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- PDB-3bdl: Crystal structure of a truncated human Tudor-SN -

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Basic information

Entry
Database: PDB / ID: 3bdl
TitleCrystal structure of a truncated human Tudor-SN
ComponentsStaphylococcal nuclease domain-containing protein 1
KeywordsHYDROLASE / Staphylococcal nuclease OB fold / Tudor domain / Cytoplasm / Host-virus interaction / Nucleus / Phosphoprotein / Transcription / Transcription regulation
Function / homology
Function and homology information


regulation of cell cycle process / miRNA catabolic process / RISC complex binding / dense body / nuclease activity / regulatory ncRNA-mediated gene silencing / RISC complex / endonuclease activity, active with either ribo- or deoxyribonucleic acids and producing 3'-phosphomonoesters / micrococcal nuclease / mRNA catabolic process ...regulation of cell cycle process / miRNA catabolic process / RISC complex binding / dense body / nuclease activity / regulatory ncRNA-mediated gene silencing / RISC complex / endonuclease activity, active with either ribo- or deoxyribonucleic acids and producing 3'-phosphomonoesters / micrococcal nuclease / mRNA catabolic process / RNA endonuclease activity / transcription coregulator activity / osteoblast differentiation / melanosome / Signaling by BRAF and RAF1 fusions / endonuclease activity / cadherin binding / RNA binding / extracellular exosome / membrane / nucleus / cytosol
Similarity search - Function
: / RNA-induced silencing complex, nuclease component Tudor-SN / Tudor domain / Tudor domain profile. / Tudor domain / Tudor domain / OB fold (Dihydrolipoamide Acetyltransferase, E2P) - #90 / SH3 type barrels. - #140 / Thermonuclease active site / Thermonuclease family signature 2. ...: / RNA-induced silencing complex, nuclease component Tudor-SN / Tudor domain / Tudor domain profile. / Tudor domain / Tudor domain / OB fold (Dihydrolipoamide Acetyltransferase, E2P) - #90 / SH3 type barrels. - #140 / Thermonuclease active site / Thermonuclease family signature 2. / Staphylococcal nuclease (SNase-like), OB-fold / Staphylococcal nuclease homologue / Thermonuclease domain profile. / Staphylococcal nuclease homologues / SNase-like, OB-fold superfamily / SH3 type barrels. / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / Roll / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
CITRIC ACID / Staphylococcal nuclease domain-containing protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.9 Å
AuthorsLi, C.L.
CitationJournal: Nucleic Acids Res. / Year: 2008
Title: Structural and functional insights into human Tudor-SN, a key component linking RNA interference and editing.
Authors: Li, C.L. / Yang, W.Z. / Chen, Y.P. / Yuan, H.S.
History
DepositionNov 15, 2007Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Aug 26, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 13, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Staphylococcal nuclease domain-containing protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,7815
Polymers64,0131
Non-polymers7684
Water12,430690
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Staphylococcal nuclease domain-containing protein 1
hetero molecules

A: Staphylococcal nuclease domain-containing protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)129,56210
Polymers128,0252
Non-polymers1,5378
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area12430 Å2
ΔGint-12 kcal/mol
Surface area46450 Å2
MethodPISA
Unit cell
Length a, b, c (Å)97.405, 91.929, 88.042
Angle α, β, γ (deg.)90.00, 91.26, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-2622-

HOH

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Components

#1: Protein Staphylococcal nuclease domain-containing protein 1 / Tudor-SN / p100 co-activator / 100 kDa coactivator / EBNA2 coactivator p100 / Tudor domain- ...Tudor-SN / p100 co-activator / 100 kDa coactivator / EBNA2 coactivator p100 / Tudor domain-containing protein 11


Mass: 64012.641 Da / Num. of mol.: 1 / Fragment: TSN-64 (SN3, SN4, Tudor, SN5 domains)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SND1, TDRD11 / Plasmid: pET28c / Production host: Escherichia coli (E. coli) / Strain (production host): B834 / References: UniProt: Q7KZF4, micrococcal nuclease
#2: Chemical
ChemComp-CIT / CITRIC ACID / Citric acid


Mass: 192.124 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C6H8O7
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 690 / 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: 3.08 Å3/Da / Density % sol: 60.04 %
Crystal growTemperature: 283 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 50mM HEPES, pH 7.0, 150mM NaCl, 10mM mercaptoethanol, 1.44M tri-ammonium citrate, VAPOR DIFFUSION, HANGING DROP, temperature 283K

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Data collection

DiffractionMean temperature: 123 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL12B2 / Wavelength: 0.979389, 0.979545, 0.964305
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Mar 7, 2007
RadiationMonochromator: Fixed-Exit Double Crystal Monochromator / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.9793891
20.9795451
30.9643051
ReflectionResolution: 1.82→23.33 Å / Num. all: 68052 / Num. obs: 68052 / % possible obs: 97.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.5 % / Biso Wilson estimate: 12.8 Å2 / Rsym value: 0.06 / Net I/σ(I): 15
Reflection shellResolution: 1.82→1.89 Å / Redundancy: 2.5 % / Mean I/σ(I) obs: 2.4 / Num. unique all: 6713 / Rsym value: 0.522 / % possible all: 97.3

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Processing

Software
NameVersionClassification
CNS1.1refinement
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
CNSphasing
RefinementMethod to determine structure: MAD / Resolution: 1.9→23.33 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 405757.73 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.209 5780 10.1 %RANDOM
Rwork0.175 ---
all-61089 --
obs-57324 93.8 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 49.6383 Å2 / ksol: 0.375852 e/Å3
Displacement parametersBiso mean: 26.3 Å2
Baniso -1Baniso -2Baniso -3
1--0.06 Å20 Å2-3.07 Å2
2---2.41 Å20 Å2
3---2.47 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.23 Å0.19 Å
Luzzati d res low-5 Å
Luzzati sigma a0.17 Å0.14 Å
Refinement stepCycle: LAST / Resolution: 1.9→23.33 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4242 0 52 690 4984
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_dihedral_angle_d23.4
X-RAY DIFFRACTIONc_improper_angle_d0.75
X-RAY DIFFRACTIONc_mcbond_it2.071.5
X-RAY DIFFRACTIONc_mcangle_it2.832
X-RAY DIFFRACTIONc_scbond_it3.462
X-RAY DIFFRACTIONc_scangle_it4.832.5
LS refinement shellResolution: 1.9→2.02 Å / Rfactor Rfree error: 0.008 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.252 910 10.3 %
Rwork0.216 7954 -
obs-8864 87.5 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater.top
X-RAY DIFFRACTION3CIT_mod.paramCIT_mod.top

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