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- PDB-4qa7: Crystal structure of H334R/Y306F HDAC8 in complex with a tetrapep... -

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Basic information

Entry
Database: PDB / ID: 4qa7
TitleCrystal structure of H334R/Y306F HDAC8 in complex with a tetrapeptide substrate
Components
  • Histone deacetylase 8
  • tetrapeptide substrate
KeywordsHYDROLASE / metalloenzyme / histone deacetylase / enzyme substrate complex / Cornelia de Lange Syndrome / arginase/deacetylase fold
Function / homology
Function and homology information


histone decrotonylase activity / histone deacetylase activity, hydrolytic mechanism / histone deacetylase / protein lysine deacetylase activity / Hydrolases; Acting on carbon-nitrogen bonds, other than peptide bonds; In linear amides / regulation of telomere maintenance / mitotic sister chromatid cohesion / histone deacetylase activity / nuclear chromosome / Notch-HLH transcription pathway ...histone decrotonylase activity / histone deacetylase activity, hydrolytic mechanism / histone deacetylase / protein lysine deacetylase activity / Hydrolases; Acting on carbon-nitrogen bonds, other than peptide bonds; In linear amides / regulation of telomere maintenance / mitotic sister chromatid cohesion / histone deacetylase activity / nuclear chromosome / Notch-HLH transcription pathway / histone deacetylase complex / Hsp70 protein binding / negative regulation of protein ubiquitination / Resolution of Sister Chromatid Cohesion / HDACs deacetylate histones / Hsp90 protein binding / regulation of protein stability / NOTCH1 Intracellular Domain Regulates Transcription / Constitutive Signaling by NOTCH1 PEST Domain Mutants / Constitutive Signaling by NOTCH1 HD+PEST Domain Mutants / Separation of Sister Chromatids / heterochromatin formation / chromatin organization / DNA-binding transcription factor binding / negative regulation of transcription by RNA polymerase II / nucleoplasm / metal ion binding / nucleus / cytoplasm
Similarity search - Function
Histone deacetylase / Histone deacetylase domain / Arginase; Chain A / : / Histone deacetylase family / Histone deacetylase domain / Histone deacetylase domain superfamily / Histone deacetylase domain / Ureohydrolase domain superfamily / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
: / 7-AMINO-4-METHYL-CHROMEN-2-ONE / Histone deacetylase 8
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.31 Å
AuthorsDecroos, C. / Bowman, C.B. / Moser, J.-A.S. / Christianson, K.E. / Deardorff, M.A. / Christianson, D.W.
CitationJournal: Acs Chem.Biol. / Year: 2014
Title: Compromised Structure and Function of HDAC8 Mutants Identified in Cornelia de Lange Syndrome Spectrum Disorders.
Authors: Decroos, C. / Bowman, C.M. / Moser, J.A. / Christianson, K.E. / Deardorff, M.A. / Christianson, D.W.
History
DepositionMay 2, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 6, 2014Provider: repository / Type: Initial release
Revision 1.1Oct 1, 2014Group: Database references
Revision 1.2Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Dec 6, 2023Group: Data collection / Derived calculations / Category: chem_comp_atom / chem_comp_bond / struct_conn
Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2 / _struct_conn.pdbx_leaving_atom_flag

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Histone deacetylase 8
B: tetrapeptide substrate
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,3267
Polymers43,9152
Non-polymers4115
Water88349
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2020 Å2
ΔGint-42 kcal/mol
Surface area14580 Å2
MethodPISA
Unit cell
Length a, b, c (Å)80.406, 80.406, 106.063
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

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Protein / Protein/peptide , 2 types, 2 molecules AB

#1: Protein Histone deacetylase 8 / HD8


Mass: 43235.043 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HDAC8, HDACL1, CDA07 / Plasmid: pHD2-Xa-His / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9BY41, histone deacetylase
#2: Protein/peptide tetrapeptide substrate


Mass: 679.811 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: synthetic peptide

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Non-polymers , 5 types, 54 molecules

#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#4: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: K
#5: Chemical ChemComp-MCM / 7-AMINO-4-METHYL-CHROMEN-2-ONE / 7-AMINO-4-METHYLCOUMARIN


Mass: 175.184 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H9NO2
#6: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 49 / 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: 2.25 Å3/Da / Density % sol: 45.42 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 0.1 M tris(hydroxymethyl)aminomethane) (TRIS, pH = 8.0), 4 mM tris(2-carboxyethyl)phosphine (TCEP), 17.5% PEG 400, VAPOR DIFFUSION, SITTING DROP, temperature 294K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1.075 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Aug 13, 2013 / Details: mirrors
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.075 Å / Relative weight: 1
ReflectionResolution: 2.31→50 Å / Num. all: 17924 / Num. obs: 17922 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 12 % / Biso Wilson estimate: 51.85 Å2 / Rmerge(I) obs: 0.082 / Net I/σ(I): 26.8
Reflection shellResolution: 2.31→2.39 Å / Redundancy: 11.5 % / Rmerge(I) obs: 1.597 / Mean I/σ(I) obs: 2 / Num. unique all: 1740 / % possible all: 100

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Processing

Software
NameVersionClassification
CBASSdata collection
PHASERphasing
PHENIX(phenix.refine: dev_1370)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3EWF

3ewf


Resolution: 2.31→42.19 Å / SU ML: 0.29 / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 28.18 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2415 1814 10.14 %random
Rwork0.2044 ---
obs0.2083 17891 99.94 %-
all-17899 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 57.99 Å2
Refinement stepCycle: LAST / Resolution: 2.31→42.19 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2862 0 22 49 2933
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0022964
X-RAY DIFFRACTIONf_angle_d0.634027
X-RAY DIFFRACTIONf_dihedral_angle_d11.4181063
X-RAY DIFFRACTIONf_chiral_restr0.042439
X-RAY DIFFRACTIONf_plane_restr0.003517
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3095-2.3720.32621420.2861201X-RAY DIFFRACTION100
2.372-2.44170.35171380.27881219X-RAY DIFFRACTION100
2.4417-2.52050.28761430.25961203X-RAY DIFFRACTION100
2.5205-2.61060.30731420.25751225X-RAY DIFFRACTION100
2.6106-2.71510.31021560.23661194X-RAY DIFFRACTION100
2.7151-2.83870.34531160.2551249X-RAY DIFFRACTION100
2.8387-2.98830.30721340.23661217X-RAY DIFFRACTION100
2.9883-3.17550.29221410.23591243X-RAY DIFFRACTION100
3.1755-3.42050.28911480.22131220X-RAY DIFFRACTION100
3.4205-3.76460.22151290.20321241X-RAY DIFFRACTION100
3.7646-4.30880.18871330.18511258X-RAY DIFFRACTION100
4.3088-5.42690.20671450.181264X-RAY DIFFRACTION100
5.4269-42.19660.20851470.1751343X-RAY DIFFRACTION100

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