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- PDB-4qa1: Crystal structure of A188T HDAC8 in complex with M344 -

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Basic information

Entry
Database: PDB / ID: 4qa1
TitleCrystal structure of A188T HDAC8 in complex with M344
ComponentsHistone deacetylase 8
KeywordsHYDROLASE / metalloenzyme / histone deacetylase / enzyme inhibitor complex / Cornelia de Lange Syndrome / arginase/deacetylase fold
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 / 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-B3N / : / Histone deacetylase 8
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.92 Å
AuthorsDecroos, C. / Bowman, C.B. / Moser, J.-A.S. / Christianson, K.E. / Deardorff, M.A. / Christianson, D.W.
CitationJournal: Acs Chem.Biol. / Year: 2014
Title: Compromised Structure and Function of HDAC8 Mutants Identified in Cornelia de Lange Syndrome Spectrum Disorders.
Authors: Decroos, C. / Bowman, C.M. / Moser, J.A. / Christianson, K.E. / Deardorff, M.A. / Christianson, D.W.
History
DepositionMay 2, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 6, 2014Provider: repository / Type: Initial release
Revision 1.1Oct 1, 2014Group: Database references
Revision 1.2Sep 20, 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_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_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
D: Histone deacetylase 8
hetero molecules


Theoretical massNumber of molelcules
Total (without water)175,22024
Polymers173,0484
Non-polymers2,17220
Water21,9961221
1
A: Histone deacetylase 8
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,8056
Polymers43,2621
Non-polymers5435
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Histone deacetylase 8
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,8977
Polymers43,2621
Non-polymers6356
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Histone deacetylase 8
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,8056
Polymers43,2621
Non-polymers5435
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Histone deacetylase 8
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,7135
Polymers43,2621
Non-polymers4514
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)98.419, 82.648, 105.649
Angle α, β, γ (deg.)90.00, 102.15, 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: 43262.016 Da / Num. of mol.: 4 / Mutation: A188T
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HDAC8, HDACL1, CDA07 / Plasmid: pHD2-Xa-His / Production host: Escherichia coli (E. coli) / Strain (production host): BL(21)DE3 / References: UniProt: Q9BY41, histone deacetylase

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Non-polymers , 5 types, 1241 molecules

#2: Chemical
ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: K
#3: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#4: 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
#5: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1221 / 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: 2.43 Å3/Da / Density % sol: 49.33 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 0.1 M (Bis(2-hydroxyethyl)-amino-tris(hydroxymethyl)-methane) (BISTRIS, pH = 6.5), 4 mM tris(2-carboxyethyl)phosphine (TCEP), 20% PEG 8000, VAPOR DIFFUSION, SITTING DROP, temperature 294K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1.075 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jan 31, 2012 / Details: mirrors
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.075 Å / Relative weight: 1
ReflectionResolution: 1.92→50 Å / Num. all: 126947 / Num. obs: 124361 / % possible obs: 98 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 3.1 % / Biso Wilson estimate: 22.66 Å2 / Rmerge(I) obs: 0.088 / Net I/σ(I): 10.7
Reflection shellResolution: 1.92→2.07 Å / Redundancy: 3 % / Rmerge(I) obs: 0.609 / Mean I/σ(I) obs: 2 / Num. unique all: 12138 / % possible all: 96.7

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Processing

Software
NameVersionClassification
CBASSdata collection
PHASERphasing
PHENIX(phenix.refine: dev_1370)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3EWF

3ewf


Resolution: 1.92→47.614 Å / SU ML: 0.21 / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 24.5 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2146 6219 5 %random
Rwork0.1745 ---
obs0.1765 124299 97.19 %-
all-127879 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 28.28 Å2
Refinement stepCycle: LAST / Resolution: 1.92→47.614 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11270 0 124 1221 12615
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00511930
X-RAY DIFFRACTIONf_angle_d0.89716238
X-RAY DIFFRACTIONf_dihedral_angle_d12.584384
X-RAY DIFFRACTIONf_chiral_restr0.0631772
X-RAY DIFFRACTIONf_plane_restr0.0042072
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9129-1.93460.34341680.27042972X-RAY DIFFRACTION74
1.9346-1.95740.2782120.24753949X-RAY DIFFRACTION97
1.9574-1.98120.26652100.23613898X-RAY DIFFRACTION97
1.9812-2.00630.28021980.22643901X-RAY DIFFRACTION96
2.0063-2.03270.27682080.22593893X-RAY DIFFRACTION97
2.0327-2.06050.27241960.21293913X-RAY DIFFRACTION97
2.0605-2.090.25542270.21223830X-RAY DIFFRACTION96
2.09-2.12120.24982200.2033889X-RAY DIFFRACTION97
2.1212-2.15430.23922000.20113901X-RAY DIFFRACTION97
2.1543-2.18960.25081900.19493877X-RAY DIFFRACTION96
2.1896-2.22740.25152070.18723927X-RAY DIFFRACTION97
2.2274-2.26790.232340.18383866X-RAY DIFFRACTION97
2.2679-2.31150.21352050.18923916X-RAY DIFFRACTION97
2.3115-2.35870.27232390.18733914X-RAY DIFFRACTION97
2.3587-2.410.22942090.18263951X-RAY DIFFRACTION98
2.41-2.46610.23592190.18413975X-RAY DIFFRACTION98
2.4661-2.52770.25962000.18393964X-RAY DIFFRACTION98
2.5277-2.59610.23192240.18313962X-RAY DIFFRACTION99
2.5961-2.67240.21091900.17394054X-RAY DIFFRACTION99
2.6724-2.75870.26092020.1773982X-RAY DIFFRACTION99
2.7587-2.85730.22392000.18154043X-RAY DIFFRACTION99
2.8573-2.97170.24012130.16933995X-RAY DIFFRACTION99
2.9717-3.10690.20631840.17454041X-RAY DIFFRACTION99
3.1069-3.27070.20922170.17564030X-RAY DIFFRACTION99
3.2707-3.47550.22452120.16844016X-RAY DIFFRACTION99
3.4755-3.74380.18511860.15444070X-RAY DIFFRACTION99
3.7438-4.12030.17541940.14084071X-RAY DIFFRACTION99
4.1203-4.71610.15192120.13184053X-RAY DIFFRACTION99
4.7161-5.940.17482270.15864091X-RAY DIFFRACTION100
5.94-47.62830.18262160.17484136X-RAY DIFFRACTION99

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