Phenix.
Authors: Dorothee Liebschner / Pavel V Afonine / Matthew L Baker / Gábor Bunkóczi / Vincent B Chen / Tristan I Croll / Bradley Hintze / Li Wei Hung / Swati Jain / Airlie J McCoy / Nigel W Moriarty ...Authors: Dorothee Liebschner / Pavel V Afonine / Matthew L Baker / Gábor Bunkóczi / Vincent B Chen / Tristan I Croll / Bradley Hintze / Li Wei Hung / Swati Jain / Airlie J McCoy / Nigel W Moriarty / Robert D Oeffner / Billy K Poon / Michael G Prisant / Randy J Read / Jane S Richardson / David C Richardson / Massimo D Sammito / Oleg V Sobolev / Duncan H Stockwell / Thomas C Terwilliger / Alexandre G Urzhumtsev / Lizbeth L Videau / Christopher J Williams / Paul D Adams /
Abstract: Diffraction (X-ray, neutron and electron) and electron cryo-microscopy are powerful methods to determine three-dimensional macromolecular structures, which are required to understand biological ...Diffraction (X-ray, neutron and electron) and electron cryo-microscopy are powerful methods to determine three-dimensional macromolecular structures, which are required to understand biological processes and to develop new therapeutics against diseases. The overall structure-solution workflow is similar for these techniques, but nuances exist because the properties of the reduced experimental data are different. Software tools for structure determination should therefore be tailored for each method. Phenix is a comprehensive software package for macromolecular structure determination that handles data from any of these techniques. Tasks performed with Phenix include data-quality assessment, map improvement, model building, the validation/rebuilding/refinement cycle and deposition. Each tool caters to the type of experimental data. The design of Phenix emphasizes the automation of procedures, where possible, to minimize repetitive and time-consuming manual tasks, while default parameters are chosen to encourage best practice. A graphical user interface provides access to many command-line features of Phenix and streamlines the transition between programs, project tracking and re-running of previous tasks.
History
DepositionOct 18, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 11, 2024Provider: repository / Type: Initial release
Revision 1.1Apr 16, 2025Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year / _citation_author.identifier_ORCID

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Protein NUCLEAR FUSION DEFECTIVE 2
B: Protein NUCLEAR FUSION DEFECTIVE 2


Theoretical massNumber of molelcules
Total (without water)35,2182
Polymers35,2182
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: SAXS
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2370 Å2
ΔGint-19 kcal/mol
Surface area13160 Å2
MethodPISA
Unit cell
Length a, b, c (Å)48.130, 101.530, 134.030
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Space group name HallC2c2
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y,-z+1/2
#4: -x,-y,z+1/2
#5: x+1/2,y+1/2,z
#6: x+1/2,-y+1/2,-z
#7: -x+1/2,y+1/2,-z+1/2
#8: -x+1/2,-y+1/2,z+1/2

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Components

#1: Protein Protein NUCLEAR FUSION DEFECTIVE 2


Mass: 17609.178 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: NFD2, At1g24450, F21J9.11 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9FYL8
Has protein modificationY

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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: 2.32 Å3/Da / Density % sol: 47.09 %
Crystal growTemperature: 293 K / Method: counter-diffusion
Details: Protein crystallized by counter-diffusion in the CrystalChip, stock solution at 4 mg/mL, in a reservoir containing 14% (w/v) PEG 3350, 50 mM Bis-TRIS-HCl at pH 6.5 to 7.0
PH range: 6.5-7.0

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Data collection

DiffractionMean temperature: 293 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM07 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 16, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.8→50 Å / Num. obs: 64222 / % possible obs: 92.5 % / Redundancy: 8.23 % / Biso Wilson estimate: 62.8 Å2 / CC1/2: 0.974 / Net I/σ(I): 4.4
Reflection shellResolution: 2.8→2.87 Å / Num. unique obs: 3046 / CC1/2: 0.303

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Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.8→47.47 Å / SU ML: 0.4522 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 27.4682
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.256 382 4.95 %
Rwork0.2136 7336 -
obs0.2157 7718 91.72 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 59.26 Å2
Refinement stepCycle: LAST / Resolution: 2.8→47.47 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2131 0 0 0 2131
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00112159
X-RAY DIFFRACTIONf_angle_d0.3142913
X-RAY DIFFRACTIONf_chiral_restr0.032351
X-RAY DIFFRACTIONf_plane_restr0.0016369
X-RAY DIFFRACTIONf_dihedral_angle_d10.6921769
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.8-3.210.351090.31672138X-RAY DIFFRACTION82.13
3.21-4.040.30511370.22292614X-RAY DIFFRACTION98.67
4.04-47.470.20721360.18382584X-RAY DIFFRACTION94.09

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