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- PDB-2xs7: Crystal structure of the RRM domain of mouse Deleted in azoosperm... -

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Basic information

Entry
Database: PDB / ID: 2xs7
TitleCrystal structure of the RRM domain of mouse Deleted in azoospermia- like in complex with Sycp3 RNA, UUGUUU
Components
  • 5'-R(*UP*UP*GP*UP*UP*UP)-3'
  • DELETED IN AZOOSPERMIA-LIKE
KeywordsRNA BINDING PROTEIN/RNA / RNA BINDING PROTEIN-RNA COMPLEX / TRANSLATION REGULATION
Function / homology
Function and homology information


female meiosis II / translation activator activity / positive regulation of meiotic nuclear division / oocyte maturation / germ cell development / positive regulation of translational initiation / mRNA 3'-UTR binding / spermatogenesis / ribosome / identical protein binding ...female meiosis II / translation activator activity / positive regulation of meiotic nuclear division / oocyte maturation / germ cell development / positive regulation of translational initiation / mRNA 3'-UTR binding / spermatogenesis / ribosome / 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 / MOLECULAR REPLACEMENT / Resolution: 1.45 Å
AuthorsJenkins, H.T. / Edwards, T.A.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2011
Title: Kinked Beta-Strands Mediate High-Affinity Recognition of Mrna Targets by the Germ-Cell Regulator Dazl
Authors: Jenkins, H.T. / 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 / Source and taxonomy
Revision 1.2Nov 23, 2011Group: Database references
Revision 1.3Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / 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 / _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_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*UP)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,6943
Polymers11,6282
Non-polymers651
Water1,856103
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1190 Å2
ΔGint-31.5 kcal/mol
Surface area6050 Å2
MethodPISA
Unit cell
Length a, b, c (Å)32.888, 37.749, 70.771
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: 9797.299 Da / Num. of mol.: 1 / Fragment: RESIDUES 32-117
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*UP)-3' / SYCP 3'-UTR / SYCP3 3'-UTR


Mass: 1831.078 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.: 103 / 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: 2.2 Å3/Da / Density % sol: 44 % / Description: NONE
Crystal growDetails: 10 MM MAGNESIUM FORMATE, 25% (W/V) PEG 3350 10 MM ZINC ACETATE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.9795
DetectorType: ADSC CCD / Detector: CCD / Date: May 16, 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: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.45→29.82 Å / Num. obs: 16096 / % possible obs: 99.1 % / Observed criterion σ(I): 6 / Redundancy: 6.9 % / Biso Wilson estimate: 15.2 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 16.1
Reflection shellResolution: 1.45→1.53 Å / Redundancy: 6.1 % / Rmerge(I) obs: 0.92 / Mean I/σ(I) obs: 2.1 / % possible all: 97.7

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Processing

Software
NameVersionClassification
REFMAC5.5.0102refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2XS2

2xs2


Resolution: 1.45→29.83 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.955 / SU B: 2.763 / SU ML: 0.048 / Cross valid method: THROUGHOUT / ESU R: 0.083 / ESU R Free: 0.073 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY.
RfactorNum. reflection% reflectionSelection details
Rfree0.20469 999 6.2 %RANDOM
Rwork0.16207 ---
obs0.16471 15097 99.15 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 18.568 Å2
Baniso -1Baniso -2Baniso -3
1-0.82 Å20 Å20 Å2
2---0.72 Å20 Å2
3----0.11 Å2
Refinement stepCycle: LAST / Resolution: 1.45→29.83 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms673 84 1 103 861
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.022787
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.6152.0951079
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.374589
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.60624.19431
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.15815127
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.401154
X-RAY DIFFRACTIONr_chiral_restr0.10.2124
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.021559
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.1990.2310
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3190.2543
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1180.271
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined0.0550.22
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2230.254
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1750.223
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined0.1090.21
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.3951.5429
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.3792697
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it3.5413358
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it4.8934.5380
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr1.7231787
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.45→1.488 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.4 71 -
Rwork0.296 1064 -
obs--95.86 %

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