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- PDB-2o94: The 97H/F mutant Structure of a glutamine-rich domain from histon... -

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Basic information

Entry
Database: PDB / ID: 2o94
TitleThe 97H/F mutant Structure of a glutamine-rich domain from histone deacetylase 4
ComponentsHistone deacetylase 4
KeywordsTRANSCRIPTION / alpha helix / polar zipper
Function / homology
Function and homology information


RUNX2 regulates chondrocyte maturation / response to denervation involved in regulation of muscle adaptation / negative regulation of myotube differentiation / peptidyl-lysine deacetylation / positive regulation of protein sumoylation / negative regulation of transcription by competitive promoter binding / regulation of protein binding / protein deacetylation / cardiac muscle hypertrophy in response to stress / histone deacetylase ...RUNX2 regulates chondrocyte maturation / response to denervation involved in regulation of muscle adaptation / negative regulation of myotube differentiation / peptidyl-lysine deacetylation / positive regulation of protein sumoylation / negative regulation of transcription by competitive promoter binding / regulation of protein binding / protein deacetylation / cardiac muscle hypertrophy in response to stress / histone deacetylase / protein lysine deacetylase activity / negative regulation of glycolytic process / SUMO transferase activity / histone deacetylase activity / negative regulation of gene expression, epigenetic / B cell activation / type I interferon-mediated signaling pathway / Notch-HLH transcription pathway / potassium ion binding / protein sumoylation / RUNX3 regulates p14-ARF / histone deacetylase complex / transcription repressor complex / SUMOylation of chromatin organization proteins / response to interleukin-1 / B cell differentiation / SUMOylation of intracellular receptors / negative regulation of DNA-binding transcription factor activity / NOTCH1 Intracellular Domain Regulates Transcription / Constitutive Signaling by NOTCH1 PEST Domain Mutants / Constitutive Signaling by NOTCH1 HD+PEST Domain Mutants / histone deacetylase binding / positive regulation of DNA-binding transcription factor activity / nervous system development / DNA-binding transcription factor binding / RNA polymerase II-specific DNA-binding transcription factor binding / molecular adaptor activity / nuclear speck / chromatin remodeling / inflammatory response / RNA polymerase II cis-regulatory region sequence-specific DNA binding / positive regulation of cell population proliferation / chromatin / positive regulation of DNA-templated transcription / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / zinc ion binding / nucleoplasm / identical protein binding / nucleus / cytosol / cytoplasm
Similarity search - Function
Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #1550 / Histone deacetylase, glutamine rich N-terminal domain / Glutamine rich N terminal domain of histone deacetylase 4 / : / Histone deacetylase family / Histone deacetylase domain / Histone deacetylase domain superfamily / Histone deacetylase domain / Ureohydrolase domain superfamily / Single alpha-helices involved in coiled-coils or other helix-helix interfaces ...Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #1550 / Histone deacetylase, glutamine rich N-terminal domain / Glutamine rich N terminal domain of histone deacetylase 4 / : / Histone deacetylase family / Histone deacetylase domain / Histone deacetylase domain superfamily / Histone deacetylase domain / Ureohydrolase domain superfamily / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Helix non-globular / Special
Similarity search - Domain/homology
Histone deacetylase 4
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsGuo, L. / Han, A. / Bates, D.L. / Chen, L.
CitationJournal: Proc.Natl.Acad.Sci.Usa / Year: 2007
Title: Crystal structure of a conserved N-terminal domain of histone deacetylase 4 reveals functional insights into glutamine-rich domains.
Authors: Guo, L. / Han, A. / Bates, D.L. / Cao, J. / Chen, L.
History
DepositionDec 13, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 27, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 18, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.4Oct 20, 2021Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.5Aug 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
A: Histone deacetylase 4
B: Histone deacetylase 4
C: Histone deacetylase 4
D: Histone deacetylase 4


Theoretical massNumber of molelcules
Total (without water)54,6494
Polymers54,6494
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10730 Å2
ΔGint-81 kcal/mol
Surface area17340 Å2
MethodPISA
Unit cell
Length a, b, c (Å)189.885, 61.023, 60.777
Angle α, β, γ (deg.)90.000, 108.610, 90.000
Int Tables number5
Space group name H-MC121
DetailsThe tetramer in the asymmetric unit is the biological assembly, no crystallographic symmetry is invovled in the tetramer formation.

