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

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Basic information

Entry
Database: PDB / ID: 6uoc
TitleCrystal structure of Danio rerio histone deacetylase 6 catalytic domain 1 (CD1) K330L mutant complexed with Givinostat
ComponentsHistone deacetylase 6HDAC6
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 / regulation of tubulin deacetylation / potassium ion binding ...: / Aggrephagy / : / tubulin deacetylase activity / swimming behavior / definitive hemopoiesis / protein lysine deacetylase activity / histone deacetylase activity / regulation of tubulin deacetylation / potassium ion binding / histone deacetylase complex / hematopoietic progenitor cell differentiation / angiogenesis / negative regulation of transcription by RNA polymerase II / 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 / 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
: / Givinostat / Histone deacetylase 6
Similarity search - Component
Biological speciesDanio rerio (zebrafish)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.40000794136 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.ptnr1_label_atom_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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,0308
Polymers40,2791
Non-polymers7517
Water7,782432
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area870 Å2
ΔGint10 kcal/mol
Surface area13190 Å2
MethodPISA
Unit cell
Length a, b, c (Å)55.160, 60.400, 122.160
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, 1 molecules A

#1: Protein Histone deacetylase 6 / HDAC6


Mass: 40278.570 Da / Num. of mol.: 1 / 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 , 5 types, 439 molecules

#2: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#4: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: K
#5: Chemical ChemComp-QCM / Givinostat / {6-[(diethylamino)methyl]naphthalen-2-yl}methyl [4-(hydroxycarbamoyl)phenyl]carbamate / Givinostat


Mass: 421.489 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C24H27N3O4 / Feature type: SUBJECT OF INVESTIGATION
Comment: medication, antineoplastic, antiinflammatory, inhibitor*YM
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 432 / 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: 2.53 Å3/Da / Density % sol: 51.31 % / Description: Thin/Thick Plate-Like Shape
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop
Details: 10 mg/ml HDAC6 CD1 2 mM Inhibitor 0.2 M magnesium formate dihydrate 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-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: 1.4→42.9476472842 Å / Num. obs: 80865 / % possible obs: 99.7 % / Redundancy: 6.5 % / Biso Wilson estimate: 11.016022672 Å2 / CC1/2: 0.995 / Rmerge(I) obs: 0.094 / Rpim(I) all: 0.04 / Net I/σ(I): 12.4
Reflection shellResolution: 1.4→1.45 Å / Redundancy: 6.7 % / Rmerge(I) obs: 0.359 / Mean I/σ(I) obs: 5.6 / Num. unique obs: 7985 / CC1/2: 0.952 / Rpim(I) all: 0.15 / % possible all: 99.7

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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: 1.40000794136→42.9476472842 Å / SU ML: 0.095673127259 / Cross valid method: FREE R-VALUE / σ(F): 1.33792355939 / Phase error: 15.2008364571
RfactorNum. reflection% reflection
Rfree0.16849740174 4046 5.00340072961 %
Rwork0.151739496756 --
obs0.152590456209 80865 99.6917955988 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 15.2124829674 Å2
Refinement stepCycle: LAST / Resolution: 1.40000794136→42.9476472842 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2756 0 46 432 3234
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.005841856928493010
X-RAY DIFFRACTIONf_angle_d0.8412883676474110
X-RAY DIFFRACTIONf_chiral_restr0.077647729394446
X-RAY DIFFRACTIONf_plane_restr0.00583739087982540
X-RAY DIFFRACTIONf_dihedral_angle_d20.94355095011095
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.40000794136-1.41650.1966034683431620.1656087178932613X-RAY DIFFRACTION99.712540424
1.4165-1.43380.1998523363351200.1659494979942606X-RAY DIFFRACTION99.6709323583
1.4338-1.45190.1907566203781390.1674518986582599X-RAY DIFFRACTION99.7086671522
1.4519-1.4710.1965368264451430.1616069421232622X-RAY DIFFRACTION99.7834716709
1.471-1.49120.1726126287781300.1579306404882645X-RAY DIFFRACTION99.5337159254
1.4912-1.51250.1706318985811400.1510773696342593X-RAY DIFFRACTION99.4903531125
1.5125-1.5350.1689091797141310.1502966329462626X-RAY DIFFRACTION99.4588744589
1.535-1.5590.1688646408531490.1494095241882568X-RAY DIFFRACTION99.3418647166
1.559-1.58460.1672214350571530.1461825326022619X-RAY DIFFRACTION99.4261119082
1.5846-1.61190.1704878706921470.1378351776362614X-RAY DIFFRACTION99.4954954955
1.6119-1.64120.1687944382211240.1453958817742637X-RAY DIFFRACTION99.6750902527
1.6412-1.67280.1659915591441390.1446719882622658X-RAY DIFFRACTION99.8571938593
1.6728-1.70690.1762002839431310.1423558518442607X-RAY DIFFRACTION99.8177178272
1.7069-1.74410.1684849854081210.1445186293332631X-RAY DIFFRACTION99.7462848858
1.7441-1.78460.169521551261440.1489651473512648X-RAY DIFFRACTION99.7142857143
1.7846-1.82930.1793870844061350.1473691313322643X-RAY DIFFRACTION99.7844827586
1.8293-1.87870.1621159732381310.1514668963542637X-RAY DIFFRACTION99.7837058399
1.8787-1.9340.1733857619331400.1523793520832645X-RAY DIFFRACTION99.7492836676
1.934-1.99640.1897624200091340.155016165082639X-RAY DIFFRACTION99.6764917326
1.9964-2.06780.1670842368341230.1548251285772649X-RAY DIFFRACTION99.604743083
2.0678-2.15060.1775561602891370.1532746182972655X-RAY DIFFRACTION99.5365418895
2.1506-2.24840.1592906363021450.1521863812092652X-RAY DIFFRACTION99.7503566334
2.2484-2.3670.187467170071460.1575925824292616X-RAY DIFFRACTION98.9964157706
2.367-2.51530.1725047966061540.1571990165922690X-RAY DIFFRACTION100
2.5153-2.70940.1782355220791440.1580883251022671X-RAY DIFFRACTION100
2.7094-2.9820.17719067211470.1610581127052698X-RAY DIFFRACTION100
2.982-3.41340.1613370197681270.1563659405132746X-RAY DIFFRACTION100
3.4134-4.29990.1490134422491590.1371204616942721X-RAY DIFFRACTION99.8266897747
4.2999-42.94764728420.1490751808161510.1495940680472871X-RAY DIFFRACTION99.9338624339

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