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- PDB-7jvu: Crystal structure of human histone deacetylase 8 (HDAC8) I45T mut... -

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Basic information

Entry
Database: PDB / ID: 7jvu
TitleCrystal structure of human histone deacetylase 8 (HDAC8) I45T mutation complexed with SAHA
ComponentsHistone deacetylase 8
KeywordsHYDROLASE / Histone deacetylase / Cornelia de Lange Syndrome (CdLS)
Function / homology
Function and homology information


histone decrotonylase activity / 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 ...histone decrotonylase activity / 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 / negative regulation of protein ubiquitination / Resolution of Sister Chromatid Cohesion / Hsp70 protein binding / epigenetic regulation of gene expression / 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 / nucleus / metal ion binding / 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
: / OCTANEDIOIC ACID HYDROXYAMIDE PHENYLAMIDE / Histone deacetylase 8
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5004765401 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)87,69017
Polymers86,4402
Non-polymers1,25015
Water11,440635
1
A: Histone deacetylase 8
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,8769
Polymers43,2201
Non-polymers6568
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Histone deacetylase 8
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,8148
Polymers43,2201
Non-polymers5947
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)53.314, 84.118, 94.281
Angle α, β, γ (deg.)90.000, 99.064, 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

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Protein , 1 types, 2 molecules AB

#1: Protein Histone deacetylase 8 / HD8


Mass: 43219.938 Da / Num. of mol.: 2 / Mutation: I45T
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

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Non-polymers , 5 types, 650 molecules

#2: Chemical ChemComp-ZN / ZINC ION


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


Mass: 39.098 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: K
#4: Chemical ChemComp-SHH / OCTANEDIOIC ACID HYDROXYAMIDE PHENYLAMIDE / SAHA


Mass: 264.320 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C14H20N2O3
#5: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C2H6O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 635 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.42 Å3/Da / Density % sol: 49.07 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / Details: 0.1 M imidazole, pH 7.0, 15% PEG35000, 4 mM TCEP / PH range: 7-8

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.98 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Aug 15, 2015
RadiationMonochromator: Cryogenically-cooled single crystal Si(220) side bounce
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.5→55.91 Å / Num. obs: 131305 / % possible obs: 99.8 % / Redundancy: 5.6 % / Biso Wilson estimate: 16.8670373583 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.074 / Rpim(I) all: 0.034 / Net I/σ(I): 19.5
Reflection shellResolution: 1.5→1.55 Å / Redundancy: 5.1 % / Rmerge(I) obs: 0.795 / Mean I/σ(I) obs: 2.3 / Num. unique obs: 130929 / CC1/2: 0.757 / Rpim(I) all: 0.389 / % possible all: 99.9

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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: 1.5004765401→15.9951076656 Å / SU ML: 0.129063430768 / Cross valid method: FREE R-VALUE / σ(F): 1.33718454107 / Phase error: 19.0740531924
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.184587196948 6593 5.03690008709 %
Rwork0.164399381995 124301 -
obs0.165440737685 130894 99.8725784177 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 22.8636882906 Å2
Refinement stepCycle: LAST / Resolution: 1.5004765401→15.9951076656 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5597 0 72 635 6304
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00523781757195914
X-RAY DIFFRACTIONf_angle_d0.8052324292828038
X-RAY DIFFRACTIONf_chiral_restr0.0527454343713875
X-RAY DIFFRACTIONf_plane_restr0.0053862959911041
X-RAY DIFFRACTIONf_dihedral_angle_d7.121198346424700
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5005-1.51750.2684836237022040.2516172539794083X-RAY DIFFRACTION98.2130584192
1.5175-1.53540.2722970553012050.240527634014157X-RAY DIFFRACTION99.9541704858
1.5354-1.55410.2740818746472090.2304206827184135X-RAY DIFFRACTION99.9769850403
1.5541-1.57370.2280021740292200.2196154945344134X-RAY DIFFRACTION99.9770378875
1.5737-1.59440.2207396934492350.2082248722254105X-RAY DIFFRACTION100
1.5944-1.61620.2496436010852310.210559364644144X-RAY DIFFRACTION99.9771480804
1.6162-1.63930.2282404153382170.1948472872734104X-RAY DIFFRACTION100
1.6393-1.66370.227739168412040.1948485259614173X-RAY DIFFRACTION99.954327472
1.6637-1.68970.203957012562110.1836541021934110X-RAY DIFFRACTION99.9768625636
1.6897-1.71740.2293339095392040.1809615087044187X-RAY DIFFRACTION100
1.7174-1.7470.1885923402892380.1766076171794123X-RAY DIFFRACTION100
1.747-1.77870.1950245791592240.1728881441094144X-RAY DIFFRACTION100
1.7787-1.81280.1890383452861950.1779543177634097X-RAY DIFFRACTION99.976706266
1.8128-1.84980.2202602079272220.1761204784644172X-RAY DIFFRACTION100
1.8498-1.890.2047649246422210.1708684702394133X-RAY DIFFRACTION100
1.89-1.93390.1980255305842000.1707404887974130X-RAY DIFFRACTION100
1.9339-1.98210.1968917596082060.1756250994254196X-RAY DIFFRACTION99.9772882126
1.9821-2.03560.188771103072090.1741624377944127X-RAY DIFFRACTION100
2.0356-2.09540.1967726123752360.1659901980314120X-RAY DIFFRACTION100
2.0954-2.16290.1899929123562300.1703559921774146X-RAY DIFFRACTION100
2.1629-2.240.1814114841432180.1650075195044145X-RAY DIFFRACTION100
2.24-2.32940.1862430718322250.1626404591494148X-RAY DIFFRACTION100
2.3294-2.43510.2034434481452210.162186132194146X-RAY DIFFRACTION100
2.4351-2.5630.1756987214952460.1623514071084148X-RAY DIFFRACTION99.9772468714
2.563-2.72280.1874206920222480.163088178584114X-RAY DIFFRACTION100
2.7228-2.93180.1800224630852290.1670592933194162X-RAY DIFFRACTION100
2.9318-3.22470.1872583685372320.1642327675854147X-RAY DIFFRACTION100
3.2247-3.68630.1790554233691920.154960767654205X-RAY DIFFRACTION100
3.6863-4.62570.1441170594542350.1306876553634181X-RAY DIFFRACTION100
4.6257-15.9950.1541580794932260.1448534894434185X-RAY DIFFRACTION98.262419247

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