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- PDB-3sxl: SEX-LETHAL RNA RECOGNITION DOMAINS 1 AND 2 FROM DROSOPHILA MELANO... -

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Basic information

Entry
Database: PDB / ID: 3sxl
TitleSEX-LETHAL RNA RECOGNITION DOMAINS 1 AND 2 FROM DROSOPHILA MELANOGASTER
ComponentsPROTEIN (SEX-LETHAL)
KeywordsRNA BINDING DOMAIN / RBD / RNA RECOGNITION MOTIF / RRM / SPLICING INHIBITOR / TRANSLATIONAL INHIBITOR / SEX DETERMINATION / X CHROMOSOME DOSAGE COMPENSATION
Function / homology
Function and homology information


sex determination, primary response to X:A ratio / germarium-derived cystoblast division / epithelium regeneration / female sex determination / somatic sex determination / female germ-line sex determination / oocyte differentiation / imaginal disc growth / negative regulation of RNA export from nucleus / sex-chromosome dosage compensation ...sex determination, primary response to X:A ratio / germarium-derived cystoblast division / epithelium regeneration / female sex determination / somatic sex determination / female germ-line sex determination / oocyte differentiation / imaginal disc growth / negative regulation of RNA export from nucleus / sex-chromosome dosage compensation / regulation of stem cell division / sex determination / poly-pyrimidine tract binding / sex differentiation / alternative mRNA splicing, via spliceosome / negative regulation of receptor signaling pathway via JAK-STAT / poly(A) binding / pre-mRNA binding / positive regulation of smoothened signaling pathway / regulation of mRNA splicing, via spliceosome / reciprocal meiotic recombination / poly(U) RNA binding / oogenesis / regulation of alternative mRNA splicing, via spliceosome / negative regulation of mRNA splicing, via spliceosome / negative regulation of translational initiation / mRNA regulatory element binding translation repressor activity / positive regulation of RNA splicing / mRNA 3'-UTR binding / mRNA 5'-UTR binding / negative regulation of translation / protein stabilization / ribonucleoprotein complex / mRNA binding / protein-containing complex / RNA binding / nucleus / cytosol / cytoplasm
Similarity search - Function
Sex-lethal splicing factor / Paraneoplastic encephalomyelitis antigen / RRM (RNA recognition motif) domain / RNA recognition motif / RNA recognition motif / Eukaryotic RNA Recognition Motif (RRM) profile. / RNA recognition motif domain / RNA-binding domain superfamily / Nucleotide-binding alpha-beta plait domain superfamily / Alpha-Beta Plaits ...Sex-lethal splicing factor / Paraneoplastic encephalomyelitis antigen / RRM (RNA recognition motif) domain / RNA recognition motif / RNA recognition motif / Eukaryotic RNA Recognition Motif (RRM) profile. / RNA recognition motif domain / RNA-binding domain superfamily / Nucleotide-binding alpha-beta plait domain superfamily / Alpha-Beta Plaits / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesDrosophila melanogaster (fruit fly)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.7 Å
AuthorsCrowder, S.M. / Kanaar, R. / Rio, D.C. / Alber, T.C.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 1999
Title: Absence of interdomain contacts in the crystal structure of the RNA recognition motifs of Sex-lethal.
Authors: Crowder, S.M. / Kanaar, R. / Rio, D.C. / Alber, T.
History
DepositionApr 4, 1999Deposition site: BNL / Processing site: RCSB
Revision 1.0Apr 27, 1999Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 3, 2021Group: Database references / Derived calculations / Category: database_2 / struct_conn / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details
Revision 1.4Dec 27, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: PROTEIN (SEX-LETHAL)
B: PROTEIN (SEX-LETHAL)
C: PROTEIN (SEX-LETHAL)


Theoretical massNumber of molelcules
Total (without water)63,0943
Polymers63,0943
Non-polymers00
Water0
1
A: PROTEIN (SEX-LETHAL)


Theoretical massNumber of molelcules
Total (without water)21,0311
Polymers21,0311
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: PROTEIN (SEX-LETHAL)


