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- PDB-2vc8: Crystal structure of the LSm domain of human EDC3 (enhancer of de... -

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Basic information

Entry
Database: PDB / ID: 2vc8
TitleCrystal structure of the LSm domain of human EDC3 (enhancer of decapping 3)
ComponentsENHANCER OF MRNA-DECAPPING PROTEIN 3
KeywordsPROTEIN BINDING / P-BODY COMPONENT / ENHANCER OF MRNA DECAPPING / RNA / CYTOPLASM / SM-LIKE PROTEIN / PROTEIN-BINDING
Function / homology
Function and homology information


deadenylation-independent decapping of nuclear-transcribed mRNA / mRNA decay by 5' to 3' exoribonuclease / P-body assembly / P-body / cytoplasmic ribonucleoprotein granule / mRNA binding / membrane / identical protein binding / cytosol
Similarity search - Function
Linker region of enhancer of mRNA-decapping protein 3 / Lsm16, N-terminal / Scd6-like Sm domain / Lsm14-like, N-terminal / Scd6-like Sm domain / FDF domain / FDF domain / DFDF domain / DFDF domain profile. / FDF ...Linker region of enhancer of mRNA-decapping protein 3 / Lsm16, N-terminal / Scd6-like Sm domain / Lsm14-like, N-terminal / Scd6-like Sm domain / FDF domain / FDF domain / DFDF domain / DFDF domain profile. / FDF / YjeF N-terminal domain superfamily / YjeF-related protein N-terminus / YjeF N-terminal domain / YjeF N-terminal domain profile. / SH3 type barrels. - #100 / : / Sm domain profile. / SH3 type barrels. / Roll / Mainly Beta
Similarity search - Domain/homology
Enhancer of mRNA-decapping protein 3
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.31 Å
AuthorsTritschler, F. / Hartmann, M.D. / Weichenrieder, O.
CitationJournal: Mol.Cell.Biol. / Year: 2007
Title: A Divergent Sm Fold in Edc3 Proteins Mediates Dcp1 Binding and P-Body Targeting.
Authors: Tritschler, F. / Eulalio, A. / Truffault, V. / Hartmann, M.D. / Helms, S. / Schmidt, S. / Coles, M. / Izaurralde, E. / Weichenrieder, O.
History
DepositionSep 19, 2007Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 16, 2007Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Remark 700 SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: ENHANCER OF MRNA-DECAPPING PROTEIN 3


Theoretical massNumber of molelcules
Total (without water)8,9881
Polymers8,9881
Non-polymers00
Water97354
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)37.300, 37.300, 79.209
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein ENHANCER OF MRNA-DECAPPING PROTEIN 3 / YJEF DOMAIN-CONTAINING PROTEIN 1 / LSM16 HOMOLOG / HUMAN EDC3 / EDC3


Mass: 8988.077 Da / Num. of mol.: 1 / Fragment: LSM DOMAIN, RESIDUES 1-82
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PETM60 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 (DE3) ROSETTA II / References: UniProt: Q96F86
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 54 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE CRYSTALLIZED SEQUENCE CORRESPONDS TO RESIDUES 1-82 OF HUMAN EDC3 PLUS TWO N-TERMINAL RESIDUES ...THE CRYSTALLIZED SEQUENCE CORRESPONDS TO RESIDUES 1-82 OF HUMAN EDC3 PLUS TWO N-TERMINAL RESIDUES (GA) REMAINING FROM THE PURIFICATION TAG

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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: 1.77 Å3/Da / Density % sol: 30.6 % / Description: NONE
Crystal growpH: 4.1
Details: 40 MM NA-PROPIONATE, 20 MM NA-CACODYLATE, 40 MM BIS-TRIS-PROPANE, PH=4.1, 32% PEG1500

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: MPG/DESY, HAMBURG / Beamline: BW6 / Wavelength: 1.05
DetectorType: MARRESEARCH / Detector: CCD / Date: Mar 9, 2007 / Details: MIRRORS
RadiationMonochromator: SI111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.05 Å / Relative weight: 1
ReflectionResolution: 1.31→18.7 Å / Num. obs: 15783 / % possible obs: 98.6 % / Redundancy: 12.9 % / Rmerge(I) obs: 0.05 / Net I/σ(I): 15.5
Reflection shellResolution: 1.31→1.33 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.28 / Mean I/σ(I) obs: 4.7 / % possible all: 99.8

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
DENZOdata reduction
SCALEPACKdata scaling
autoSHARPphasing
RefinementMethod to determine structure: SAD
Starting model: NONE

Resolution: 1.31→18.65 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.954 / SU B: 2.467 / SU ML: 0.049 / Cross valid method: THROUGHOUT / ESU R: 0.071 / ESU R Free: 0.066 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.231 758 4.9 %RANDOM
Rwork0.196 ---
obs0.198 14787 97.3 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 18.3 Å2
Baniso -1Baniso -2Baniso -3
1--0.54 Å2-0.27 Å20 Å2
2---0.54 Å20 Å2
3---0.81 Å2
Refinement stepCycle: LAST / Resolution: 1.31→18.65 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms541 0 0 54 595
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.022632
X-RAY DIFFRACTIONr_bond_other_d0.0030.02426
X-RAY DIFFRACTIONr_angle_refined_deg1.7521.973882
X-RAY DIFFRACTIONr_angle_other_deg1.0231070
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.084596
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.0492526
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.70215114
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.732154
X-RAY DIFFRACTIONr_chiral_restr0.1140.2108
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.02732
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02119
X-RAY DIFFRACTIONr_nbd_refined0.2050.2118
X-RAY DIFFRACTIONr_nbd_other0.2090.2438
X-RAY DIFFRACTIONr_nbtor_refined0.1670.2324
X-RAY DIFFRACTIONr_nbtor_other0.0870.2359
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1860.241
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2430.211
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2120.239
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1770.27
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it6.27624545
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it6.72132672
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it7.77348278
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it9.18572197
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.31→1.34 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.383 52
Rwork0.313 1109

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