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- PDB-4uut: Crystal structure of the Ultrabithorax protein -

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Basic information

Entry
Database: PDB / ID: 4uut
TitleCrystal structure of the Ultrabithorax protein
ComponentsHOMEOTIC PROTEIN ULTRABITHORAX
KeywordsTRANSCRIPTION / UBX / HOMEOTIC PROTEIN / TRANSCRIPTION FACTOR
Function / homology
Function and homology information


dorsal vessel aortic cell fate commitment / positive regulation of muscle organ development / anterior Malpighian tubule development / specification of animal organ identity / regulation of imaginal disc growth / haltere development / mesodermal cell fate specification / specification of segmental identity, thorax / open tracheal system development / imaginal disc-derived leg morphogenesis ...dorsal vessel aortic cell fate commitment / positive regulation of muscle organ development / anterior Malpighian tubule development / specification of animal organ identity / regulation of imaginal disc growth / haltere development / mesodermal cell fate specification / specification of segmental identity, thorax / open tracheal system development / imaginal disc-derived leg morphogenesis / somatic muscle development / muscle cell fate specification / polytene chromosome band / endoderm formation / regulation of cell fate specification / cell fate determination / anterior/posterior pattern specification / midgut development / cis-regulatory region sequence-specific DNA binding / transcription repressor complex / transcription coregulator binding / protein-DNA complex / heart development / transcription regulator complex / sequence-specific DNA binding / DNA-binding transcription factor activity, RNA polymerase II-specific / RNA polymerase II cis-regulatory region sequence-specific DNA binding / protein domain specific binding / negative regulation of DNA-templated transcription / regulation of DNA-templated transcription / positive regulation of DNA-templated transcription / negative regulation of transcription by RNA polymerase II / DNA binding / nucleus
Similarity search - Function
Homeobox protein, antennapedia type, conserved site / 'Homeobox' antennapedia-type protein signature. / Homeobox domain, metazoa / Homeobox, conserved site / 'Homeobox' domain signature. / Homeodomain / 'Homeobox' domain profile. / Homeodomain / Homeobox domain / Homeodomain-like ...Homeobox protein, antennapedia type, conserved site / 'Homeobox' antennapedia-type protein signature. / Homeobox domain, metazoa / Homeobox, conserved site / 'Homeobox' domain signature. / Homeodomain / 'Homeobox' domain profile. / Homeodomain / Homeobox domain / Homeodomain-like / Homeobox-like domain superfamily / Arc Repressor Mutant, subunit A / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Homeotic protein ultrabithorax
Similarity search - Component
Biological speciesDROSOPHILA MELANOGASTER (fruit fly)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsFoos, N. / Mate, M.J. / Ortiz-Lombardia, M.
CitationJournal: Structure / Year: 2015
Title: A Flexible Extension of the Drosophila Ultrabithorax Homeodomain Defines a Novel Hox/Pbc Interaction Mode.
Authors: Foos, N. / Maurel-Zaffran, C. / Mate, M.J. / Vincentelli, R. / Hainaut, M. / Berenger, H. / Pradel, J. / Saurin, A.J. / Ortiz-Lombardia, M. / Graba, Y.
History
DepositionJul 31, 2014Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 18, 2015Provider: repository / Type: Initial release
Revision 1.1May 1, 2024Group: 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 / software / 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 / _software.name / _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: HOMEOTIC PROTEIN ULTRABITHORAX
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,9147
Polymers11,4591
Non-polymers4556
Water1267
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)98.648, 98.648, 98.648
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number213
Space group name H-MP4132
Components on special symmetry positions
IDModelComponents
11A-2002-

HOH

21A-2004-

HOH

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Components

#1: Protein HOMEOTIC PROTEIN ULTRABITHORAX


Mass: 11459.246 Da / Num. of mol.: 1 / Fragment: HOMEODOMAIN AND UBDA, RESIDUES 233-324
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) DROSOPHILA MELANOGASTER (fruit fly) / Plasmid: UBXIVA PDEST14 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): ROSETTA PLYSS / References: UniProt: P83949
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 7 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 3.5 Å3/Da / Density % sol: 64.86 % / Description: NONE
Crystal growDetails: 20% 1-4 BUTANEDIOL, 0.2M LISO4, 0.1M MES PH 6

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.974716
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 21, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.974716 Å / Relative weight: 1
ReflectionResolution: 2.8→69.75 Å / Num. obs: 4428 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 8.7 % / Biso Wilson estimate: 101.67 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 25.8
Reflection shellResolution: 2.8→3.13 Å / Redundancy: 8.8 % / Rmerge(I) obs: 0.58 / Mean I/σ(I) obs: 3.9 / % possible all: 100

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Processing

Software
NameVersionClassification
BUSTER2.11.5refinement
autoPROCdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: LOCAL STRUCTURE OF UBX

Resolution: 2.8→69.75 Å / Cor.coef. Fo:Fc: 0.9378 / Cor.coef. Fo:Fc free: 0.9407 / SU R Cruickshank DPI: 0.346 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.386 / SU Rfree Blow DPI: 0.257 / SU Rfree Cruickshank DPI: 0.248
RfactorNum. reflection% reflectionSelection details
Rfree0.2366 406 9.25 %RANDOM
Rwork0.2175 ---
obs0.2192 4390 99.68 %-
Displacement parametersBiso mean: 88.31 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refine analyzeLuzzati coordinate error obs: 0.503 Å
Refinement stepCycle: LAST / Resolution: 2.8→69.75 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms593 0 22 7 622
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.01618HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.03827HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d240SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes19HARMONIC2
X-RAY DIFFRACTIONt_gen_planes83HARMONIC5
X-RAY DIFFRACTIONt_it618HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion2.31
X-RAY DIFFRACTIONt_other_torsion20.69
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion78SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact698SEMIHARMONIC4
LS refinement shellResolution: 2.8→3.13 Å / Total num. of bins used: 5
RfactorNum. reflection% reflection
Rfree0.2882 106 8.85 %
Rwork0.2401 1092 -
all0.2439 1198 -
obs--99.68 %
Refinement TLS params.Method: refined / Origin x: -12.0782 Å / Origin y: 15.4626 Å / Origin z: -3.2635 Å
111213212223313233
T-0.1874 Å20.0998 Å2-0.0117 Å2-0.038 Å20.0851 Å2---0.1093 Å2
L5.2072 °2-1.9989 °2-2.9831 °2-2.4925 °21.335 °2--1.6875 °2
S-0.0211 Å °0.3164 Å °0.1117 Å °-0.4276 Å °-0.1226 Å °0.0817 Å °0.1926 Å °-0.3112 Å °0.1437 Å °
Refinement TLS groupSelection details: CHAIN A

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