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

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Basic information

Entry
Database: PDB / ID: 6uob
TitleCrystal structure of Danio rerio histone deacetylase 6 catalytic domain 1 (CD1) K330L mutant complexed with Resminostat
ComponentsHistone deacetylase 6
KeywordsHydrolase/Hydrolase Inhibitor / Histone Deacetylase / Hydrolase-Hydrolase Inhibitor complex
Function / homology
Function and homology information


Aggrephagy / tubulin deacetylase activity / swimming behavior / definitive hemopoiesis / protein lysine deacetylase activity / histone deacetylase activity / potassium ion binding / histone deacetylase complex / hematopoietic progenitor cell differentiation / epigenetic regulation of gene expression ...Aggrephagy / tubulin deacetylase activity / swimming behavior / definitive hemopoiesis / protein lysine deacetylase activity / 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
: / Resminostat / PHENYLALANINE / Protein deacetylase HDAC6
Similarity search - Component
Biological speciesDanio rerio (zebrafish)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.58000577636 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: Biochemistry / Year: 2019
Title: Structural Basis of Catalysis and Inhibition of HDAC6 CD1, the Enigmatic Catalytic Domain of Histone Deacetylase 6.
Authors: Osko, J.D. / Christianson, D.W.
History
DepositionOct 14, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 4, 2019Provider: repository / Type: Initial release
Revision 1.1Dec 18, 2019Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.2Oct 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.pdbx_ptnr2_label_alt_id / _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

Downloads & links

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Assembly

Deposited unit
A: Histone deacetylase 6
B: Histone deacetylase 6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)81,89514
Polymers80,5572
Non-polymers1,33712
Water8,953497
1
A: Histone deacetylase 6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,9997
Polymers40,2791
Non-polymers7206
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Histone deacetylase 6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,8967
Polymers40,2791
Non-polymers6176
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)67.270, 102.620, 112.900
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Histone deacetylase 6


Mass: 40278.570 Da / Num. of mol.: 2 / Mutation: K330L
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Danio rerio (zebrafish) / Gene: hdac6 / Production host: Escherichia coli (E. coli) / References: UniProt: F8W4B7

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Non-polymers , 6 types, 509 molecules

#2: Chemical ChemComp-PHE / PHENYLALANINE


Type: L-peptide linking / Mass: 165.189 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H11NO2
#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: Chemical ChemComp-P7D / Resminostat / (2E)-3-[1-({4-[(dimethylamino)methyl]phenyl}sulfonyl)-1H-pyrrol-3-yl]-N-hydroxyprop-2-enamide


Mass: 349.405 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C16H19N3O4S / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 497 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 49.15 % / Description: Thick rod-like shape
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop
Details: 10 mg/ml HDAC6 CD1 2 mM Inhibitor 0.1 M ammonium citrate tribasic (pH 7.0) 12% PEG 3350 1:1 ratio protein to precipitant

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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: Jul 8, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.58→56.45 Å / Num. obs: 106861 / % possible obs: 99.8 % / Redundancy: 6.5 % / Biso Wilson estimate: 16.2335760404 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.145 / Rpim(I) all: 0.062 / Net I/σ(I): 9.8
Reflection shellResolution: 1.58→1.63 Å / Redundancy: 6.2 % / Rmerge(I) obs: 2.032 / Mean I/σ(I) obs: 1.9 / Num. unique obs: 10560 / CC1/2: 0.502 / Rpim(I) all: 0.88 / % possible all: 99.6

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Processing

Software
NameVersionClassification
PHENIX1.11.1_2575refinement
PHENIX1.11.1_2575refinement
iMOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5EEF

5eef


Resolution: 1.58000577636→56.45 Å / SU ML: 0.164229763548 / Cross valid method: FREE R-VALUE / σ(F): 1.33451691593 / Phase error: 21.6677009037
RfactorNum. reflection% reflection
Rfree0.207736124672 5192 4.8586481504 %
Rwork0.184031372273 --
obs0.185207062797 106861 99.3686070299 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 20.3097732547 Å2
Refinement stepCycle: LAST / Resolution: 1.58000577636→56.45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5489 0 77 497 6063
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.006094576189075838
X-RAY DIFFRACTIONf_angle_d0.8749989198397952
X-RAY DIFFRACTIONf_chiral_restr0.055376984754864
X-RAY DIFFRACTIONf_plane_restr0.005402558488791038
X-RAY DIFFRACTIONf_dihedral_angle_d18.24763892743441
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.58000577636-1.5980.2782349387011670.2584690476143356X-RAY DIFFRACTION99.2114897212
1.598-1.61680.318652892491800.2529513865883340X-RAY DIFFRACTION99.1828684136
1.6168-1.63650.2587556272161690.2460576017233348X-RAY DIFFRACTION98.5982618447
1.6365-1.65720.2724320884511480.243077647153288X-RAY DIFFRACTION97.1719457014
1.6572-1.6790.2604307657911780.2282105435413351X-RAY DIFFRACTION99.2686357243
1.679-1.7020.2626772996631810.2231522749413332X-RAY DIFFRACTION99.9146757679
1.702-1.72630.2561388968781580.2137883129833411X-RAY DIFFRACTION99.9160134378
1.7263-1.75210.2707638392921610.2075133898533370X-RAY DIFFRACTION99.8303647159
1.7521-1.77950.239931845581820.2109017986433362X-RAY DIFFRACTION99.8309859155
1.7795-1.80860.2595316282721730.2158876812933366X-RAY DIFFRACTION99.8871013266
1.8086-1.83980.2370171318081490.2072028339023387X-RAY DIFFRACTION99.915230291
1.8398-1.87330.2383349427571570.2006863124473406X-RAY DIFFRACTION99.9158721256
1.8733-1.90930.2756870230431690.2200624054453360X-RAY DIFFRACTION99.073554183
1.9093-1.94830.3008743447031540.2656797477023304X-RAY DIFFRACTION97.3536036036
1.9483-1.99070.2057321339151740.1945793713523380X-RAY DIFFRACTION99.8875772906
1.9907-2.0370.2392347482311530.1882743625583428X-RAY DIFFRACTION99.944180854
2.037-2.08790.2232459711551780.1928071500433386X-RAY DIFFRACTION99.8599047352
2.0879-2.14440.2046825027161720.1901218868843392X-RAY DIFFRACTION99.9158957107
2.1444-2.20750.206282500331750.1896449928463348X-RAY DIFFRACTION99.858276644
2.2075-2.27870.2845627587991810.2573033106963207X-RAY DIFFRACTION93.591160221
2.2787-2.36020.206168711931640.1829423010693383X-RAY DIFFRACTION99.4950911641
2.3602-2.45470.1758213605641650.1728905959013449X-RAY DIFFRACTION100
2.4547-2.56640.2180003228071740.1786552427243414X-RAY DIFFRACTION100
2.5664-2.70170.1736930569451920.1750525815963395X-RAY DIFFRACTION100
2.7017-2.8710.2266504555091850.1739407813973419X-RAY DIFFRACTION100
2.871-3.09260.1983003220591760.1828646249523440X-RAY DIFFRACTION99.9447208402
3.0926-3.40380.2015445570251860.1748357913913455X-RAY DIFFRACTION99.972542559
3.4038-3.89620.1867591856692080.1564375710823430X-RAY DIFFRACTION99.725877193
3.8962-4.90840.1467275309661980.1332508289463506X-RAY DIFFRACTION100
4.9084-56.450.1625419758311850.1547695422263656X-RAY DIFFRACTION99.7921538062

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