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

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Basic information

Entry
Database: PDB / ID: 6dvn
TitleCrystal structure of Danio rerio histone deacetylase 6 catalytic domain 2 in complex with DDK-137
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 / 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
Chem-HB7 / : / Hdac6 protein / Histone deacetylase 6
Similarity search - Component
Biological speciesDanio rerio (zebrafish)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 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: 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 / 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_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_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: Hdac6 protein
B: Hdac6 protein
C: Hdac6 protein
D: Hdac6 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)163,86925
Polymers161,1424
Non-polymers2,72721
Water3,477193
1
A: Hdac6 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,0147
Polymers40,2851
Non-polymers7286
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Hdac6 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,9526
Polymers40,2851
Non-polymers6665
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Hdac6 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,9526
Polymers40,2851
Non-polymers6665
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Hdac6 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,9526
Polymers40,2851
Non-polymers6665
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)78.550, 95.500, 98.250
Angle α, β, γ (deg.)90.00, 98.60, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 4 molecules ABCD

#1: Protein
Hdac6 protein /


Mass: 40285.484 Da / Num. of mol.: 4
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 , 5 types, 214 molecules

#2: Chemical
ChemComp-ZN / ZINC ION


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


Mass: 39.098 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: K
#4: Chemical
ChemComp-HB7 / N-[2-(benzylamino)-2-oxoethyl]-4-(dimethylamino)-N-{[4-(hydroxycarbamoyl)phenyl]methyl}benzamide


Mass: 460.525 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C26H28N4O4
#5: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H6O2
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 193 / 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: 2.26 Å3/Da / Density % sol: 45.6 % / Description: Plate crystals
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 0.2M ammonium tartrate dibasic (7.0), 20% w/v PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 1.18 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 8, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.18 Å / Relative weight: 1
ReflectionResolution: 2.2→95.5 Å / Num. obs: 69939 / % possible obs: 96 % / Redundancy: 5.8 % / CC1/2: 0.987 / Rmerge(I) obs: 0.228 / Rpim(I) all: 0.102 / Net I/σ(I): 7
Reflection shellResolution: 2.2→2.25 Å / Redundancy: 5 % / Rmerge(I) obs: 0.764 / Mean I/σ(I) obs: 2.6 / Num. unique obs: 6728 / CC1/2: 0.721 / Rpim(I) all: 0.371 / % possible all: 92.6

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Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575: ???)refinement
MOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5EEM

5eem


Resolution: 2.2→48.573 Å / SU ML: 0.25 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 22.51
RfactorNum. reflection% reflection
Rfree0.2228 3459 4.95 %
Rwork0.1881 --
obs0.1899 69939 95.93 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.2→48.573 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11062 0 168 193 11423
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00311564
X-RAY DIFFRACTIONf_angle_d0.59815713
X-RAY DIFFRACTIONf_dihedral_angle_d16.3636838
X-RAY DIFFRACTIONf_chiral_restr0.0431704
X-RAY DIFFRACTIONf_plane_restr0.0042058
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2-2.23010.32441550.24622579X-RAY DIFFRACTION94
2.2301-2.2620.29751450.23982479X-RAY DIFFRACTION91
2.262-2.29580.2581310.22122609X-RAY DIFFRACTION93
2.2958-2.33160.25981320.21472704X-RAY DIFFRACTION98
2.3316-2.36990.25711550.22462676X-RAY DIFFRACTION98
2.3699-2.41070.31431300.21192681X-RAY DIFFRACTION97
2.4107-2.45460.2591480.21222721X-RAY DIFFRACTION98
2.4546-2.50180.24271390.21322656X-RAY DIFFRACTION97
2.5018-2.55280.23781360.20442695X-RAY DIFFRACTION97
2.5528-2.60830.26231560.20622626X-RAY DIFFRACTION96
2.6083-2.6690.26451370.20512670X-RAY DIFFRACTION96
2.669-2.73580.25531330.21132698X-RAY DIFFRACTION96
2.7358-2.80970.27431150.21582663X-RAY DIFFRACTION95
2.8097-2.89240.25071020.21392530X-RAY DIFFRACTION90
2.8924-2.98570.28011350.22032687X-RAY DIFFRACTION97
2.9857-3.09240.24271450.21172694X-RAY DIFFRACTION98
3.0924-3.21620.21461390.20612713X-RAY DIFFRACTION98
3.2162-3.36260.23771470.2032717X-RAY DIFFRACTION98
3.3626-3.53980.22761520.1882686X-RAY DIFFRACTION97
3.5398-3.76150.21291350.16712680X-RAY DIFFRACTION96
3.7615-4.05180.17241170.15772560X-RAY DIFFRACTION92
4.0518-4.45930.15681360.1412575X-RAY DIFFRACTION92
4.4593-5.10390.14651600.13282724X-RAY DIFFRACTION99
5.1039-6.42810.16511390.15852758X-RAY DIFFRACTION98
6.4281-48.58450.14861400.12882699X-RAY DIFFRACTION94

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