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- PDB-5d1d: Crystal structure of P91L-Y306F HDAC8 in complex with a tetrapept... -

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Basic information

Entry
Database: PDB / ID: 5d1d
TitleCrystal structure of P91L-Y306F HDAC8 in complex with a tetrapeptide substrate
Components
  • HDAC8 Fluor de Lys tetrapeptide substrate
  • Histone deacetylase 8
KeywordsHYDROLASE / histone deacetylase / arginase/deacetylase fold / enzyme substrate complex
Function / homology
Function and homology information


histone decrotonylase activity / histone H4K16 deacetylase activity, hydrolytic mechanism / histone H4K5 deacetylase activity, hydrolytic mechanism / histone H4K8 deacetylase activity, hydrolytic mechanism / histone H3K4 deacetylase activity, hydrolytic mechanism / histone H3K14 deacetylase activity, hydrolytic mechanism / histone H4K12 deacetylase activity, hydrolytic mechanism / histone deacetylase / histone H3K9 deacetylase activity, hydrolytic mechanism / regulation of telomere maintenance ...histone decrotonylase activity / histone H4K16 deacetylase activity, hydrolytic mechanism / histone H4K5 deacetylase activity, hydrolytic mechanism / histone H4K8 deacetylase activity, hydrolytic mechanism / histone H3K4 deacetylase activity, hydrolytic mechanism / histone H3K14 deacetylase activity, hydrolytic mechanism / histone H4K12 deacetylase activity, hydrolytic mechanism / histone deacetylase / histone H3K9 deacetylase activity, hydrolytic mechanism / regulation of telomere maintenance / protein lysine deacetylase activity / Hydrolases; Acting on carbon-nitrogen bonds, other than peptide bonds; In linear amides / 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
: / Histone deacetylase 8
Similarity search - Component
Biological speciesHomo sapiens (human)
unidentified (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.011 Å
AuthorsDecroos, C. / Christianson, N.H. / Gullett, L.E. / Bowman, C.M. / Christianson, K.E. / Deardorff, M.A. / Christianson, D.W.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM49758 United States
Doris Duke Charitable Foundation United States
CitationJournal: Biochemistry / Year: 2015
Title: Biochemical and Structural Characterization of HDAC8 Mutants Associated with Cornelia de Lange Syndrome Spectrum Disorders.
Authors: Decroos, C. / Christianson, N.H. / Gullett, L.E. / Bowman, C.M. / Christianson, K.E. / Deardorff, M.A. / Christianson, D.W.
History
DepositionAug 4, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 21, 2015Provider: repository / Type: Initial release
Revision 1.1Oct 28, 2015Group: Database references
Revision 1.2Nov 11, 2015Group: Database references
Revision 1.3Sep 13, 2017Group: Author supporting evidence / Derived calculations
Category: pdbx_audit_support / pdbx_struct_assembly ...pdbx_audit_support / pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / pdbx_struct_oper_list
Item: _pdbx_audit_support.funding_organization / _pdbx_struct_assembly.oligomeric_details ..._pdbx_audit_support.funding_organization / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_assembly_prop.type / _pdbx_struct_assembly_prop.value / _pdbx_struct_oper_list.symmetry_operation
Revision 1.4Dec 25, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5Sep 27, 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_conn_type
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.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.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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_conn.ptnr2_label_seq_id / _struct_conn_type.id
Revision 1.6Nov 15, 2023Group: Data collection / Derived calculations / Category: chem_comp_atom / chem_comp_bond / struct_conn
Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2 / _struct_conn.pdbx_leaving_atom_flag
Revision 1.7Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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: HDAC8 Fluor de Lys tetrapeptide substrate
D: HDAC8 Fluor de Lys tetrapeptide substrate
hetero molecules


