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- PDB-3f0r: Crystal Structure Analysis of Human HDAC8 complexed with trichost... -

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Basic information

Entry
Database: PDB / ID: 3f0r
TitleCrystal Structure Analysis of Human HDAC8 complexed with trichostatin A in a new monoclinic crystal form
ComponentsHistone deacetylase 8
KeywordsHYDROLASE / HDAC / metalloenzyme / acetylation / arginase fold / HDAC8 / histone deacetylase 8 / hydroxamate inhibitor / Alternative splicing / Chromatin regulator / Nucleus / Repressor / Transcription / Transcription regulation
Function / homology
Function and homology information


histone decrotonylase activity / histone deacetylase / protein lysine deacetylase activity / regulation of telomere maintenance / Hydrolases; Acting on carbon-nitrogen bonds, other than peptide bonds; In linear amides / histone deacetylase activity / mitotic sister chromatid cohesion / nuclear chromosome / Notch-HLH transcription pathway / histone deacetylase complex ...histone decrotonylase activity / histone deacetylase / protein lysine deacetylase activity / regulation of telomere maintenance / Hydrolases; Acting on carbon-nitrogen bonds, other than peptide bonds; In linear amides / histone deacetylase activity / mitotic sister chromatid cohesion / 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 / 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
: / TRICHOSTATIN A / Histone deacetylase 8
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.54 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 25, 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 / 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_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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_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)131,77018
Polymers129,5253
Non-polymers2,24515
Water1,820101
1
A: Histone deacetylase 8
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,9236
Polymers43,1751
Non-polymers7485
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Histone deacetylase 8
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,9236
Polymers43,1751
Non-polymers7485
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Histone deacetylase 8
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,9236
Polymers43,1751
Non-polymers7485
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)87.895, 90.705, 92.141
Angle α, β, γ (deg.)90.00, 94.63, 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.: 3 / 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-TSN / TRICHOSTATIN A / 7-[4-(DIMETHYLAMINO)PHENYL]-N-HYDROXY-4,6-DIMETHYL-7-OXO-2,4-HEPTADIENAMIDE / Trichostatin A


Mass: 302.368 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C17H22N2O3 / Comment: antifungal, antibiotic*YM
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 101 / 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: 56.48 %
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 ...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: CHESS / Beamline: F1 / Wavelength: 0.9124 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Feb 3, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9124 Å / Relative weight: 1
ReflectionResolution: 2.54→50 Å / Num. all: 45639 / Num. obs: 45639 / % possible obs: 96.8 % / Redundancy: 3.2 % / Biso Wilson estimate: 63.4 Å2 / Rmerge(I) obs: 0.097 / Net I/σ(I): 11.7
Reflection shellResolution: 2.54→2.63 Å / Redundancy: 3 % / Rmerge(I) obs: 0.508 / Mean I/σ(I) obs: 2.3 / Num. unique all: 4566 / % possible all: 97.4

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Processing

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

1w22


Resolution: 2.54→40.97 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 87356.13 / 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
Rfree0.258 2177 5.1 %RANDOM
Rwork0.21 ---
obs0.21 43041 90 %-
all-45639 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 43.55 Å2 / ksol: 0.35 e/Å3
Displacement parametersBiso mean: 57.9 Å2
Baniso -1Baniso -2Baniso -3
1-10.12 Å20 Å2-3.51 Å2
2---2.73 Å20 Å2
3----7.39 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.41 Å0.33 Å
Luzzati d res low-5 Å
Luzzati sigma a0.47 Å0.4 Å
Refinement stepCycle: LAST / Resolution: 2.54→40.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8461 0 141 101 8703
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_deg1.2
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d22.2
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.82
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.381.5
X-RAY DIFFRACTIONc_mcangle_it2.332
X-RAY DIFFRACTIONc_scbond_it1.892
X-RAY DIFFRACTIONc_scangle_it2.92.5
LS refinement shellResolution: 2.54→2.7 Å / Rfactor Rfree error: 0.02 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.35 313 5.3 %
Rwork0.32 5562 -
obs--74.2 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2tsn.partsn.top
X-RAY DIFFRACTION3water_rep.paramwater.top
X-RAY DIFFRACTION4ion.paramion.top
X-RAY DIFFRACTION5prosthetics.parprosthetics.top

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