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- PDB-1l8r: Structure of the Retinal Determination Protein Dachshund Reveals ... -

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Basic information

Entry
Database: PDB / ID: 1l8r
TitleStructure of the Retinal Determination Protein Dachshund Reveals a DNA-Binding Motif
ComponentsDachshund
KeywordsTRANSCRIPTION / winged-helix
Function / homology
Function and homology information


development of primary female sexual characteristics / negative regulation of cell proliferation involved in contact inhibition / negative regulation of DNA biosynthetic process / regulation of nuclear cell cycle DNA replication / respiratory gaseous exchange by respiratory system / negative regulation of transcription by competitive promoter binding / type B pancreatic cell proliferation / suckling behavior / negative regulation of fibroblast proliferation / negative regulation of cell migration ...development of primary female sexual characteristics / negative regulation of cell proliferation involved in contact inhibition / negative regulation of DNA biosynthetic process / regulation of nuclear cell cycle DNA replication / respiratory gaseous exchange by respiratory system / negative regulation of transcription by competitive promoter binding / type B pancreatic cell proliferation / suckling behavior / negative regulation of fibroblast proliferation / negative regulation of cell migration / RNA polymerase II transcription regulatory region sequence-specific DNA binding / DNA-binding transcription repressor activity, RNA polymerase II-specific / transcription regulator complex / DNA-binding transcription factor activity, RNA polymerase II-specific / nuclear speck / RNA polymerase II cis-regulatory region sequence-specific DNA binding / negative regulation of DNA-templated transcription / regulation of transcription by RNA polymerase II / negative regulation of transcription by RNA polymerase II / Golgi apparatus / nucleoplasm / nucleus / cytosol
Similarity search - Function
: / Ski / SKI/SNO/DAC domain / Ski-like, DNA-binding domain superfamily / SKI/SNO/DAC Dachshund homology domain / Mlu1-box Binding Protein; DNA-binding Domain / Putative DNA-binding domain superfamily / Roll / Alpha Beta
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.65 Å
AuthorsKim, S.S. / Zhang, R. / Braunstein, S.E. / Joachimiak, A. / Cvekl, A. / Hegde, R.S.
CitationJournal: Structure / Year: 2002
Title: Structure of the retinal determination protein Dachshund reveals a DNA binding motif.
Authors: Kim, S.S. / Zhang, R.G. / Braunstein, S.E. / Joachimiak, A. / Cvekl, A. / Hegde, R.S.
History
DepositionMar 21, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 26, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 30, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Dachshund
B: Dachshund


Theoretical massNumber of molelcules
Total (without water)22,5702
Polymers22,5702
Non-polymers00
Water2,756153
1
A: Dachshund


Theoretical massNumber of molelcules
Total (without water)11,2851
Polymers11,2851
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Dachshund


Theoretical massNumber of molelcules
Total (without water)11,2851
Polymers11,2851
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)28.797, 47.731, 50.436
Angle α, β, γ (deg.)60.75, 86.86, 84.55
Int Tables number1
Space group name H-MP1

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Components

#1: Protein Dachshund


Mass: 11285.039 Da / Num. of mol.: 2 / Fragment: DACHbox-N
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / References: UniProt: Q9UI36
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 153 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.67 Å3/Da / Density % sol: 53.88 %
Crystal growTemperature: 277 K / Method: vapor diffusion / pH: 7.5
Details: PEG 10000, Ammonium Sulphate, pH 7.5, VAPOR DIFFUSION, temperature 277K
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
125-30 %PEG100001reservoir
20.25 Mammonium sulfate1reservoir
35 mMdithiothreitol1reservoir
48 mg/mlprotein1drop

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97981, 0.97904, 0.95366
DetectorType: CUSTOM-MADE / Detector: CCD / Date: May 1, 2001
RadiationMonochromator: Double crystal monochromator / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.979811
20.979041
30.953661
ReflectionResolution: 1.65→25.14 Å / Num. all: 56014 / Num. obs: 53166 / % possible obs: 96.5 % / Observed criterion σ(I): 0
Reflection shellResolution: 1.65→1.71 Å / % possible all: 91.5
Reflection
*PLUS
Lowest resolution: 50 Å / Num. obs: 26123 / Num. measured all: 227661 / Rmerge(I) obs: 0.064
Reflection shell
*PLUS
% possible obs: 91.5 % / Rmerge(I) obs: 0.233

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Processing

Software
NameClassification
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: MAD / Resolution: 1.65→50 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.259 5009 9.8 %RANDOM
Rwork0.237 ---
all0.237 56284 --
obs0.237 51275 --
Refinement stepCycle: LAST / Resolution: 1.65→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1539 0 0 153 1692
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d22.1
X-RAY DIFFRACTIONx_bond_d0.0049
X-RAY DIFFRACTIONx_angle_d1.12
X-RAY DIFFRACTIONx_improper_angle_d0.71
Refinement
*PLUS
Lowest resolution: 6 Å / % reflection Rfree: 9 % / Rfactor obs: 0.237 / Rfactor Rfree: 0.251 / Rfactor Rwork: 0.23
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.0049
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_deg1.12
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg22.1
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg0.71
LS refinement shell
*PLUS
Rfactor Rfree: 0.365 / Rfactor Rwork: 0.318

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