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- PDB-3h8z: The Crystal Structure of the Tudor Domains from FXR2 -

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Basic information

Entry
Database: PDB / ID: 3h8z
TitleThe Crystal Structure of the Tudor Domains from FXR2
ComponentsFragile X mental retardation syndrome-related protein 2
KeywordsPROTEIN BINDING / Tudor domains / Fragile X mental retardation / FXR2 / Structural Genomics / Structural Genomics Consortium / SGC / Phosphoprotein / RNA-binding
Function / homology
Function and homology information


: / ribonucleoprotein granule / : / dendritic filopodium / regulation of filopodium assembly / dendritic spine neck / regulation of alternative mRNA splicing, via spliceosome / translation regulator activity / regulation of mRNA stability / mRNA 3'-UTR binding ...: / ribonucleoprotein granule / : / dendritic filopodium / regulation of filopodium assembly / dendritic spine neck / regulation of alternative mRNA splicing, via spliceosome / translation regulator activity / regulation of mRNA stability / mRNA 3'-UTR binding / positive regulation of translation / cytoplasmic ribonucleoprotein granule / presynapse / growth cone / cytosolic large ribosomal subunit / dendritic spine / postsynaptic density / negative regulation of translation / positive regulation of protein phosphorylation / protein heterodimerization activity / axon / mRNA binding / neuronal cell body / protein homodimerization activity / RNA binding / membrane / identical protein binding / nucleus / cytosol / cytoplasm
Similarity search - Function
Fragile X-related protein 1, C-terminal region 1 / Fragile X-related 1 protein C-terminal region 2 / Fragile X messenger ribonucleoprotein 1, C-terminal core / Fragile X messenger ribonucleoprotein 1 / Synaptic functional regulator FMRP, KH0 domain / FMR1, tudor domain / Fragile X-related 1 protein core C terminal / FMRP KH0 domain / Fragile X messenger ribonucleoprotein 1, Tudor domain / Agenet-like domain profile. ...Fragile X-related protein 1, C-terminal region 1 / Fragile X-related 1 protein C-terminal region 2 / Fragile X messenger ribonucleoprotein 1, C-terminal core / Fragile X messenger ribonucleoprotein 1 / Synaptic functional regulator FMRP, KH0 domain / FMR1, tudor domain / Fragile X-related 1 protein core C terminal / FMRP KH0 domain / Fragile X messenger ribonucleoprotein 1, Tudor domain / Agenet-like domain profile. / Agenet-like domain / Agenet domain / KH domain / K Homology domain, type 1 / Type-1 KH domain profile. / SH3 type barrels. - #140 / K Homology domain, type 1 superfamily / K Homology domain / K homology RNA-binding domain / SH3 type barrels. / Roll / Mainly Beta
Similarity search - Domain/homology
Fragile X mental retardation syndrome-related protein 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.92 Å
AuthorsAmaya, M.F. / Dong, A. / Adams-Cioaba, M.A. / Guo, Y. / MacKenzie, F. / Kozieradzki, I. / Edwards, A.M. / Arrowsmith, C.H. / Bochkarev, A. / Min, J. / Structural Genomics Consortium (SGC)
CitationJournal: Plos One / Year: 2010
Title: Structural Studies of the Tandem Tudor Domains of Fragile X Mental Retardation Related Proteins FXR1 and FXR2.
Authors: Adams-Cioaba, M.A. / Guo, Y. / Bian, C. / Amaya, M.F. / Lam, R. / Wasney, G.A. / Vedadi, M. / Xu, C. / Min, J.
History
DepositionApr 29, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 16, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 2017Group: Refinement description / Category: software

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Fragile X mental retardation syndrome-related protein 2


Theoretical massNumber of molelcules
Total (without water)14,8121
Polymers14,8121
Non-polymers00
Water1,13563
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)34.563, 54.676, 70.171
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Fragile X mental retardation syndrome-related protein 2


Mass: 14812.163 Da / Num. of mol.: 1 / Fragment: UNP residues 13-136
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: FXR2, FMR1L2 / Production host: Escherichia coli (E. coli) / References: UniProt: P51116
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 63 / 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: 2.24 Å3/Da / Density % sol: 45.04 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 10 mg/ml protein in 20 mM Tris, pH 8.0, 200 mM NaCl, 1 mM DTT; Hanging drop vapour diffusion,20-30% Peg 3350, 0.2M MgCl2, Hepes 7.5., VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97942 Å
DetectorDate: Mar 18, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97942 Å / Relative weight: 1
ReflectionResolution: 1.92→100 Å / Num. obs: 10551 / % possible obs: 99 % / Redundancy: 6.1 % / Rmerge(I) obs: 0.09 / Χ2: 1.682 / Net I/σ(I): 24.231
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
1.92-1.962.50.6484561.07387
1.96-230.6524781.26596.4
2-2.043.70.6285381.14998.7
2.04-2.085.10.5725021.92899.4
2.08-2.1260.4725051.2599.8
2.12-2.176.20.415491.48699.6
2.17-2.236.40.4025051.57399.6
2.23-2.296.50.3815311.87899.8
2.29-2.366.80.2685251.362100
2.36-2.436.90.2495081.6100
2.43-2.5270.2125341.46100
2.52-2.6270.1755361.262100
2.62-2.7470.155331.254100
2.74-2.8870.1125271.28100
2.88-3.0670.0875291.199100
3.06-3.36.90.075371.322100
3.3-3.636.80.0595391.546100
3.63-4.166.70.065482.219100
4.16-5.246.50.0545582.171100
5.24-10060.0656134.40699.5

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMAC5.2.0019refinement
PDB_EXTRACT3.005data extraction
RefinementMethod to determine structure: SAD / Resolution: 1.92→43.11 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.925 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 3.498 / SU ML: 0.103 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.161 / ESU R Free: 0.151 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25 498 4.8 %RANDOM
Rwork0.21 ---
obs0.212 10430 97.72 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 70.61 Å2 / Biso mean: 32.047 Å2 / Biso min: 16.57 Å2
Baniso -1Baniso -2Baniso -3
1--1.18 Å20 Å20 Å2
2--1.88 Å20 Å2
3----0.7 Å2
Refinement stepCycle: LAST / Resolution: 1.92→43.11 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms873 0 0 63 936
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0210.022897
X-RAY DIFFRACTIONr_angle_refined_deg1.7291.9391222
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8195108
X-RAY DIFFRACTIONr_dihedral_angle_2_deg26.75623.02343
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.30815123
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.748157
X-RAY DIFFRACTIONr_chiral_restr0.1350.2130
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.02708
X-RAY DIFFRACTIONr_nbd_refined0.2210.2328
X-RAY DIFFRACTIONr_nbtor_refined0.3140.2593
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1210.259
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1520.223
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1020.27
X-RAY DIFFRACTIONr_mcbond_it1.5251.5573
X-RAY DIFFRACTIONr_mcangle_it2.3212890
X-RAY DIFFRACTIONr_scbond_it3.3493386
X-RAY DIFFRACTIONr_scangle_it4.634.5332
LS refinement shellResolution: 1.92→1.969 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.336 28 -
Rwork0.263 589 -
all-617 -
obs--80.76 %

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