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- PDB-8tq0: Crystal structure of Danio rerio histone deacetylase 6 catalytic ... -

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Basic information

Entry
Database: PDB / ID: 8tq0
TitleCrystal structure of Danio rerio histone deacetylase 6 catalytic domain 2 complexed with (R)-Lipoic Acid
ComponentsHdac6 protein
KeywordsHYDROLASE/INHIBITOR / Hydrolase / histone deacetylase / inhibitor / metallohydrolase / HYDROLASE-INHIBITOR complex
Function / homology
Function and homology information


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 family / Histone deacetylase domain / Histone deacetylase domain superfamily / Histone deacetylase domain / Ureohydrolase domain superfamily / Zinc finger, RING/FYVE/PHD-type
Similarity search - Domain/homology
: / DIHYDROLIPOIC ACID / Protein deacetylase HDAC6
Similarity search - Component
Biological speciesDanio rerio (zebrafish)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsWatson, P.R. / Christianson, D.W.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM49758 United States
CitationJournal: J.Biol.Chem. / Year: 2023
Title: Crystal structure of histone deacetylase 6 complexed with (R)-lipoic acid, an essential cofactor in central carbon metabolism.
Authors: Watson, P.R. / Stollmaier, J.G. / Christianson, D.W.
History
DepositionAug 6, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 20, 2023Provider: repository / Type: Initial release
Revision 1.1Oct 4, 2023Group: Structure summary / Category: struct / Item: _struct.title
Revision 1.2Apr 3, 2024Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)81,27510
Polymers80,5712
Non-polymers7048
Water2,378132
1
A: Hdac6 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,6375
Polymers40,2851
Non-polymers3524
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Hdac6 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,6375
Polymers40,2851
Non-polymers3524
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)74.894, 92.156, 96.666
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
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1(chain "A" and (resid 442 through 450 or resid 452...
d_2ens_1(chain "B" and (resid 442 through 450 or resid 452...

NCS domain segments:

Ens-ID: ens_1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
d_11PROPROGLNGLNAA442 - 4508 - 16
d_12METMETMETMETAA452 - 45818 - 24
d_13ASPASPTHRTHRAA460 - 74826 - 314
d_14ILEILEMETMETAA750 - 754316 - 320
d_15METMETASPASPAA756 - 770322 - 336
d_16PROPROLEULEUAA774 - 797340 - 363
d_17RLARLARLARLAAC801
d_21PROPROGLNGLNBB442 - 4508 - 16
d_22METMETMETMETBB452 - 45818 - 24
d_23ASPASPTHRTHRBB460 - 74826 - 314
d_24ILEILEMETMETBB750 - 754316 - 320
d_25METMETLEULEUBB756 - 797322 - 363
d_26RLARLARLARLABD801

NCS oper: (Code: givenMatrix: (-0.99992316308, -0.00962145118213, -0.00781636822633), (-0.00973070720516, 0.999853773379, 0.0140621903389), (0.00767992658736, 0.0141371686341, -0.999870571219)Vector: ...NCS oper: (Code: given
Matrix: (-0.99992316308, -0.00962145118213, -0.00781636822633), (-0.00973070720516, 0.999853773379, 0.0140621903389), (0.00767992658736, 0.0141371686341, -0.999870571219)
Vector: 74.8779383517, 0.228196033112, 22.1704033196)

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Components

#1: Protein Hdac6 protein / Histone Deacetylase 6


Mass: 40285.484 Da / Num. of mol.: 2 / Fragment: catalytic domain 2
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
#2: Chemical ChemComp-RED / DIHYDROLIPOIC ACID


Mass: 208.341 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H16O2S2 / Feature type: SUBJECT OF INVESTIGATION
#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.: 132 / 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: 40.58 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop
Details: 10 mg/mL HDAC6, 0.2 M potassium citrate tribasic and 20% (w/v) polyethylene glycol 3,350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSLS-II / Beamline: 17-ID-2 / Wavelength: 0.98 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jul 10, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.4→29.6 Å / Num. obs: 26674 / % possible obs: 98.65 % / Redundancy: 9.2 % / Biso Wilson estimate: 17.94 Å2 / CC1/2: 0.993 / Rmerge(I) obs: 0.218 / Net I/σ(I): 8.7
Reflection shellResolution: 2.4→2.49 Å / Rmerge(I) obs: 0.665 / Mean I/σ(I) obs: 4.9 / Num. unique obs: 2782 / CC1/2: 0.965

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.4→29.6 Å / SU ML: 0.2764 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 29.924
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2484 3731 7.52 %
Rwork0.2067 26451 -
obs0.2099 26452 98.22 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 18.19 Å2
Refinement stepCycle: LAST / Resolution: 2.4→29.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5402 0 27 132 5561
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00285567
X-RAY DIFFRACTIONf_angle_d0.55447566
X-RAY DIFFRACTIONf_chiral_restr0.042840
X-RAY DIFFRACTIONf_plane_restr0.0043983
X-RAY DIFFRACTIONf_dihedral_angle_d7.7125771
Refine LS restraints NCSType: Torsion NCS / Rms dev position: 0.406366706465 Å
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4-2.430.37371490.23861737X-RAY DIFFRACTION99.89
2.43-2.460.26881450.23191680X-RAY DIFFRACTION100
2.46-2.50.28961550.22571741X-RAY DIFFRACTION99.89
2.5-2.530.3011180.22981720X-RAY DIFFRACTION99.46
2.53-2.570.2551450.23821736X-RAY DIFFRACTION99.63
2.57-2.610.28531520.2131723X-RAY DIFFRACTION99.52
2.61-2.650.3541370.23921672X-RAY DIFFRACTION98.37
2.65-2.70.34641220.26871743X-RAY DIFFRACTION97.39
2.7-2.750.26031540.23341692X-RAY DIFFRACTION99.73
2.75-2.80.24021190.23351740X-RAY DIFFRACTION99.79
2.8-2.860.31251560.22541701X-RAY DIFFRACTION99.73
2.86-2.920.25951450.22871711X-RAY DIFFRACTION99.84
2.92-2.990.23491360.22371788X-RAY DIFFRACTION99.84
2.99-3.060.25021410.22151692X-RAY DIFFRACTION99.78
3.06-3.140.30381310.22331743X-RAY DIFFRACTION99.95
3.14-3.240.26931400.22071737X-RAY DIFFRACTION99.84
3.24-3.340.28661360.22151721X-RAY DIFFRACTION99.89
3.34-3.460.30611350.22641692X-RAY DIFFRACTION97.91
3.46-3.60.26861300.21581669X-RAY DIFFRACTION95.19
3.6-3.760.25241110.22461399X-RAY DIFFRACTION81.84
3.76-3.960.23211300.23271490X-RAY DIFFRACTION85.81
3.96-4.210.21131330.15911744X-RAY DIFFRACTION99.95
4.21-4.530.15071440.14511704X-RAY DIFFRACTION99.95
4.53-4.990.16891410.15121730X-RAY DIFFRACTION99.79
4.99-5.70.15751460.16321733X-RAY DIFFRACTION100
5.7-7.160.21911340.18621727X-RAY DIFFRACTION99.89
7.17-29.60.21411460.1611716X-RAY DIFFRACTION99.15

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