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- PDB-4e5r: Crystal Structure of Frog DGCR8 Dimerization Domain -

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Basic information

Entry
Database: PDB / ID: 4e5r
TitleCrystal Structure of Frog DGCR8 Dimerization Domain
ComponentsMGC78846 protein
KeywordsRNA BINDING PROTEIN / Dimerization / WW motif / domain swapping
Function / homology
Function and homology information


primary miRNA processing / microprocessor complex / heme binding / RNA binding / identical protein binding
Similarity search - Function
Microprocessor complex subunit DGCR8 / Ubiquitin Ligase Nedd4; Chain: W; - #10 / Ubiquitin Ligase Nedd4; Chain: W; / Double-stranded RNA binding motif / Double-stranded RNA binding motif / Double stranded RNA-binding domain (dsRBD) profile. / Double-stranded RNA-binding domain / WW domain superfamily / WW/rsp5/WWP domain profile. / Domain with 2 conserved Trp (W) residues ...Microprocessor complex subunit DGCR8 / Ubiquitin Ligase Nedd4; Chain: W; - #10 / Ubiquitin Ligase Nedd4; Chain: W; / Double-stranded RNA binding motif / Double-stranded RNA binding motif / Double stranded RNA-binding domain (dsRBD) profile. / Double-stranded RNA-binding domain / WW domain superfamily / WW/rsp5/WWP domain profile. / Domain with 2 conserved Trp (W) residues / WW domain / Single Sheet / Mainly Beta
Similarity search - Domain/homology
Biological speciesXenopus laevis (African clawed frog)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsGuo, F. / Senturia, R. / Laganowsky, A. / Barr, I. / Scheidemantle, B.D.
CitationJournal: Plos One / Year: 2012
Title: Dimerization and heme binding are conserved in amphibian and starfish homologues of the microRNA processing protein DGCR8.
Authors: Senturia, R. / Laganowsky, A. / Barr, I. / Scheidemantle, B.D. / Guo, F.
History
DepositionMar 14, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 27, 2013Provider: repository / Type: Initial release
Revision 1.1Feb 28, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: MGC78846 protein


Theoretical massNumber of molelcules
Total (without water)6,3791
Polymers6,3791
Non-polymers00
Water48627
1
A: MGC78846 protein

A: MGC78846 protein


Theoretical massNumber of molelcules
Total (without water)12,7592
Polymers12,7592
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_645y+1,x-1,-z1
Buried area2860 Å2
ΔGint-19 kcal/mol
Surface area6690 Å2
MethodPISA
Unit cell
Length a, b, c (Å)39.891, 39.891, 82.125
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212
Components on special symmetry positions
IDModelComponents
11A-417-

HOH

21A-427-

HOH

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Components

#1: Protein MGC78846 protein


Mass: 6379.329 Da / Num. of mol.: 1 / Fragment: Dimerization Domain (UNP residues 300-355)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Xenopus laevis (African clawed frog) / Gene: dgcr8, MGC78846 / Plasmid: pET24a+ / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q6IRB5
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 27 / Source method: isolated from a natural source / Formula: H2O

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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: 2.56 Å3/Da / Density % sol: 51.97 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 20% (w/v) PEG-1000, 0.1 M imidazole pH 8.0, 0.2 M calcium acetate, 100 mM tribasic sodium citrate, vapor diffusion, hanging drop, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E+ SUPERBRIGHT / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS HTC / Detector: IMAGE PLATE / Date: Nov 1, 2010
RadiationMonochromator: CONFOCAL MIRRORS Varimax HF / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.9→80 Å / Num. all: 5691 / Num. obs: 5640 / % possible obs: 98.99 % / Redundancy: 11.5 % / Biso Wilson estimate: 33.21 Å2 / Rsym value: 0.1 / Net I/σ(I): 1.23
Reflection shellResolution: 1.9→1.97 Å / % possible obs: 99.6 % / Redundancy: 6.6 % / Mean I/σ(I) obs: 3.38 / Rsym value: 0.459

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
PHENIX1.7.3_928refinement
PDB_EXTRACT3.1data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.9→35.882 Å / Occupancy max: 1 / Occupancy min: 0.46 / FOM work R set: 0.8483 / SU ML: 0.24 / σ(F): 0 / Phase error: 20.41 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.228 560 10.01 %
Rwork0.2068 --
obs0.2088 5593 98.99 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 45.004 Å2 / ksol: 0.387 e/Å3
Displacement parametersBiso max: 81.82 Å2 / Biso mean: 34.9949 Å2 / Biso min: 22.72 Å2
Baniso -1Baniso -2Baniso -3
1-6.2576 Å20 Å2-0 Å2
2--6.2576 Å2-0 Å2
3----12.5151 Å2
Refinement stepCycle: LAST / Resolution: 1.9→35.882 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms450 0 0 27 477
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.007469
X-RAY DIFFRACTIONf_angle_d1.109644
X-RAY DIFFRACTIONf_chiral_restr0.06969
X-RAY DIFFRACTIONf_plane_restr0.00581
X-RAY DIFFRACTIONf_dihedral_angle_d11.561173
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 4

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.9002-2.09140.2651360.242712231359100
2.0914-2.3940.25021370.185212311368100
2.394-3.0160.23111410.204512591400100
3.016-35.88840.21691460.20751320146697

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