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- PDB-7jvw: Crystal structure of human histone deacetylase 8 (HDAC8) G320R mu... -

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Basic information

Entry
Database: PDB / ID: 7jvw
TitleCrystal structure of human histone deacetylase 8 (HDAC8) G320R mutation complexed with M344
ComponentsHistone deacetylase 8
KeywordsHYDROLASE / Histone deacetylase / Cornelia de Lange Syndrome (CdLS)
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 / histone deacetylase activity / mitotic sister chromatid cohesion / 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 / 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 / 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 family / Histone deacetylase domain / Histone deacetylase domain superfamily / Histone deacetylase domain / Ureohydrolase domain superfamily
Similarity search - Domain/homology
Chem-B3N / : / Histone deacetylase 8
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.40301779656 Å
AuthorsOsko, J.D. / Christianson, D.W. / Decroos, C. / Porter, N.J. / Lee, M.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM49758 United States
CitationJournal: J.Struct.Biol. / Year: 2020
Title: Structural analysis of histone deacetylase 8 mutants associated with Cornelia de Lange Syndrome spectrum disorders.
Authors: Osko, J.D. / Porter, N.J. / Decroos, C. / Lee, M.S. / Watson, P.R. / Raible, S.E. / Krantz, I.D. / Deardorff, M.A. / Christianson, D.W.
History
DepositionAug 24, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 16, 2020Provider: repository / Type: Initial release
Revision 1.1Dec 30, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Oct 18, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)87,56610
Polymers86,6642
Non-polymers9028
Water2,576143
1
A: Histone deacetylase 8
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,7835
Polymers43,3321
Non-polymers4514
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Histone deacetylase 8
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,7835
Polymers43,3321
Non-polymers4514
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)52.980, 82.750, 94.520
Angle α, β, γ (deg.)90.000, 98.840, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

#1: Protein Histone deacetylase 8 / HD8


Mass: 43332.137 Da / Num. of mol.: 2 / Mutation: G320R
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HDAC8, HDACL1, CDA07 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9BY41, histone deacetylase
#2: Chemical ChemComp-B3N / 4-(dimethylamino)-N-[7-(hydroxyamino)-7-oxoheptyl]benzamide / M344


Mass: 307.388 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C16H25N3O3
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#4: Chemical
ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: K
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 143 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 47.93 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / pH: 5.3 / Details: 0.1 M MES, pH 5.3, 3% PEG1500, 4 mM TCEP

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL14-1 / Wavelength: 1 Å
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Dec 9, 2015
RadiationMonochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.4→82.75 Å / Num. obs: 31564 / % possible obs: 97.4 % / Redundancy: 3.8 % / Biso Wilson estimate: 34.6910203953 Å2 / CC1/2: 0.981 / Rmerge(I) obs: 0.148 / Rpim(I) all: 0.09 / Net I/σ(I): 8.7
Reflection shellResolution: 2.4→2.49 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.961 / Mean I/σ(I) obs: 1.7 / Num. unique obs: 30670 / CC1/2: 0.578 / Rpim(I) all: 0.571 / % possible all: 96

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Processing

Software
NameVersionClassification
PHENIX1.11.1_2575refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 3EWF

3ewf


Resolution: 2.40301779656→48.9900201109 Å / SU ML: 0.381622707936 / Cross valid method: FREE R-VALUE / σ(F): 1.33674203891 / Phase error: 29.5397908894
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.254332779861 1566 5.12484864352 %
Rwork0.195250273152 28991 -
obs0.198349862029 30557 96.818858718 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 40.6687983774 Å2
Refinement stepCycle: LAST / Resolution: 2.40301779656→48.9900201109 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5376 0 50 143 5569
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.007770213140425599
X-RAY DIFFRACTIONf_angle_d0.933757187347610
X-RAY DIFFRACTIONf_chiral_restr0.0531953909583839
X-RAY DIFFRACTIONf_plane_restr0.00601023546547967
X-RAY DIFFRACTIONf_dihedral_angle_d7.597674280074425
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.404-2.48060.3633732737521440.2840912745412545X-RAY DIFFRACTION95.253276656
2.4806-2.56920.3696618609621450.2846493326492609X-RAY DIFFRACTION96.2600489339
2.5692-2.67210.3343417889141350.2790483098932623X-RAY DIFFRACTION95.4986149584
2.6721-2.79370.3199999550151400.2398280879192607X-RAY DIFFRACTION96.5893108298
2.7937-2.9410.3370730881341360.2171128459662624X-RAY DIFFRACTION96.7402733964
2.941-3.12520.2892052861671370.2071693852512630X-RAY DIFFRACTION97.1558988764
3.1252-3.36640.2523531158191390.1953603200242634X-RAY DIFFRACTION97.1278458844
3.3664-3.70510.2749035813091400.2056252973612648X-RAY DIFFRACTION97.2105997211
3.7051-4.2410.2193718517841410.1653046230382661X-RAY DIFFRACTION97.2916666667
4.241-5.34220.2020702670431630.1492540042322667X-RAY DIFFRACTION97.957770855
5.3422-48.980.1941902126261460.1663106756952743X-RAY DIFFRACTION97.8990172823

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