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- PDB-4r9p: An Expansion to the Smad MH2-family: The structure of the N-MH2 e... -

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Basic information

Entry
Database: PDB / ID: 4r9p
TitleAn Expansion to the Smad MH2-family: The structure of the N-MH2 expanded domain
ComponentsRE28239p
KeywordsTRANSCRIPTION / MH2-like domain / Beta-sandwich / Smad/FHA family
Function / homology
Function and homology information


chitin-based embryonic cuticle biosynthetic process / regulation of multicellular organismal process / cytoplasmic side of apical plasma membrane / trachea morphogenesis / regulation of developmental process / post-embryonic development / apical part of cell / regulation of DNA-templated transcription / cytoplasm
Similarity search - Function
Tumour Suppressor Smad4 - #10 / SMAD domain, Dwarfin-type / MH2 domain / MAD homology domain 2 (MH2) profile. / Domain B in dwarfin family proteins / SMAD-like domain superfamily / Tumour Suppressor Smad4 / SMAD/FHA domain superfamily / Sandwich / Mainly Beta
Similarity search - Domain/homology
Expansion, isoform A / RE28239p
Similarity search - Component
Biological speciesDrosophila melanogaster (fruit fly)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.592 Å
AuthorsBeich-Frandsen, M. / Aragon, E. / Llimargas, M. / Benach, J. / Riera, A. / Macias, M.J.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2015
Title: Structure of the N-terminal domain of the protein Expansion: an 'Expansion' to the Smad MH2
Authors: Beich-Frandsen, M. / Aragon, E. / Llimargas, M. / Benach, J. / Riera, A. / Pous, J. / Macias, M.J.
History
DepositionSep 6, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 8, 2015Provider: repository / Type: Initial release
Revision 1.1Feb 28, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: RE28239p


Theoretical massNumber of molelcules
Total (without water)27,9971
Polymers27,9971
Non-polymers00
Water1,35175
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)36.84, 45.67, 54.19
Angle α, β, γ (deg.)90.00, 93.31, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein RE28239p / Expansion N-MH2


Mass: 27997.189 Da / Num. of mol.: 1 / Fragment: N-terminal MH2-like domain, UNP residues 1-240
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Gene: CG13188 / Plasmid: pETM11 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) Rosetta / References: UniProt: Q7YU38, UniProt: A1Z8R1*PLUS
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 75 / 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: 1.63 Å3/Da / Density % sol: 24.33 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 9
Details: 12% v/v 1,2-Propanediol, 9% w/v PEG 20000, 0.1M Glycine, pH 9.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.97952 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 18, 2013
RadiationMonochromator: Si(111) channel-cut, cryocooled / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97952 Å / Relative weight: 1
ReflectionResolution: 1.59→31.27 Å / Num. all: 24247 / Num. obs: 23152 / % possible obs: 95.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 5.89 % / Biso Wilson estimate: 33 Å2 / Rmerge(I) obs: 0.069 / Net I/σ(I): 13.58

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Processing

Software
NameVersionClassification
XDSdata scaling
PHASERphasing
PHENIX(phenix.refine: dev_1701)refinement
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.592→31.267 Å / SU ML: 0.2 / σ(F): 1.39 / Phase error: 23.75 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.1978 1987 8.59 %Random
Rwork0.1765 ---
obs0.1783 23144 95.48 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.592→31.267 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1693 0 0 75 1768
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0191777
X-RAY DIFFRACTIONf_angle_d1.4622406
X-RAY DIFFRACTIONf_dihedral_angle_d13.677711
X-RAY DIFFRACTIONf_chiral_restr0.125266
X-RAY DIFFRACTIONf_plane_restr0.008313
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.592-1.63130.3227920.3469947X-RAY DIFFRACTION61
1.6313-1.67540.35861200.32041327X-RAY DIFFRACTION84
1.6754-1.72470.33331420.30191478X-RAY DIFFRACTION94
1.7247-1.78040.29691460.26021563X-RAY DIFFRACTION100
1.7804-1.8440.23161520.23681581X-RAY DIFFRACTION100
1.844-1.91780.27091470.20321566X-RAY DIFFRACTION100
1.9178-2.00510.20681360.19861580X-RAY DIFFRACTION100
2.0051-2.11080.21051510.17091567X-RAY DIFFRACTION100
2.1108-2.2430.24071490.17251579X-RAY DIFFRACTION100
2.243-2.41610.221520.17781576X-RAY DIFFRACTION100
2.4161-2.65910.20951420.1771593X-RAY DIFFRACTION100
2.6591-3.04360.18071480.17131590X-RAY DIFFRACTION100
3.0436-3.83360.18041550.15311576X-RAY DIFFRACTION100
3.8336-31.27320.1531550.15531634X-RAY DIFFRACTION99

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