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- PDB-2r5z: Structure of Scr/Exd complex bound to a DNA sequence derived from... -

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Basic information

Entry
Database: PDB / ID: 2r5z
TitleStructure of Scr/Exd complex bound to a DNA sequence derived from the fkh gene
Components
  • DNA (5'-D(*DAP*DCP*DTP*DCP*DTP*DAP*DAP*DGP*DAP*DTP*DTP*DAP*DAP*DTP*DCP*DGP*DGP*DCP*DTP*DG)-3')
  • DNA (5'-D(*DTP*DCP*DAP*DGP*DCP*DCP*DGP*DAP*DTP*DTP*DAP*DAP*DTP*DCP*DTP*DTP*DAP*DGP*DAP*DG)-3')
  • Homeobox protein extradenticle
  • Homeotic protein Sex combs reduced
KeywordsTRANSCRIPTION/DNA / Homeodomain / homeotic proteins / specificity / Developmental protein / DNA-binding / Homeobox / Nucleus / Transcription / Transcription regulation / Transcription-DNA COMPLEX
Function / homology
Function and homology information


sex comb development / salivary gland boundary specification / oenocyte development / somatic muscle development / midgut development / eye development / regulation of cell fate specification / peripheral nervous system development / anterior/posterior pattern specification / embryonic organ development ...sex comb development / salivary gland boundary specification / oenocyte development / somatic muscle development / midgut development / eye development / regulation of cell fate specification / peripheral nervous system development / anterior/posterior pattern specification / embryonic organ development / neuron development / cis-regulatory region sequence-specific DNA binding / animal organ morphogenesis / transcription coregulator activity / RNA polymerase II transcription regulatory region sequence-specific DNA binding / protein-DNA complex / brain development / RNA polymerase II transcription regulator complex / transcription regulator complex / DNA-binding transcription factor binding / sequence-specific DNA binding / DNA-binding transcription factor activity, RNA polymerase II-specific / transcription coactivator activity / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / protein heterodimerization activity / regulation of transcription by RNA polymerase II / positive regulation of DNA-templated transcription / protein homodimerization activity / positive regulation of transcription by RNA polymerase II / DNA binding / nucleoplasm / nucleus / cytoplasm
Similarity search - Function
: / PBX, PBC domain / PBC domain / PBC domain profile. / Homeobox protein, antennapedia type / Homeobox protein, antennapedia type, conserved site / 'Homeobox' antennapedia-type protein signature. / : / Homeobox KN domain / Homeobox KN domain ...: / PBX, PBC domain / PBC domain / PBC domain profile. / Homeobox protein, antennapedia type / Homeobox protein, antennapedia type, conserved site / 'Homeobox' antennapedia-type protein signature. / : / Homeobox KN domain / Homeobox KN domain / 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
DNA / DNA (> 10) / Homeotic protein Sex combs reduced / Homeobox protein extradenticle
Similarity search - Component
Biological speciesDrosophila melanogaster (fruit fly)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsAggarwal, A.K. / Passner, J.M. / Jain, R.
CitationJournal: Cell(Cambridge,Mass.) / Year: 2007
Title: Functional specificity of a Hox protein mediated by the recognition of minor groove structure
Authors: Joshi, R. / Passner, J.M. / Rohs, R. / Jain, R. / Sosinsky, A. / Crickmore, M.A. / Jacob, V. / Aggarwal, A.K. / Honig, B. / Mann, R.S.
History
DepositionSep 4, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 5, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 2.0Oct 20, 2021Group: Database references / Polymer sequence / Source and taxonomy
Category: database_2 / entity_poly ...database_2 / entity_poly / pdbx_entity_src_syn / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity_poly.pdbx_target_identifier / _struct_ref_seq_dif.details
Revision 2.1Aug 30, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
C: DNA (5'-D(*DAP*DCP*DTP*DCP*DTP*DAP*DAP*DGP*DAP*DTP*DTP*DAP*DAP*DTP*DCP*DGP*DGP*DCP*DTP*DG)-3')
D: DNA (5'-D(*DTP*DCP*DAP*DGP*DCP*DCP*DGP*DAP*DTP*DTP*DAP*DAP*DTP*DCP*DTP*DTP*DAP*DGP*DAP*DG)-3')
A: Homeotic protein Sex combs reduced
B: Homeobox protein extradenticle


