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- PDB-2xs2: Crystal structure of the RRM domain of mouse Deleted in azoosperm... -

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Basic information

Entry
Database: PDB / ID: 2xs2
TitleCrystal structure of the RRM domain of mouse Deleted in azoospermia-like in complex with RNA, UUGUUCUU
Components
  • 5'-R(*UP*UP*GP*UP*UP*CP*UP*U)-3'
  • DELETED IN AZOOSPERMIA-LIKE
KeywordsRNA BINDING PROTEIN/RNA / RNA BINDING PROTEIN-RNA COMPLEX
Function / homology
Function and homology information


female meiosis II / translation activator activity / positive regulation of meiotic nuclear division / oocyte maturation / 3'-UTR-mediated mRNA stabilization / germ cell development / positive regulation of translational initiation / mRNA 3'-UTR binding / spermatogenesis / ribosome ...female meiosis II / translation activator activity / positive regulation of meiotic nuclear division / oocyte maturation / 3'-UTR-mediated mRNA stabilization / germ cell development / positive regulation of translational initiation / mRNA 3'-UTR binding / spermatogenesis / ribosome / protein-containing complex / identical protein binding / nucleus / cytoplasm
Similarity search - Function
DAZ, RNA recognition motif, vertebrates / DAZ domain / Daz repeat / DAZ domain profile. / 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 ...DAZ, RNA recognition motif, vertebrates / DAZ domain / Daz repeat / DAZ domain profile. / 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
RNA / Deleted in azoospermia-like
Similarity search - Component
Biological speciesMUS MUSCULUS (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.35 Å
AuthorsJenkins, H.T. / Edwards, T.A.
CitationJournal: Proc. Natl. Acad. Sci. U.S.A. / Year: 2011
Title: Kinked beta-strands mediate high-affinity recognition of mRNA targets by the germ-cell regulator DAZL.
Authors: Jenkins, H.T. / Malkova, B. / Edwards, T.A.
History
DepositionSep 24, 2010Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 5, 2011Provider: repository / Type: Initial release
Revision 1.1Nov 2, 2011Group: Database references
Revision 1.2Nov 23, 2011Group: Database references
Revision 1.3Jun 13, 2018Group: Data collection / Database references
Category: citation / citation_author ...citation / citation_author / diffrn_radiation / diffrn_source
Item: _citation.journal_abbrev / _citation.journal_id_ISSN ..._citation.journal_abbrev / _citation.journal_id_ISSN / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.title / _diffrn_radiation.pdbx_diffrn_protocol / _diffrn_source.pdbx_wavelength_list
Revision 1.4May 8, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr1_symmetry / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry / _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

Downloads & links

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Assembly

Deposited unit
A: DELETED IN AZOOSPERMIA-LIKE
B: 5'-R(*UP*UP*GP*UP*UP*CP*UP*U)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,0883
Polymers14,0232
Non-polymers651
Water2,324129
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1350 Å2
ΔGint-25.9 kcal/mol
Surface area6640 Å2
MethodPISA
Unit cell
Length a, b, c (Å)38.100, 52.060, 60.490
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein DELETED IN AZOOSPERMIA-LIKE / DAZ-LIKE AUTOSOMAL / DELETED IN AZOOSPERMIA-LIKE 1


Mass: 11580.338 Da / Num. of mol.: 1 / Fragment: RESIDUES 32-132 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) MUS MUSCULUS (house mouse) / Plasmid: PET-SUMO-28A / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): ROSETTA-2 PLYSS / References: UniProt: Q64368
#2: RNA chain 5'-R(*UP*UP*GP*UP*UP*CP*UP*U)-3'


Mass: 2442.425 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) MUS MUSCULUS (house mouse)
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 129 / Source method: isolated from a natural source / Formula: H2O
Compound detailsENGINEERED RESIDUE IN CHAIN A, CYS 120 TO SER

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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: 2.73 Å3/Da / Density % sol: 55 % / Description: NONE
Crystal growDetails: 10 MM MAGNESIUM FORMATE, 20 % (W/V) PEG 3350, 0.1 MM ZINC ACETATE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9763 / Wavelength: 0.9763 Å
DetectorType: ADSC CCD / Detector: CCD / Date: Apr 14, 2010
Details: KIRKPATRICK BAEZ BIMORPH MIRROR PAIR FOR HORIZONTAL AND VERTICAL FOCUSSING
RadiationMonochromator: DOUBLE CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 1.35→27.41 Å / Num. obs: 26034 / % possible obs: 96 % / Observed criterion σ(I): 6 / Redundancy: 5.4 % / Biso Wilson estimate: 16.33 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 15
Reflection shellResolution: 1.35→1.42 Å / Redundancy: 5.1 % / Rmerge(I) obs: 0.65 / Mean I/σ(I) obs: 2.4 / % possible all: 87.3

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Processing

Software
NameVersionClassification
REFMAC5.5.0102refinement
MOSFLMdata reduction
SCALAdata scaling
SHELXphasing
RefinementMethod to determine structure: SAD
Starting model: NONE

Resolution: 1.35→27.41 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.963 / SU B: 1.679 / SU ML: 0.031 / Cross valid method: THROUGHOUT / ESU R: 0.055 / ESU R Free: 0.053 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.19267 1313 5 %RANDOM
Rwork0.16131 ---
obs0.16292 24721 96.05 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 19.382 Å2
Baniso -1Baniso -2Baniso -3
1--0.08 Å20 Å20 Å2
2--0.23 Å20 Å2
3----0.16 Å2
Refinement stepCycle: LAST / Resolution: 1.35→27.41 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms679 124 1 129 933
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.022870
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.6422.1331203
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.297596
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.72922.85735
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.85815134
X-RAY DIFFRACTIONr_dihedral_angle_4_deg26.313157
X-RAY DIFFRACTIONr_chiral_restr0.110.2137
X-RAY DIFFRACTIONr_gen_planes_refined0.010.021622
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.1980.2306
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3130.2573
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1090.273
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined0.030.22
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1710.245
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1180.217
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined0.0620.22
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.831.5448
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.8642728
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it3.8073422
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it5.3424.5470
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr1.9713870
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.35→1.385 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.321 67 -
Rwork0.325 1445 -
obs--77.22 %

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