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

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Basic information

Entry
Database: PDB / ID: 6dvo
TitleCrystal structure of Danio rerio histone deacetylase 6 catalytic domain 2 in complex with Bavarostat
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 / 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
Chem-HBV / : / PROLINE / Hdac6 protein / Histone deacetylase 6
Similarity search - Component
Biological speciesDanio rerio (zebrafish)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.98 Å
AuthorsPorter, N.J. / 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: 2018
Title: Histone Deacetylase 6-Selective Inhibitors and the Influence of Capping Groups on Hydroxamate-Zinc Denticity.
Authors: Porter, N.J. / Osko, J.D. / Diedrich, D. / Kurz, T. / Hooker, J.M. / Hansen, F.K. / Christianson, D.W.
History
DepositionJun 24, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 29, 2018Provider: repository / Type: Initial release
Revision 1.1Sep 26, 2018Group: Data collection / 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 1.2Dec 18, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Oct 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: Hdac6 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,38714
Polymers40,2851
Non-polymers1,10213
Water3,999222
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1510 Å2
ΔGint17 kcal/mol
Surface area13160 Å2
Unit cell
Length a, b, c (Å)97.230, 97.230, 78.900
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number170
Space group name H-MP65

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Hdac6 protein


Mass: 40285.484 Da / Num. of mol.: 1
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

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Non-polymers , 6 types, 235 molecules

#2: Chemical ChemComp-ZN / ZINC ION


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


Mass: 39.098 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: K
#4: Chemical ChemComp-PRO / PROLINE


Type: L-peptide linking / Mass: 115.130 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H9NO2
#5: Chemical ChemComp-HBV / 3-fluoro-N-hydroxy-4-[(methyl{[(3s,5s,7s)-tricyclo[3.3.1.1~3,7~]decan-1-yl]methyl}amino)methyl]benzamide / Bavarostat


Mass: 346.439 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H27FN2O2
#6: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C2H6O2
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 222 / 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: 2.72 Å3/Da / Density % sol: 54.73 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop
Details: 200 mM L-proline; 100 mM HEPES (pH 7.5); 24% PEG 1,500

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.97946 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jun 15, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97946 Å / Relative weight: 1
ReflectionResolution: 1.98→84.2 Å / Num. obs: 29613 / % possible obs: 100 % / Redundancy: 9.5 % / Biso Wilson estimate: 17.83 Å2 / CC1/2: 0.99 / Rmerge(I) obs: 0.312 / Net I/σ(I): 8 / Num. measured all: 282074 / Scaling rejects: 188
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Net I/σ(I) obs% possible all
1.98-2.039.61.741986320790.6551.9100
9.07-84.210.60.05835783370.99931.399.9

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Processing

Software
NameVersionClassification
Aimless0.5.32data scaling
PHENIX1.12_2829refinement
PDB_EXTRACT3.24data extraction
iMOSFLMdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5EEM

5eem


Resolution: 1.98→42.102 Å / SU ML: 0.19 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 21.89
RfactorNum. reflection% reflection
Rfree0.2158 1422 4.81 %
Rwork0.1683 --
obs0.1706 29563 99.93 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 69.9 Å2 / Biso mean: 22.9751 Å2 / Biso min: 7.03 Å2
Refinement stepCycle: final / Resolution: 1.98→42.102 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2750 0 68 222 3040
Biso mean--30.95 29.2 -
Num. residues----352
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0042932
X-RAY DIFFRACTIONf_angle_d0.7143972
X-RAY DIFFRACTIONf_chiral_restr0.046429
X-RAY DIFFRACTIONf_plane_restr0.004517
X-RAY DIFFRACTIONf_dihedral_angle_d18.941737
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 10 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
1.9802-2.05090.27271450.234927792924
2.0509-2.1330.32011390.238228152954
2.133-2.23010.30391220.217528052927
2.2301-2.34770.27211620.205827792941
2.3477-2.49480.2421390.183228432982
2.4948-2.68740.25961230.17428102933
2.6874-2.95770.20361650.170328002965
2.9577-3.38560.20531280.155928292957
3.3856-4.26480.1591450.129828162961
4.2648-42.11150.16781540.13628653019

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