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- PDB-5w5k: Crystal structure of Danio rerio histone deacetylase 6 catalytic ... -

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Basic information

Entry
Database: PDB / ID: 5w5k
TitleCrystal structure of Danio rerio histone deacetylase 6 catalytic domain 2 in complex with KV70
ComponentsHistone deacetylase 6HDAC6
KeywordsHYDROLASE / histone deacetylase / tubulin deacetylase
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-K70 / Hdac6 protein / Histone deacetylase 6
Similarity search - Component
Biological speciesDanio rerio (zebrafish)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsPorter, N.J. / Christianson, D.W.
CitationJournal: J.Med.Chem. / Year: 2019
Title: Synthesis and Biological Investigation of Phenothiazine-Based Benzhydroxamic Acids as Selective Histone Deacetylase 6 Inhibitors.
Authors: Vogerl, K. / Ong, N. / Senger, J. / Herp, D. / Schmidtkunz, K. / Marek, M. / Muller, M. / Bartel, K. / Shaik, T.B. / Porter, N.J. / Robaa, D. / Christianson, D.W. / