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- PDB-5wgm: Crystal structure of Danio rerio histone deacetylase 6 catalytic ... -

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Basic information

Entry
Database: PDB / ID: 5wgm
TitleCrystal structure of Danio rerio histone deacetylase 6 catalytic domain 2 in complex with ACY-1083
ComponentsHdac6 protein
KeywordsHYDROLASE/HYDROLASE INHIBITOR / histone deacetylase / hydrolase inhibitor / HYDROLASE-HYDROLASE INHIBITOR complex
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 / chromatin organization / actin binding / angiogenesis / perikaryon / axon / dendrite / centrosome / zinc ion binding / nucleus / cytosol / cytoplasm
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-AH7 / : / DI(HYDROXYETHYL)ETHER / TRIETHYLENE GLYCOL / Protein deacetylase HDAC6 / Protein deacetylase HDAC6
Similarity search - Component
Biological speciesDanio rerio (zebrafish)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 Å
AuthorsPorter, N.J. / Christianson, D.W.
CitationJournal: Proc. Natl. Acad. Sci. U.S.A. / Year: 2017
Title: Unusual zinc-binding mode of HDAC6-selective hydroxamate inhibitors.
Authors: Porter, N.J. / Mahendran, A. / Breslow, R. / Christianson, D.W.
History
DepositionJul 14, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 6, 2017Provider: repository / Type: Initial release
Revision 1.1Dec 20, 2017Group: Database references / Category: citation
Item: _citation.journal_abbrev / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Jan 3, 2018Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Oct 4, 2023Group: Advisory / Data collection ...Advisory / 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 / pdbx_unobs_or_zero_occ_residues / struct_conn / struct_conn_type
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.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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.ptnr1_symmetry / _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 / _struct_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry / _struct_conn_type.id
Revision 1.4Dec 25, 2024Group: Advisory / Derived calculations / Structure summary
Category: pdbx_entry_details / pdbx_validate_symm_contact ...pdbx_entry_details / pdbx_validate_symm_contact / struct_conn / struct_conn_type

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)125,14156
Polymers120,8563
Non-polymers4,28553
Water17,330962
1
A: Hdac6 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,71618
Polymers40,2851
Non-polymers1,43117
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Hdac6 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,70820
Polymers40,2851
Non-polymers1,42319
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Hdac6 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,71618
Polymers40,2851
Non-polymers1,43117
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)97.813, 174.304, 149.064
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11B-1176-

HOH

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Components

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Protein , 1 types, 3 molecules ABC

#1: Protein Hdac6 protein / histone deacetylase 6


Mass: 40285.484 Da / Num. of mol.: 3 / Fragment: catalytic domain 2 (UNP residues 288-646)
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 , 7 types, 1015 molecules

#2: Chemical ChemComp-ZN / ZINC ION


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


Mass: 39.098 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: K
#4: Chemical ChemComp-AH7 / 2-[(4,4-difluoro-1-phenylcyclohexyl)amino]-N-hydroxypyrimidine-5-carboxamide


Mass: 348.347 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C17H18F2N4O2
#5: Chemical...
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 37 / Source method: obtained synthetically / Formula: C2H6O2
#6: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H14O4
#7: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 962 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationN

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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: 2.63 Å3/Da / Density % sol: 53.21 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / Details: magnesium acetate, sodium cacodylate, PEG8000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.97946 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 6, 2017
RadiationMonochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97946 Å / Relative weight: 1
ReflectionResolution: 1.75→49.953 Å / Num. obs: 127773 / % possible obs: 99.9 % / Redundancy: 6.8 % / Net I/σ(I): 8
Reflection shellHighest resolution: 1.75 Å

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Processing

Software
NameVersionClassification
PHENIX(dev_2776: ???)refinement
iMOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 5EEM

5eem


Resolution: 1.75→49.953 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 17.75
RfactorNum. reflection% reflection
Rfree0.1852 6481 5.07 %
Rwork0.1587 --
obs0.1601 127727 99.92 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.75→49.953 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8391 0 266 962 9619
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0129097
X-RAY DIFFRACTIONf_angle_d1.11912303
X-RAY DIFFRACTIONf_dihedral_angle_d19.6275369
X-RAY DIFFRACTIONf_chiral_restr0.0731315
X-RAY DIFFRACTIONf_plane_restr0.0081614
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.75-1.76990.30982180.26953989X-RAY DIFFRACTION100
1.7699-1.79070.25152100.25524003X-RAY DIFFRACTION100
1.7907-1.81260.26362080.23724037X-RAY DIFFRACTION100
1.8126-1.83550.2551970.21733993X-RAY DIFFRACTION100
1.8355-1.85970.26032090.20374012X-RAY DIFFRACTION100
1.8597-1.88510.22322160.19294019X-RAY DIFFRACTION100
1.8851-1.91210.22742020.18514000X-RAY DIFFRACTION100
1.9121-1.94060.2181900.1774048X-RAY DIFFRACTION100
1.9406-1.97090.21732120.16954003X-RAY DIFFRACTION100
1.9709-2.00320.19862370.17564010X-RAY DIFFRACTION100
2.0032-2.03780.2171970.17964053X-RAY DIFFRACTION100
2.0378-2.07480.21192340.17543966X-RAY DIFFRACTION100
2.0748-2.11470.18641850.17024036X-RAY DIFFRACTION100
2.1147-2.15790.20792480.16164015X-RAY DIFFRACTION100
2.1579-2.20480.20442020.15764018X-RAY DIFFRACTION100
2.2048-2.25610.18012360.14994031X-RAY DIFFRACTION100
2.2561-2.31250.1862180.14854012X-RAY DIFFRACTION100
2.3125-2.37510.20322150.1564041X-RAY DIFFRACTION100
2.3751-2.4450.17922170.15114036X-RAY DIFFRACTION100
2.445-2.52390.19572080.14964024X-RAY DIFFRACTION100
2.5239-2.61410.17181940.14974066X-RAY DIFFRACTION100
2.6141-2.71870.18172060.15014066X-RAY DIFFRACTION100
2.7187-2.84240.17822380.15294008X-RAY DIFFRACTION100
2.8424-2.99230.20212170.15474071X-RAY DIFFRACTION100
2.9923-3.17970.17452500.1574026X-RAY DIFFRACTION100
3.1797-3.42520.1822210.15694084X-RAY DIFFRACTION100
3.4252-3.76980.15631990.13334094X-RAY DIFFRACTION100
3.7698-4.3150.11662140.12864096X-RAY DIFFRACTION100
4.315-5.43540.12942310.12724141X-RAY DIFFRACTION100
5.4354-49.97350.19252520.16374248X-RAY DIFFRACTION100

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