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- PDB-1zv1: Crystal structure of the dimerization domain of doublesex protein... -

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Basic information

Entry
Database: PDB / ID: 1zv1
TitleCrystal structure of the dimerization domain of doublesex protein from D. melanogaster
ComponentsDoublesex protein
KeywordsPROTEIN BINDING / doublesex / uba domain / dimerization / sex determination / transcription factor
Function / homology
Function and homology information


imaginal disc-derived male genitalia development / male analia development / female analia development / female sex differentiation / sex-specific pigmentation / female somatic sex determination / imaginal disc-derived female genitalia development / sex comb development / negative regulation of developmental pigmentation / somatic sex determination ...imaginal disc-derived male genitalia development / male analia development / female analia development / female sex differentiation / sex-specific pigmentation / female somatic sex determination / imaginal disc-derived female genitalia development / sex comb development / negative regulation of developmental pigmentation / somatic sex determination / genital disc development / male sex differentiation / courtship behavior / male courtship behavior, veined wing generated song production / sex determination / male courtship behavior / sex differentiation / axon midline choice point recognition / RNA polymerase II transcription regulatory region sequence-specific DNA binding / DNA-binding transcription repressor activity, RNA polymerase II-specific / DNA-binding transcription activator activity, RNA polymerase II-specific / DNA-binding transcription factor activity, RNA polymerase II-specific / RNA polymerase II cis-regulatory region sequence-specific DNA binding / negative regulation of DNA-templated transcription / regulation of transcription by RNA polymerase II / positive regulation of DNA-templated transcription / protein homodimerization activity / positive regulation of transcription by RNA polymerase II / zinc ion binding / nucleus
Similarity search - Function
Doublesex dimerisation / Doublesex dimerisation domain / Doublesex dimerisation domain / DM DNA-binding domain / DMRT family / DM DNA-binding domain superfamily / DM DNA binding domain / DM DNA-binding domain signature. / DM DNA-binding domain profile. / Doublesex DNA-binding motif ...Doublesex dimerisation / Doublesex dimerisation domain / Doublesex dimerisation domain / DM DNA-binding domain / DMRT family / DM DNA-binding domain superfamily / DM DNA binding domain / DM DNA-binding domain signature. / DM DNA-binding domain profile. / Doublesex DNA-binding motif / Ubiquitin-associated (UBA) domain / Helicase, Ruva Protein; domain 3 / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Biological speciesDrosophila melanogaster (fruit fly)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.6 Å
AuthorsWeiss, M.A. / Bayrer, J.R. / Wan, Z. / Li, B. / Phillips, N.B.
CitationJournal: J.Biol.Chem. / Year: 2005
Title: Dimerization of doublesex is mediated by a cryptic ubiquitin-associated domain fold: implications for sex-specific gene regulation
Authors: Bayrer, J.R. / Zhang, W. / Weiss, M.A.
History
DepositionJun 1, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 9, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jul 24, 2019Group: Data collection / Refinement description / Category: software / Item: _software.name / _software.version
Revision 1.4Feb 14, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Doublesex protein
B: Doublesex protein


Theoretical massNumber of molelcules
Total (without water)15,4912
Polymers15,4912
Non-polymers00
Water2,270126
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2260 Å2
ΔGint-20 kcal/mol
Surface area6780 Å2
MethodPISA
Unit cell
Length a, b, c (Å)39.773, 46.623, 59.771
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
DetailsThe biological assembly is a dimer found entirely in the asymmetric unit.

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Components

#1: Protein Doublesex protein


Mass: 7745.735 Da / Num. of mol.: 2 / Fragment: DIMERIZATION DOMAIN
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Gene: dsx / Production host: Escherichia coli (E. coli) / References: UniProt: P23023
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 126 / 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: 2

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Sample preparation

CrystalDensity Matthews: 1.787 Å3/Da / Density % sol: 28.53 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.4
Details: ammonium sulfate, isopropanol, tris, sodium chloride , pH 7.4, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
12001
21
Diffraction source
SourceSiteBeamlineIDWavelengthWavelength (Å)
SYNCHROTRONNSLS X9B10.97880.9788
SYNCHROTRONAPS 14-BM-C20.90.9
Detector
TypeIDDetectorDate
ADSC QUANTUM 41CCDApr 11, 2003
ADSC QUANTUM 42CCDNov 26, 2002
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SINGLE WAVELENGTHMx-ray1
2Mx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
10.97881
20.91
ReflectionResolution: 1.6→20 Å / Num. all: 15159 / Num. obs: 15159 / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 10.9 % / Rmerge(I) obs: 0.038 / Net I/σ(I): 62.3
Reflection shellResolution: 1.6→1.66 Å / Rmerge(I) obs: 0.182 / Mean I/σ(I) obs: 11 / % possible all: 96.9

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
HKL-2000data reduction
SCALEPACKdata scaling
SHELXSphasing
CNS1.1refinement
RefinementMethod to determine structure: SAD / Resolution: 1.6→10.86 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.925 / SU B: 1.707 / SU ML: 0.063 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / ESU R: 0.115 / ESU R Free: 0.118
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25722 752 5 %RANDOM
Rwork0.2085 ---
obs0.21084 14294 99.21 %-
all-14844 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 27.969 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2---0.01 Å20 Å2
3---0.01 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.23 Å0.19 Å
Luzzati d res low-5 Å
Luzzati sigma a-0.09 Å
Refinement stepCycle: LAST / Resolution: 1.6→10.86 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms994 0 0 126 1120
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0221015
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.3941.971372
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg3.885116
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.6132558
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.67215181
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.551156
X-RAY DIFFRACTIONr_chiral_restr0.0920.2143
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.02786
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.240.2568
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3220.2707
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.290.2112
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2250.233
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2140.221
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.3191.5608
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.192945
X-RAY DIFFRACTIONr_scbond_it2.7753479
X-RAY DIFFRACTIONr_scangle_it3.984.5427
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.6→1.641 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.337 44 -
Rwork0.242 1003 -
obs--96.85 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater.param

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