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- PDB-5tht: Crystal Structure of G303A HDAC8 in complex with M344 -

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Basic information

Entry
Database: PDB / ID: 5tht
TitleCrystal Structure of G303A HDAC8 in complex with M344
ComponentsHistone deacetylase 8
KeywordsHYDROLASE / Zinc Histone Deacetylase
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
Chem-B3N / : / Histone deacetylase 8
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.407 Å
AuthorsPorter, N.J. / Christianson, D.W.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM49758 United States
CitationJournal: Biochemistry / Year: 2016
Title: Structural and Functional Influence of the Glycine-Rich Loop G302GGGY on the Catalytic Tyrosine of Histone Deacetylase 8.
Authors: Porter, N.J. / Christianson, N.H. / Decroos, C. / Christianson, D.W.
History
DepositionSep 30, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 21, 2016Provider: repository / Type: Initial release
Revision 1.1Sep 27, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Apr 18, 2018Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp / citation ...chem_comp / citation / entity / pdbx_entity_nonpoly
Item: _chem_comp.name / _citation.journal_id_ISSN ..._chem_comp.name / _citation.journal_id_ISSN / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _entity.pdbx_description / _pdbx_entity_nonpoly.name
Revision 1.3Dec 25, 2019Group: Author supporting evidence / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_audit_support / pdbx_entity_nonpoly
Item: _chem_comp.name / _entity.pdbx_description ..._chem_comp.name / _entity.pdbx_description / _pdbx_audit_support.funding_organization / _pdbx_entity_nonpoly.name
Revision 1.4Oct 4, 2023Group: Advisory / Data collection ...Advisory / 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 / pdbx_unobs_or_zero_occ_atoms / struct_conn
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

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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
D: Histone deacetylase 8
hetero molecules


Theoretical massNumber of molelcules
Total (without water)176,46447
Polymers172,9844
Non-polymers3,48043
Water3,783210
1
A: Histone deacetylase 8
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,06911
Polymers43,2461
Non-polymers82310
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Histone deacetylase 8
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,00710
Polymers43,2461
Non-polymers7619
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Histone deacetylase 8
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,31815
Polymers43,2461
Non-polymers1,07214
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Histone deacetylase 8
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,06911
Polymers43,2461
Non-polymers82310
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)97.700, 83.810, 99.780
Angle α, β, γ (deg.)90.00, 91.72, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 4 molecules ABCD

#1: Protein
Histone deacetylase 8 / HD8


Mass: 43246.020 Da / Num. of mol.: 4 / Mutation: G303A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HDAC8, HDACL1, CDA07 / Plasmid: pET20b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) / References: UniProt: Q9BY41, histone deacetylase

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Non-polymers , 5 types, 253 molecules

#2: Chemical
ChemComp-B3N / 4-(dimethylamino)-N-[7-(hydroxyamino)-7-oxoheptyl]benzamide / M344


Mass: 307.388 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C16H25N3O3
#3: Chemical
ChemComp-ZN / ZINC ION


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


Mass: 39.098 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: K
#5: Chemical...
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 27 / Source method: obtained synthetically / Formula: C2H6O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 210 / 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: 2.36 Å3/Da / Density % sol: 47.89 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / Details: 100 mM HEPES (pH 7.5), 22% w/v PEG 6000, 4 mM TCEP

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.97923 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 9, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97923 Å / Relative weight: 1
ReflectionResolution: 2.407→97.66 Å / Num. obs: 62588 / % possible obs: 99.9 % / Redundancy: 3.5 % / CC1/2: 0.996 / Rmerge(I) obs: 0.068 / Rsym value: 0.066 / Net I/σ(I): 12.5

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
iMOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3EWF

3ewf


Resolution: 2.407→97.656 Å / SU ML: 0.23 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 20.06
RfactorNum. reflection% reflection
Rfree0.2123 2928 4.68 %
Rwork0.1802 --
obs0.1817 62558 99.87 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.407→97.656 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10950 0 208 210 11368
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00211502
X-RAY DIFFRACTIONf_angle_d0.46515582
X-RAY DIFFRACTIONf_dihedral_angle_d15.6466726
X-RAY DIFFRACTIONf_chiral_restr0.041709
X-RAY DIFFRACTIONf_plane_restr0.0031997
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.407-2.44650.27461270.22752835X-RAY DIFFRACTION99
2.4465-2.48870.28271220.22052795X-RAY DIFFRACTION100
2.4887-2.53390.27321300.20832822X-RAY DIFFRACTION100
2.5339-2.58270.21891810.20012813X-RAY DIFFRACTION100
2.5827-2.63540.24721160.18892820X-RAY DIFFRACTION100
2.6354-2.69270.22831410.1992834X-RAY DIFFRACTION100
2.6927-2.75530.23491460.20142789X-RAY DIFFRACTION100
2.7553-2.82420.2461500.19932813X-RAY DIFFRACTION100
2.8242-2.90060.26781130.19682882X-RAY DIFFRACTION100
2.9006-2.9860.24121430.19052835X-RAY DIFFRACTION100
2.986-3.08230.19381530.19072814X-RAY DIFFRACTION100
3.0823-3.19250.24981230.19012825X-RAY DIFFRACTION100
3.1925-3.32030.2081630.19322832X-RAY DIFFRACTION100
3.3203-3.47150.20971620.18812824X-RAY DIFFRACTION100
3.4715-3.65450.21541250.17392872X-RAY DIFFRACTION100
3.6545-3.88350.19271420.16492821X-RAY DIFFRACTION100
3.8835-4.18330.19811150.16022888X-RAY DIFFRACTION100
4.1833-4.60430.15251830.14432819X-RAY DIFFRACTION100
4.6043-5.27050.17431340.15762872X-RAY DIFFRACTION100
5.2705-6.64010.21411320.17782874X-RAY DIFFRACTION100
6.6401-97.73630.20361270.1652951X-RAY DIFFRACTION99

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