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- PDB-6uo4: Crystal structure of Danio rerio histone deacetylase 6 catalytic ... -

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Basic information

Entry
Database: PDB / ID: 6uo4
TitleCrystal structure of Danio rerio histone deacetylase 6 catalytic domain 1 (CD1) Y363F mutant complexed with Trichostatin A
ComponentsHistone deacetylase 6
KeywordsHYDROLASE / Histone Deacetylase
Function / homology
Function and homology information


Aggrephagy / negative regulation of cellular component organization / positive regulation of cellular component organization / regulation of biological quality / deacetylase activity / tubulin deacetylase activity / mitochondrion localization / swimming behavior / definitive hemopoiesis / regulation of microtubule-based process ...Aggrephagy / negative regulation of cellular component organization / positive regulation of cellular component organization / regulation of biological quality / deacetylase activity / tubulin deacetylase activity / mitochondrion localization / swimming behavior / definitive hemopoiesis / regulation of microtubule-based process / protein lysine deacetylase activity / potassium ion binding / response to stress / hematopoietic progenitor cell differentiation / transferase activity / actin binding / chromatin organization / angiogenesis / perikaryon / axon / dendrite / centrosome / zinc ion binding / nucleus / cytoplasm / cytosol
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 / Histone deacetylase domain ...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
: / TRICHOSTATIN A / Protein deacetylase HDAC6
Similarity search - Component
Biological speciesDanio rerio (zebrafish)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.26830986453 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 / pdbx_struct_conn_angle / struct_conn
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_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_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

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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)81,44910
Polymers80,5572
Non-polymers8928
Water10,124562
1
A: Histone deacetylase 6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,7255
Polymers40,2791
Non-polymers4464
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Histone deacetylase 6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,7255
Polymers40,2791
Non-polymers4464
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)52.892, 124.407, 55.630
Angle α, β, γ (deg.)90.000, 114.462, 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

#1: Protein Histone deacetylase 6


Mass: 40278.594 Da / Num. of mol.: 2 / Mutation: Y363F
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
#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-TSN / TRICHOSTATIN A / 7-[4-(DIMETHYLAMINO)PHENYL]-N-HYDROXY-4,6-DIMETHYL-7-OXO-2,4-HEPTADIENAMIDE


Mass: 302.368 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C17H22N2O3 / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 562 / Source method: isolated from a natural source / Formula: H2O
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: 2.07 Å3/Da / Density % sol: 40.52 % / Description: Perfect Diamond Shape
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop
Details: 10 mg/ml HDAC6 CD1 2 mM Inhibitor 0.2 M sodium malonate (pH 7.0) 20% 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-C / Wavelength: 0.98 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Jun 8, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.26830986453→62.2035 Å / Num. obs: 162601 / % possible obs: 94.5 % / Redundancy: 3.5 % / Biso Wilson estimate: 13.0998328981 Å2 / CC1/2: 0.995 / Rmerge(I) obs: 0.076 / Rpim(I) all: 0.048 / Net I/σ(I): 10.1
Reflection shellResolution: 1.27→1.31 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.578 / Mean I/σ(I) obs: 1.8 / Num. unique obs: 15378 / CC1/2: 0.731 / Rpim(I) all: 0.378 / % possible all: 87.9

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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: 1.26830986453→62.2035 Å / SU ML: 0.134358508977 / Cross valid method: FREE R-VALUE / σ(F): 1.3472700715 / Phase error: 21.4415458187
RfactorNum. reflection% reflection
Rfree0.196446701692 7662 4.71217712177 %
Rwork0.181584811089 --
obs0.182294719231 162600 94.3478336554 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 18.1736205762 Å2
Refinement stepCycle: LAST / Resolution: 1.26830986453→62.2035 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5459 0 50 562 6071
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.004569205187985732
X-RAY DIFFRACTIONf_angle_d0.7681141402317817
X-RAY DIFFRACTIONf_chiral_restr0.074768551924862
X-RAY DIFFRACTIONf_plane_restr0.005132721069981025
X-RAY DIFFRACTIONf_dihedral_angle_d20.36332757722041
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.26830986453-1.28270.2837537751492270.2710537026954697X-RAY DIFFRACTION85.6794849487
1.2827-1.29780.2488504963082350.2668007779674946X-RAY DIFFRACTION90.1356993737
1.2978-1.31360.2743014666662420.256027764135031X-RAY DIFFRACTION92.5087719298
1.3136-1.33030.284729183312800.2408041342075050X-RAY DIFFRACTION92.970521542
1.3303-1.34780.2641744324122540.2401623185845137X-RAY DIFFRACTION93.9853556485
1.3478-1.36620.260962232052550.2387864863635126X-RAY DIFFRACTION93.7783199721
1.3662-1.38580.2356827558932770.2333348810215138X-RAY DIFFRACTION94.2886992861
1.3858-1.40640.2425979537052540.2286130670095142X-RAY DIFFRACTION94.3191749694
1.4064-1.42840.2480473718272460.2234816424435160X-RAY DIFFRACTION93.8541666667
1.4284-1.45180.2452603584632490.2234289807275114X-RAY DIFFRACTION94.4356400775
1.4518-1.47690.2575977607742300.2235290466655187X-RAY DIFFRACTION94.061469005
1.4769-1.50370.2420625363912160.2124864655765199X-RAY DIFFRACTION93.9614783967
1.5037-1.53270.2272939816152480.2080100705895075X-RAY DIFFRACTION94.0127163546
1.5327-1.5640.2250845532762610.2031049417555142X-RAY DIFFRACTION93.3483068417
1.564-1.5980.2300272164432070.1919927736064912X-RAY DIFFRACTION89.2589363557
1.598-1.63510.2275541688982530.1887593583275260X-RAY DIFFRACTION96.0787730917
1.6351-1.6760.212222119172570.194179437325267X-RAY DIFFRACTION96.4722319246
1.676-1.72140.2019294114852750.1868130948835256X-RAY DIFFRACTION96.0743442765
1.7214-1.7720.2066943335842700.1875261764745245X-RAY DIFFRACTION96.6018567175
1.772-1.82920.1975781164782640.1811928980475320X-RAY DIFFRACTION96.8267730189
1.8292-1.89460.199013526032530.182648800055298X-RAY DIFFRACTION96.5895249695
1.8946-1.97050.1984353553272490.1844224190575277X-RAY DIFFRACTION96.4566241927
1.9705-2.06010.2156095906752410.1808619614945314X-RAY DIFFRACTION96.3740458015
2.0601-2.16880.185108298732410.1785052303484932X-RAY DIFFRACTION90.1376546437
2.1688-2.30460.2014580790882800.1771597882435120X-RAY DIFFRACTION93.8477580813
2.3046-2.48260.1952847399373210.180741771045311X-RAY DIFFRACTION98.0160111382
2.4826-2.73240.1913263152263210.1786360954085321X-RAY DIFFRACTION98.138806749
2.7324-3.12780.1941453264492680.1752571958935428X-RAY DIFFRACTION98.3425414365
3.1278-3.94060.1617807371322500.1535326418285288X-RAY DIFFRACTION95.9459459459
3.9406-62.20350.1442611053872380.14792662445245X-RAY DIFFRACTION93.9352407058

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