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- PDB-6q0z: Crystal structure of Danio rerio histone deacetylase 6 catalytic ... -

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Basic information

Entry
Database: PDB / ID: 6q0z
TitleCrystal structure of Danio rerio histone deacetylase 6 catalytic domain 2 complexed with JS28
ComponentsHdac6 protein
KeywordsHYDROLASE/HYDROLASE INHIBITOR / Histone deacetylase / metallohydrolase / HYDROLASE-HYDROLASE INHIBITOR complex
Function / homology
Function and homology information


Aggrephagy / tubulin deacetylase activity / swimming behavior / definitive hemopoiesis / protein lysine deacetylase activity / regulation of tubulin deacetylation / histone deacetylase activity / potassium ion binding / histone deacetylase complex / hematopoietic progenitor cell differentiation ...Aggrephagy / tubulin deacetylase activity / swimming behavior / definitive hemopoiesis / protein lysine deacetylase activity / regulation of tubulin deacetylation / histone deacetylase activity / potassium ion binding / histone deacetylase complex / hematopoietic progenitor cell differentiation / epigenetic regulation of gene expression / angiogenesis / zinc ion binding
Similarity search - Function
Ubiquitin Carboxyl-terminal Hydrolase-like zinc finger / Zinc finger, UBP-type / Zn-finger in ubiquitin-hydrolases and other protein / Zinc finger UBP-type profile. / Histone deacetylase domain / Arginase; Chain A / : / Histone deacetylase family / Histone deacetylase domain / Histone deacetylase domain superfamily ...Ubiquitin Carboxyl-terminal Hydrolase-like zinc finger / Zinc finger, UBP-type / Zn-finger in ubiquitin-hydrolases and other protein / Zinc finger UBP-type profile. / Histone deacetylase domain / Arginase; Chain A / : / Histone deacetylase family / Histone deacetylase domain / Histone deacetylase domain superfamily / Histone deacetylase domain / Ureohydrolase domain superfamily / Zinc finger, RING/FYVE/PHD-type / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
: / Chem-P7V / Hdac6 protein / Histone deacetylase 6
Similarity search - Component
Biological speciesDanio rerio (zebrafish)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 Å
AuthorsOsko, J.D. / Christianson, D.W.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI)GM49758 United States
CitationJournal: J.Med.Chem. / Year: 2020
Title: Exploring Structural Determinants of Inhibitor Affinity and Selectivity in Complexes with Histone Deacetylase 6.
Authors: Osko, J.D. / Porter, N.J. / Narayana Reddy, P.A. / Xiao, Y.C. / Rokka, J. / Jung, M. / Hooker, J.M. / Salvino, J.M. / Christianson, D.W.
History
DepositionAug 2, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 5, 2020Provider: repository / Type: Initial release
Revision 1.1Oct 11, 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 / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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

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Assembly

Deposited unit
A: Hdac6 protein
B: Hdac6 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)80,30310
Polymers79,4502
Non-polymers8538
Water10,052558
1
A: Hdac6 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,1525
Polymers39,7251
Non-polymers4274
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Hdac6 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,1525
Polymers39,7251
Non-polymers4274
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)48.170, 55.340, 74.240
Angle α, β, γ (deg.)73.04, 89.86, 83.01
Int Tables number1
Space group name H-MP1

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Components

#1: Protein Hdac6 protein / Histone Deacetylase 6


Mass: 39724.973 Da / Num. of mol.: 2 / Fragment: catalytic domain 2 (UNP residues 290-646)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Danio rerio (zebrafish) / Gene: hdac6 / Production host: Escherichia coli (E. coli) / References: UniProt: A7YT55, UniProt: F8W4B7*PLUS
#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-P7V / 2-(4-bromophenyl)-N-hydroxy-1,3-oxazole-4-carboxamide


Mass: 283.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H7BrN2O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 558 / 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: 2.39 Å3/Da / Density % sol: 48.43 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop
Details: 10 mg/mL zCD2 protein, 2.0 mM JS28 inhibitor, 0.2 M sodium citrate, 20% w/v PEG3350, 1:1 ratio of protein to precipitant

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.98 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 15, 2017
RadiationMonochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.75→37.8 Å / Num. obs: 73413 / % possible obs: 81.7 % / Redundancy: 3.8 % / CC1/2: 0.995 / Rmerge(I) obs: 0.12 / Rpim(I) all: 0.07 / Net I/σ(I): 8.5
Reflection shellResolution: 1.75→1.81 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.735 / Mean I/σ(I) obs: 1.9 / Num. unique obs: 5538 / CC1/2: 0.766 / Rpim(I) all: 0.435 / % possible all: 78.4

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Processing

Software
NameClassification
PHENIXrefinement
MOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 5EEM

5eem


Resolution: 1.75→37.8 Å / Cross valid method: FREE R-VALUE /
Num. reflection% reflection
obs59962 78.4 %
Refinement stepCycle: LAST / Resolution: 1.75→37.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5460 0 38 558 6056

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