Theoretical massNumber of molelcules
Total (without water)21,0311
Polymers21,0311
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: PROTEIN (SEX-LETHAL)


Theoretical massNumber of molelcules
Total (without water)21,0311
Polymers21,0311
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)50.910, 124.470, 50.930
Angle α, β, γ (deg.)90.00, 120.00, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS oper: (Code: given / Matrix: (1, 1), (1), (-1) / Vector: 0.16667)

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Components

#1: Protein PROTEIN (SEX-LETHAL)


Mass: 21031.182 Da / Num. of mol.: 3
Fragment: RNA BINDING DOMAINS 1 AND 2 (RESIDUES 112-294 OF FULL LENGTH)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Plasmid: PET-3B / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL-21(DE3) / References: UniProt: P19339

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.21 Å3/Da / Density % sol: 44.45 %
Crystal growpH: 7.8 / Details: pH 7.80
Crystal grow
*PLUS
pH: 7.8 / Method: vapor diffusion, hanging drop / Details: used to seeding
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
118 mg/mlprotein1drop
210 %glycerol1drop
35 mMHEPES1drop
420 %PEG2000 MME1reservoir
50.1 MHEPES1reservoir
60.2 Mammonium sulfate1reservoir

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Data collection

DiffractionMean temperature: 120 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL1-5 / Wavelength: 1.06879, 0.98001, 0.97957, 1.2000
DetectorDetector: CCD
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
11.068791
20.980011
30.979571
41.21
ReflectionResolution: 2.7→20 Å / Num. obs: 16847 / % possible obs: 99.8 % / Observed criterion σ(I): 2 / Redundancy: 6.7 % / Biso Wilson estimate: 68.5 Å2 / Rsym value: 0.069 / Net I/σ(I): 13.4
Reflection shellHighest resolution: 2.7 Å / Mean I/σ(I) obs: 5.7
Reflection
*PLUS
Highest resolution: 2.7 Å / Lowest resolution: 20 Å / % possible obs: 99.8 % / Observed criterion σ(I): 2 / Redundancy: 6.7 % / Rmerge(I) obs: 0.069 / Biso Wilson estimate: 68.5 Å2
Reflection shell
*PLUS
Highest resolution: 2.7 Å / Mean I/σ(I) obs: 5.7

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Processing

Software
NameVersionClassification
CNS0.4refinement
MOSFLMdata reduction
CCP4(SCALA)data scaling
RefinementMethod to determine structure: MAD / Resolution: 2.7→20 Å / Rfactor Rfree error: 0.007 / Data cutoff high rms absF: 1604575.59 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2
RfactorNum. reflection% reflectionSelection details
Rfree0.264 1494 10 %RANDOM
Rwork0.221 ---
obs-14901 99.1 %-
Solvent computationSolvent model: FLAT MODEL
Displacement parametersBiso mean: 56.5 Å2
Baniso -1Baniso -2Baniso -3
1-0.17 Å20 Å24.91 Å2
2---0.53 Å20 Å2
3---0.37 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.47 Å0.4 Å
Luzzati d res low-5.5 Å
Luzzati sigma a0.5 Å0.57 Å
Refinement stepCycle: LAST / Resolution: 2.7→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3696 0 0 0 3696
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.015
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg2
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d25.1
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1.12
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
LS refinement shellResolution: 2.7→2.87 Å / Rfactor Rfree error: 0.03 / Total num. of bins used: 6
Num. reflection% reflection
Rfree258 10.6 %
Rwork2168 -
obs-98.2 %
Xplor fileSerial no: 1 / Param file: PROTEIN_REP.PARAM / Topol file: PROTEIN.TOP
Refinement
*PLUS
Highest resolution: 2.7 Å / Lowest resolution: 20 Å / σ(F): 2 / % reflection Rfree: 10 % / Rfactor obs: 0.218
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 56.5 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg2
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg25.1
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg1.12
LS refinement shell
*PLUS
Highest resolution: 2.7 Å / % reflection Rfree: 10.6 %

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