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- PDB-3d3j: Crystal structure of human Edc3p -

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Basic information

Entry
Database: PDB / ID: 3d3j
TitleCrystal structure of human Edc3p
ComponentsEnhancer of mRNA-decapping protein 3
KeywordsPROTEIN BINDING / hEdc3 / Phosphoprotein
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
Lsm16, N-terminal / Scd6-like Sm domain / Scd6-like Sm domain / Lsm14-like, N-terminal / FDF domain / FDF domain / DFDF domain profile. / DFDF domain / FDF / YjeF N-terminal domain ...Lsm16, N-terminal / Scd6-like Sm domain / Scd6-like Sm domain / Lsm14-like, N-terminal / FDF domain / FDF domain / DFDF domain profile. / DFDF domain / FDF / YjeF N-terminal domain / YjeF N-terminal domain superfamily / YjeF-related protein N-terminus / YjeF N-terminal domain profile. / YjeF N-terminal domain / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Enhancer of mRNA-decapping protein 3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsLing, S.H.M.
CitationJournal: Mol.Cell.Biol. / Year: 2008
Title: Crystal structure of human Edc3 and its functional implications
Authors: Ling, S.H.M. / Decker, C.J. / Walsh, M.A. / She, M. / Parker, R. / Song, H.
History
DepositionMay 12, 2008Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Aug 26, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance

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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)34,1701
Polymers34,1701
Non-polymers00
Water54030
1
A: Enhancer of mRNA-decapping protein 3

A: Enhancer of mRNA-decapping protein 3


Theoretical massNumber of molelcules
Total (without water)68,3402
Polymers68,3402
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation15_545y+1/2,x-1/2,-z+1/21
Buried area3520 Å2
ΔGint-2 kcal/mol
Surface area19980 Å2
MethodPISA
Unit cell
Length a, b, c (Å)119.741, 119.741, 93.923
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number97
Space group name H-MI422
Components on special symmetry positions
IDModelComponents
11A-12-

HOH

21A-22-

HOH

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Components

#1: Protein Enhancer of mRNA-decapping protein 3 / YjeF domain-containing protein 1 / LSM16 homolog


Mass: 34170.098 Da / Num. of mol.: 1 / Fragment: C-terminal Residues, UNP 203-508
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: EDC3 / Plasmid: pGEX-6p1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q96F86
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 30 / 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: 2.46 Å3/Da / Density % sol: 50.06 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: PEG 6000, sodium cacodylate, magnesium acetate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 10, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionHighest resolution: 2.8 Å / Num. all: 9673 / Num. obs: 9673

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3D3K
Resolution: 2.8→20 Å / Cor.coef. Fo:Fc: 0.941 / Cor.coef. Fo:Fc free: 0.9 / SU B: 48.974 / SU ML: 0.426 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.887 / ESU R Free: 0.388 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.29062 419 4.8 %RANDOM
Rwork0.22901 ---
obs0.23197 8273 99.97 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 76.149 Å2
Baniso -1Baniso -2Baniso -3
1-3.94 Å2-0 Å2-0 Å2
2--3.94 Å20 Å2
3----7.87 Å2
Refinement stepCycle: LAST / Resolution: 2.8→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1791 0 0 30 1821
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0221833
X-RAY DIFFRACTIONr_angle_refined_deg0.9781.9772492
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.9545227
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.37524.1173
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.58615309
X-RAY DIFFRACTIONr_dihedral_angle_4_deg8.721159
X-RAY DIFFRACTIONr_chiral_restr0.0660.2289
X-RAY DIFFRACTIONr_gen_planes_refined0.0020.021361
X-RAY DIFFRACTIONr_nbd_refined0.1810.2849
X-RAY DIFFRACTIONr_nbtor_refined0.2990.21229
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1710.262
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2330.248
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1590.26
X-RAY DIFFRACTIONr_mcbond_it0.211.51180
X-RAY DIFFRACTIONr_mcangle_it0.39621872
X-RAY DIFFRACTIONr_scbond_it0.4723725
X-RAY DIFFRACTIONr_scangle_it0.7924.5620
LS refinement shellResolution: 2.8→2.871 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.383 33 -
Rwork0.309 609 -
obs--100 %
Refinement TLS params.Method: refined / Origin x: 19.5418 Å / Origin y: -40.6056 Å / Origin z: 9.4753 Å
111213212223313233
T-0.2128 Å2-0.2717 Å2-0.0524 Å2-0.2172 Å2-0.0493 Å2---0.205 Å2
L7.069 °2-1.7571 °2-0.5983 °2-4.3856 °2-0.7318 °2--7.3908 °2
S0.1968 Å °1.4222 Å °-0.3399 Å °-0.352 Å °-0.2431 Å °0.1725 Å °1.0336 Å °-1.3006 Å °0.0463 Å °

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