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- PDB-3f07: Crystal Structure Analysis of Human HDAC8 complexed with APHA in ... -

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Basic information

Entry
Database: PDB / ID: 3f07
TitleCrystal Structure Analysis of Human HDAC8 complexed with APHA in a new monoclinic crystal form
ComponentsHistone deacetylase 8
KeywordsHYDROLASE / HDAC / metalloenzyme / acetylation / arginase fold / HDAC8 / histone deacetylase 8 / hydroxamate inhibitor / mutant / Alternative splicing / Chromatin regulator / Nucleus / Repressor / Transcription / Transcription regulation
Function / homology
Function and homology information


histone decrotonylase activity / histone H4K16 deacetylase activity, hydrolytic mechanism / histone H4K5 deacetylase activity, hydrolytic mechanism / histone H4K8 deacetylase activity, hydrolytic mechanism / histone H3K4 deacetylase activity, hydrolytic mechanism / histone H3K14 deacetylase activity, hydrolytic mechanism / histone H4K12 deacetylase activity, hydrolytic mechanism / histone deacetylase / histone H3K9 deacetylase activity, hydrolytic mechanism / regulation of telomere maintenance ...histone decrotonylase activity / histone H4K16 deacetylase activity, hydrolytic mechanism / histone H4K5 deacetylase activity, hydrolytic mechanism / histone H4K8 deacetylase activity, hydrolytic mechanism / histone H3K4 deacetylase activity, hydrolytic mechanism / histone H3K14 deacetylase activity, hydrolytic mechanism / histone H4K12 deacetylase activity, hydrolytic mechanism / histone deacetylase / histone H3K9 deacetylase activity, hydrolytic mechanism / regulation of telomere maintenance / protein lysine deacetylase activity / Hydrolases; Acting on carbon-nitrogen bonds, other than peptide bonds; In linear amides / mitotic sister chromatid cohesion / histone deacetylase activity / nuclear chromosome / Notch-HLH transcription pathway / histone deacetylase complex / negative regulation of protein ubiquitination / Hsp70 protein binding / 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
Chem-AGE / : / Histone deacetylase 8
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.3 Å
AuthorsDowling, D.P. / Gantt, S.L. / Gattis, S.G. / Fierke, C.A. / Christianson, D.W.
CitationJournal: Biochemistry / Year: 2008
Title: Structural studies of human histone deacetylase 8 and its site-specific variants complexed with substrate and inhibitors.
Authors: Dowling, D.P. / Gantt, S.L. / Gattis, S.G. / Fierke, C.A. / Christianson, D.W.
History
DepositionOct 24, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 30, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Sep 6, 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 / 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 / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_label_atom_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_ref_seq_dif.details / _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: Histone deacetylase 8
B: Histone deacetylase 8
C: Histone deacetylase 8
hetero molecules


Theoretical massNumber of molelcules
Total (without water)130,59015
Polymers129,5253
Non-polymers1,06512
Water25214
1
A: Histone deacetylase 8
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,6686
Polymers43,1751
Non-polymers4935
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Histone deacetylase 8
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,6035
Polymers43,1751
Non-polymers4284
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Histone deacetylase 8
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,3194
Polymers43,1751
Non-polymers1443
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)88.381, 90.171, 92.267
Angle α, β, γ (deg.)90.00, 94.74, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Histone deacetylase 8 / HD8


Mass: 43174.941 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CDA07, HDAC8, HDACL1 / Plasmid: pHD2-Xa-His / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9BY41, histone deacetylase
#2: Chemical
ChemComp-ZN / ZINC ION


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


Mass: 39.098 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: K
#4: Chemical ChemComp-AGE / (2E)-N-hydroxy-3-[1-methyl-4-(phenylacetyl)-1H-pyrrol-2-yl]prop-2-enamide / APHA Compound 8 / 3-(1-Methyl-4-phenylacetyl-1H-2-pyrrolyl)-N-hydroxypropenamide


Mass: 284.310 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C16H16N2O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 14 / 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: 2.83 Å3/Da / Density % sol: 56.52 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 5.8
Details: Final drop concentrations of 25 mM Tris, 2.5% glycerol, 75 mM KCl, 1-5% PEG 6000, 50 mM MES, 1 mM tri(2-carboxyethyl)phosphine (TCEP), 0.03 mM gly-gly-gly, pH 5.8, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X12B / Wavelength: 1.0085 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jul 20, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0085 Å / Relative weight: 1
ReflectionResolution: 3.3→32 Å / Num. all: 21912 / Num. obs: 21912 / % possible obs: 98.8 % / Redundancy: 3.1 % / Biso Wilson estimate: 66.9 Å2 / Rmerge(I) obs: 0.136 / Net I/σ(I): 8
Reflection shellResolution: 3.3→3.42 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.435 / Mean I/σ(I) obs: 3.2 / Num. unique all: 2212 / % possible all: 99.5

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Processing

Software
NameVersionClassification
CBASSdata collection
AMoREphasing
CNS1.2refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1W22

1w22


Resolution: 3.3→31.5 Å / Rfactor Rfree error: 0.009 / Data cutoff high absF: 63030.99 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber / Details: BULK SOLVENT MODEL USED
RfactorNum. reflection% reflectionSelection details
Rfree0.26 828 4 %RANDOM
Rwork0.216 ---
obs0.216 20842 95.2 %-
all-21881 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 20.7651 Å2 / ksol: 0.3 e/Å3
Displacement parametersBiso mean: 60.1 Å2
Baniso -1Baniso -2Baniso -3
1--4.6 Å20 Å2-5.59 Å2
2---3.51 Å20 Å2
3---8.12 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.51 Å0.4 Å
Luzzati d res low-5 Å
Luzzati sigma a0.71 Å0.62 Å
Refinement stepCycle: LAST / Resolution: 3.3→31.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8377 0 52 14 8443
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.008
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_deg1.3
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d22
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.89
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.021.5
X-RAY DIFFRACTIONc_mcangle_it1.822
X-RAY DIFFRACTIONc_scbond_it1.332
X-RAY DIFFRACTIONc_scangle_it2.22.5
LS refinement shellResolution: 3.3→3.51 Å / Rfactor Rfree error: 0.032 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.386 145 4.4 %
Rwork0.315 3170 -
obs--91.9 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2HOHer_rep.paramunk.top
X-RAY DIFFRACTION3ion.paramHOHer.top
X-RAY DIFFRACTION4unk.parion.top

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