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- PDB-1mhn: High resolution crystal structure of the SMN Tudor domain -

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Basic information

Entry
Database: PDB / ID: 1mhn
TitleHigh resolution crystal structure of the SMN Tudor domain
ComponentsSurvival motor neuron protein
KeywordsRNA BINDING PROTEIN / SMN / SMA / spinal muscular atrophy
Function / homology
Function and homology information


Gemini of Cajal bodies / SMN complex / SMN-Sm protein complex / spliceosomal complex assembly / spliceosomal snRNP assembly / Cajal body / DNA-templated transcription termination / Z disc / cytoplasmic ribonucleoprotein granule / nervous system development ...Gemini of Cajal bodies / SMN complex / SMN-Sm protein complex / spliceosomal complex assembly / spliceosomal snRNP assembly / Cajal body / DNA-templated transcription termination / Z disc / cytoplasmic ribonucleoprotein granule / nervous system development / snRNP Assembly / SARS-CoV-2 modulates host translation machinery / perikaryon / neuron projection / nuclear body / axon / RNA binding / nucleoplasm / identical protein binding / nucleus / cytosol / cytoplasm
Similarity search - Function
: / : / Survival Motor Neuron, YG-box / Survival Motor Neuron, Gemin2-binding domain / SMN complex subunit Smn1 / : / Survival motor neuron, Tudor domain / Survival motor neuron protein (SMN), Tudor domain / Tudor domain profile. / Tudor domain ...: / : / Survival Motor Neuron, YG-box / Survival Motor Neuron, Gemin2-binding domain / SMN complex subunit Smn1 / : / Survival motor neuron, Tudor domain / Survival motor neuron protein (SMN), Tudor domain / Tudor domain profile. / Tudor domain / Tudor domain / SH3 type barrels. - #140 / SH3 type barrels. / Roll / Mainly Beta
Similarity search - Domain/homology
Survival motor neuron protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsSprangers, R. / Groves, M.R. / Sinning, I. / Sattler, M.
Citation
Journal: J.Mol.Biol. / Year: 2003
Title: High Resolution X-ray and NMR Structures of the SMN Tudor Domain: conformational variation in the binding site for symmetrically dimethylated arginine residues
Authors: Sprangers, R. / Groves, M.R. / Sinning, I. / Sattler, M.
#1: Journal: To be Published
Title: Definition of domain boundaries and crystallization of the SMN Tudor domain
Authors: Sprangers, R. / Selenko, P. / Sattler, M. / Sinning, I. / Groves, M.R.
History
DepositionAug 20, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 25, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 14, 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: Survival motor neuron protein


Theoretical massNumber of molelcules
Total (without water)6,6491
Polymers6,6491
Non-polymers00
Water1,17165
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)27.652, 27.652, 110.299
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number170
Space group name H-MP65

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Components

#1: Protein Survival motor neuron protein / SMN / Component of gems 1 / Gemin1


Mass: 6649.454 Da / Num. of mol.: 1 / Fragment: Tudor domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: smn1 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: Q16637
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 65 / 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: 1.83 Å3/Da / Density % sol: 32.79 %
Crystal growTemperature: 285 K / Method: vapor diffusion, hanging drop / pH: 4.5
Details: Amonium Sulphate, pH 4.5, VAPOR DIFFUSION, HANGING DROP, temperature 285K
Crystal grow
*PLUS
Details: Sprangers, R., (2003) Acta Crystallogr., D59, 366.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.934 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Dec 1, 2001
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.934 Å / Relative weight: 1
ReflectionResolution: 1.8→23.95 Å / Num. all: 4489 / Num. obs: 4499 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 1 / Redundancy: 11.4 %
Reflection shellResolution: 1.8→1.9 Å / % possible all: 100

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
SCALAdata scaling
CNSrefinement
REFMACrefinement
CCP4(SCALA)data scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.8→23.947 Å / Isotropic thermal model: Isotropic / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.1871 465 -RANDOM
Rwork0.1445 ---
all0.1466 4440 --
obs0.1466 4440 100 %-
Refinement stepCycle: LAST / Resolution: 1.8→23.947 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms465 0 0 65 530
LS refinement shellResolution: 1.8→1.9 Å
Refinement
*PLUS
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.0143
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_deg1.341
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg3.42

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