Theoretical massNumber of molelcules
Total (without water)30,7874
Polymers30,7874
Non-polymers00
Water2,018112
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6820 Å2
MethodPISA
Unit cell
Length a, b, c (Å)88.840, 92.600, 78.840
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: DNA chain DNA (5'-D(*DAP*DCP*DTP*DCP*DTP*DAP*DAP*DGP*DAP*DTP*DTP*DAP*DAP*DTP*DCP*DGP*DGP*DCP*DTP*DG)-3')


Mass: 6132.991 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) / References: PDB-2R5Y
#2: DNA chain DNA (5'-D(*DTP*DCP*DAP*DGP*DCP*DCP*DGP*DAP*DTP*DTP*DAP*DAP*DTP*DCP*DTP*DTP*DAP*DGP*DAP*DG)-3')


Mass: 6132.991 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) / References: PDB-2R5Y
#3: Protein Homeotic protein Sex combs reduced


Mass: 10967.711 Da / Num. of mol.: 1 / Fragment: Homeobox DNA-binding domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Gene: Scr / Plasmid: pET-3A / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pLysS / References: UniProt: P09077
#4: Protein Homeobox protein extradenticle / Dpbx


Mass: 7553.561 Da / Num. of mol.: 1 / Fragment: Homeobox TALE-type DNA-binding domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Gene: exd / Plasmid: pET-3A / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pLysS / References: UniProt: P40427
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 112 / 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: 2.63 Å3/Da / Density % sol: 53.29 %
Crystal growpH: 8.7
Details: 10-14 % PEG 4K, 20 % MPD, 0.1 M Tris, pH 8.7-8.9, 0.2 M Sodium Acetate, 0.2 M Potassium Chloride

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 1.1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Sep 10, 2004
Details: Rosenbaum-Rock high-resolution double-crystal monochromator.
RadiationMonochromator: Rosenbaum-Rock high-resolution double-crystal monochromator.
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 2.6→50 Å / Num. all: 10408 / Num. obs: 10189 / % possible obs: 97.9 % / Observed criterion σ(F): -3 / Redundancy: 33.6 % / Biso Wilson estimate: 41.7 Å2 / Rmerge(I) obs: 0.063 / Rsym value: 0.063 / Net I/σ(I): 36
Reflection shellResolution: 2.6→2.69 Å / Redundancy: 1.86 % / Rmerge(I) obs: 0.32 / Mean I/σ(I) obs: 9.7 / Num. unique all: 1008 / Rsym value: 0.32 / % possible all: 100

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Processing

Software
NameVersionClassification
CNS1.1refinement
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1B8I

1b8i


Resolution: 2.6→11.98 Å / Rfactor Rfree error: 0.013 / Data cutoff high absF: 1949550.74 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.303 539 5.5 %RANDOM
Rwork0.233 ---
obs0.233 9733 95.4 %-
all-10272 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 45.4238 Å2 / ksol: 0.325294 e/Å3
Displacement parametersBiso mean: 57.3 Å2
Baniso -1Baniso -2Baniso -3
1--17.29 Å20 Å20 Å2
2---5.57 Å20 Å2
3---22.87 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.48 Å0.38 Å
Luzzati d res low-5 Å
Luzzati sigma a0.39 Å0.39 Å
Refinement stepCycle: LAST / Resolution: 2.6→11.98 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1160 814 0 112 2086
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.1
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d18.4
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1.14
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.491.5
X-RAY DIFFRACTIONc_mcangle_it2.632
X-RAY DIFFRACTIONc_scbond_it2.082
X-RAY DIFFRACTIONc_scangle_it3.352.5
LS refinement shellResolution: 2.6→2.76 Å / Rfactor Rfree error: 0.042 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.386 85 5.6 %
Rwork0.349 1432 -
obs-1517 90.8 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2dna-rna_rep.paramdna-rna.top
X-RAY DIFFRACTION3water_rep.paramwater.top

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