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Components

#1: Protein
Histone deacetylase 4 / / HD4


Mass: 13662.374 Da / Num. of mol.: 4 / Fragment: N-terminal glutamine-rich domain, residues 62-129 / Mutation: H97F
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HDAC4, KIAA0288 / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta PlysS / References: UniProt: P56524

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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: 3.05 Å3/Da / Density % sol: 59.71 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.540M LITHIUM SULFATE 55mM HEPES PH7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Nov 19, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionRedundancy: 3.7 % / Av σ(I) over netI: 11 / Number: 50424 / Rmerge(I) obs: 0.053 / Χ2: 1.02 / D res high: 2.95 Å / D res low: 30 Å / Num. obs: 13769 / % possible obs: 97.5
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsChi squaredRedundancy
6.34309210.031.8483.5
5.046.3499.310.0381.4473.6
4.45.0498.310.0421.533.7
44.499.110.0481.0833.7
3.72498.910.060.953.7
3.53.7298.710.0940.7483.7
3.323.598.810.1350.7183.7
3.183.3298.710.2230.6633.7
3.063.1897.110.5040.6413.6
2.953.0694.210.7580.5843.6
ReflectionResolution: 3→30 Å / Num. all: 13433 / Num. obs: 13083 / % possible obs: 97.6 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Rsym value: 0.053
Reflection shellResolution: 3→3.19 Å / Mean I/σ(I) obs: 1.99 / Rsym value: 0.504 / % possible all: 97.1

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
PDB_EXTRACT2data extraction
ADSCQUANTUMdata collection
HKL-2000data reduction
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 2H8N

2h8n


Resolution: 3→30 Å / FOM work R set: 0.727 / Cross valid method: THROUGHOUT / σ(F): 1481 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.327 1038 7.7 %random
Rwork0.305 ---
obs0.3239 10088 75.1 %-
Solvent computationBsol: 63.431 Å2
Displacement parametersBiso mean: 108.763 Å2
Baniso -1Baniso -2Baniso -3
1--25.021 Å20 Å2-21.585 Å2
2--16.219 Å20 Å2
3---8.801 Å2
Refinement stepCycle: LAST / Resolution: 3→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2332 0 0 0 2332
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_mcbond_it5.2731.5
X-RAY DIFFRACTIONc_scbond_it8.4342
X-RAY DIFFRACTIONc_mcangle_it8.692
X-RAY DIFFRACTIONc_scangle_it14.8432.5
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-IDNum. reflection obs
3-3.050.421240.441214X-RAY DIFFRACTION238
3.05-3.110.446250.369X-RAY DIFFRACTION214
3.11-3.170.251290.42X-RAY DIFFRACTION304
3.17-3.230.264370.33X-RAY DIFFRACTION364
3.23-3.30.298340.34X-RAY DIFFRACTION399
3.3-3.380.293450.313X-RAY DIFFRACTION447
3.38-3.460.313490.32X-RAY DIFFRACTION437
3.46-3.560.332660.354X-RAY DIFFRACTION511
3.56-3.660.374520.349X-RAY DIFFRACTION523
3.66-3.780.357490.335X-RAY DIFFRACTION546
3.78-3.910.333610.323X-RAY DIFFRACTION533
3.91-4.070.348540.271X-RAY DIFFRACTION597
4.07-4.260.217590.214X-RAY DIFFRACTION596
4.26-4.480.287640.244X-RAY DIFFRACTION592
4.48-4.760.35620.239X-RAY DIFFRACTION638
4.76-5.130.265530.257X-RAY DIFFRACTION628
5.13-5.650.387700.32X-RAY DIFFRACTION632
5.65-6.460.357710.318X-RAY DIFFRACTION648
6.46-8.140.315760.325X-RAY DIFFRACTION667
8.14-500.010.36580.369X-RAY DIFFRACTION574
Xplor fileSerial no: 1 / Param file: protein_rep.param

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