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- PDB-8suc: NHL-2 NHL domain -

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Basic information

Entry
Database: PDB / ID: 8suc
TitleNHL-2 NHL domain
ComponentsNHL (Ring finger b-box coiled coil) domain containing protein
KeywordsRNA BINDING PROTEIN / TRIM / NHL
Function / homology
Function and homology information


positive regulation of development, heterochronic / protein localization to cell cortex / regulation of development, heterochronic / DEAD/H-box RNA helicase binding / P granule / regulation of establishment of cell polarity / P-body / RING-type E3 ubiquitin transferase / ubiquitin protein ligase activity / zinc ion binding
Similarity search - Function
: / NHL repeat / NHL repeat / B-box, C-terminal / B-Box C-terminal domain / Zinc finger, RING-type, eukaryotic / RING-type zinc-finger / B-box zinc finger / B-Box-type zinc finger / B-box-type zinc finger ...: / NHL repeat / NHL repeat / B-box, C-terminal / B-Box C-terminal domain / Zinc finger, RING-type, eukaryotic / RING-type zinc-finger / B-box zinc finger / B-Box-type zinc finger / B-box-type zinc finger / Zinc finger B-box type profile. / Six-bladed beta-propeller, TolB-like / Zinc finger, RING-type, conserved site / Zinc finger RING-type signature. / Ring finger / Zinc finger, RING-type / Zinc finger, RING/FYVE/PHD-type
Similarity search - Domain/homology
RING-type E3 ubiquitin transferase
Similarity search - Component
Biological speciesCaenorhabditis elegans (invertebrata)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 Å
AuthorsColson, R.N. / Wilce, J.A.
Funding support Australia, 1items
OrganizationGrant numberCountry
Australian Research Council (ARC) Australia
CitationJournal: To Be Published
Title: NHL-2 NHL domain
Authors: Colson, R.N. / Wilce, J.A.
History
DepositionMay 12, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 8, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: NHL (Ring finger b-box coiled coil) domain containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,1854
Polymers31,1131
Non-polymers733
Water6,593366
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)82.666, 82.666, 110.048
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212
Space group name HallP4abw2nw
Symmetry operation#1: x,y,z
#2: -y+1/2,x+1/2,z+1/4
#3: y+1/2,-x+1/2,z+3/4
#4: x+1/2,-y+1/2,-z+3/4
#5: -x+1/2,y+1/2,-z+1/4
#6: -x,-y,z+1/2
#7: y,x,-z
#8: -y,-x,-z+1/2
Components on special symmetry positions
IDModelComponents
11A-1437-

HOH

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Components

#1: Protein NHL (Ring finger b-box coiled coil) domain containing protein


Mass: 31112.529 Da / Num. of mol.: 1 / Fragment: NHL domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Caenorhabditis elegans (invertebrata) / Gene: nhl-2, CELE_F26F4.7, F26F4.7 / Production host: Escherichia coli (E. coli) / References: UniProt: Q19818
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 366 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 3.02 Å3/Da / Density % sol: 59.29 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, hanging drop / Details: 0.1 mM Hepes, PEG 4000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Mar 16, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.4→33.53 Å / Num. obs: 75045 / % possible obs: 99.36 % / Redundancy: 9.4 % / Biso Wilson estimate: 16.37 Å2 / CC1/2: 0.999 / Net I/σ(I): 22.13
Reflection shellResolution: 1.4→1.45 Å / Num. unique obs: 7400 / CC1/2: 0.852

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XDSdata reduction
XSCALEdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.4→33.53 Å / SU ML: 0.1437 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 16.5313
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1765 2000 2.67 %
Rwork0.1596 73045 -
obs0.1601 75045 99.29 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 24.91 Å2
Refinement stepCycle: LAST / Resolution: 1.4→33.53 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2184 0 3 366 2553
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00552273
X-RAY DIFFRACTIONf_angle_d0.87033092
X-RAY DIFFRACTIONf_chiral_restr0.0931347
X-RAY DIFFRACTIONf_plane_restr0.0084403
X-RAY DIFFRACTIONf_dihedral_angle_d6.3009314
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.4-1.430.25271380.2135052X-RAY DIFFRACTION97.81
1.43-1.470.24141420.19355170X-RAY DIFFRACTION99.96
1.47-1.520.18171410.1755171X-RAY DIFFRACTION100
1.52-1.570.2041430.18045195X-RAY DIFFRACTION99.96
1.57-1.620.21251420.16455220X-RAY DIFFRACTION99.96
1.62-1.690.17741420.15195174X-RAY DIFFRACTION100
1.69-1.760.16191430.14225217X-RAY DIFFRACTION100
1.76-1.860.16161430.14375204X-RAY DIFFRACTION100
1.86-1.970.15861430.1565244X-RAY DIFFRACTION99.96
1.97-2.120.18221440.14475248X-RAY DIFFRACTION99.98
2.12-2.340.16721440.14355273X-RAY DIFFRACTION99.89
2.34-2.680.1871450.16385292X-RAY DIFFRACTION99.96
2.68-3.370.17941470.16395357X-RAY DIFFRACTION99.89
3.37-33.530.1641430.16395228X-RAY DIFFRACTION93.17

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