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

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Basic information

Entry
Database: PDB / ID: 2xsf
TitleCrystal structure of the RRM domain of mouse Deleted in azoospermia- like
ComponentsDELETED IN AZOOSPERMIA-LIKE
KeywordsRNA BINDING PROTEIN
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
Deleted in azoospermia-like
Similarity search - Component
Biological speciesMUS MUSCULUS (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 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 28, 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_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_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: DELETED IN AZOOSPERMIA-LIKE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)10,1774
Polymers9,8961
Non-polymers2803
Water1,62190
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)53.900, 53.900, 65.930
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

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


Mass: 9896.392 Da / Num. of mol.: 1 / Fragment: RESIDUES 35-118
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) MUS MUSCULUS (house mouse) / Plasmid: PGEX-6P-2 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): CODONPLUS / References: UniProt: Q64368
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 90 / 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: 2.76 Å3/Da / Density % sol: 55 % / Description: NONE
Crystal growpH: 7.5
Details: 2.1 M LITHIUM SULPHATE, 50 MM HEPES PH 7.5, 5 % (V/V) GLYCEROL

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX14.2 / Wavelength: 0.979
DetectorType: ADSC CCD / Detector: CCD / Date: Sep 18, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.7→20 Å / Num. obs: 12616 / % possible obs: 99.9 % / Observed criterion σ(I): 6 / Redundancy: 11.8 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 21.9
Reflection shellResolution: 1.7→1.79 Å / Redundancy: 12 % / Rmerge(I) obs: 0.6 / Mean I/σ(I) obs: 4.7 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.5.0102refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3BS9

3bs9


Resolution: 1.7→22 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.949 / SU B: 3.617 / SU ML: 0.056 / Cross valid method: THROUGHOUT / ESU R: 0.095 / ESU R Free: 0.088 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.202 614 4.9 %RANDOM
Rwork0.189 ---
obs0.189 12002 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 25.67 Å2
Baniso -1Baniso -2Baniso -3
1-1.16 Å20.58 Å20 Å2
2--1.16 Å20 Å2
3----1.74 Å2
Refinement stepCycle: LAST / Resolution: 1.7→22 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms631 0 17 90 738
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.022682
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.5871.969919
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.482588
X-RAY DIFFRACTIONr_dihedral_angle_2_deg27.89323.33330
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.50615123
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.031155
X-RAY DIFFRACTIONr_chiral_restr0.0960.2101
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.02501
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2060.2292
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3160.2461
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1740.267
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.160.245
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2280.211
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.9611.5409
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.7092667
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.6063273
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it4.2674.5248
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.7→1.74 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.211 51 -
Rwork0.225 870 -
obs--100 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.0908-0.2601-0.94692.03620.83574.75330.04860.1501-0.0645-0.0586-0.04990.07880.0870.01920.00140.059-0.03440.00790.047-0.01630.029925.1691-15.6185-5.3366
21.1876-0.10170.87760.99040.39550.88620.10340.0841-0.0310.0446-0.013-0.07470.09590.0959-0.09040.1073-0.0581-0.00230.1252-0.02560.086426.311-18.4727-1.6732
33.884-2.52590.104611.6381-0.14855.4425-0.2159-0.1784-0.08910.41340.30040.3390.00860.0757-0.08440.0855-0.0357-0.00010.05210.01640.036927.0624-9.17154.7486
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A35 - 71
2X-RAY DIFFRACTION2A72 - 97
3X-RAY DIFFRACTION3A98 - 115

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