Theoretical massNumber of molelcules
Total (without water)88,42510
Polymers88,1384
Non-polymers2876
Water4,900272
1
A: Histone deacetylase 8
C: HDAC8 Fluor de Lys tetrapeptide substrate
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,2135
Polymers44,0692
Non-polymers1443
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area820 Å2
ΔGint-4 kcal/mol
Surface area14330 Å2
MethodPISA
2
B: Histone deacetylase 8
D: HDAC8 Fluor de Lys tetrapeptide substrate
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,2135
Polymers44,0692
Non-polymers1443
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area760 Å2
ΔGint-6 kcal/mol
Surface area14100 Å2
MethodPISA
Unit cell
Length a, b, c (Å)82.281, 97.987, 105.933
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Histone deacetylase 8 / HD8


Mass: 43232.035 Da / Num. of mol.: 2 / Mutation: P91L Y306F
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): BL21(DE3) / References: UniProt: Q9BY41, histone deacetylase
#2: Protein/peptide HDAC8 Fluor de Lys tetrapeptide substrate


Mass: 836.980 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) unidentified (others)
#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.: 272 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 49.23 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 100 mM Tris (pH 8.0), 10% (w/v) PEG 35000, 4 mM TCEP

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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: Feb 23, 2014
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.075 Å / Relative weight: 1
ReflectionResolution: 2.01→44.5 Å / Num. obs: 57560 / % possible obs: 99.9 % / Redundancy: 9.5 % / Rmerge(I) obs: 0.135 / Net I/σ(I): 13.2
Reflection shellResolution: 2.01→2.08 Å / Redundancy: 9.1 % / Rmerge(I) obs: 1.153 / Mean I/σ(I) obs: 2.1 / % possible all: 98.8

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Processing

Software
NameVersionClassification
PHENIXdev_1833refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3EWF

3ewf


Resolution: 2.011→44.5 Å / SU ML: 0.21 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 20.13 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2064 2915 5.07 %random
Rwork0.1749 ---
obs0.1765 57481 99.82 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.011→44.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5649 0 6 272 5927
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0035858
X-RAY DIFFRACTIONf_angle_d0.7227965
X-RAY DIFFRACTIONf_dihedral_angle_d11.1372073
X-RAY DIFFRACTIONf_chiral_restr0.027871
X-RAY DIFFRACTIONf_plane_restr0.0031021
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.0109-2.04390.28561490.25022498X-RAY DIFFRACTION98
2.0439-2.07910.28571420.24692537X-RAY DIFFRACTION99
2.0791-2.11690.29031390.23382555X-RAY DIFFRACTION100
2.1169-2.15760.2691240.22152604X-RAY DIFFRACTION100
2.1576-2.20170.26851350.21992558X-RAY DIFFRACTION100
2.2017-2.24950.27861400.20412582X-RAY DIFFRACTION100
2.2495-2.30190.2241560.20542528X-RAY DIFFRACTION100
2.3019-2.35940.24661320.20322612X-RAY DIFFRACTION100
2.3594-2.42320.25291480.19752559X-RAY DIFFRACTION100
2.4232-2.49450.22441330.18942569X-RAY DIFFRACTION100
2.4945-2.5750.22491270.18052618X-RAY DIFFRACTION100
2.575-2.6670.19891260.18262599X-RAY DIFFRACTION100
2.667-2.77380.24091320.18342584X-RAY DIFFRACTION100
2.7738-2.90.2251460.18492578X-RAY DIFFRACTION100
2.9-3.05290.21731340.18062624X-RAY DIFFRACTION100
3.0529-3.24410.19891340.18162598X-RAY DIFFRACTION100
3.2441-3.49450.22421290.1762637X-RAY DIFFRACTION100
3.4945-3.8460.17281440.15622624X-RAY DIFFRACTION100
3.846-4.40210.17051230.13672668X-RAY DIFFRACTION100
4.4021-5.54450.16931540.14872666X-RAY DIFFRACTION100
5.5445-44.54760.17581680.16212768X-RAY DIFFRACTION100

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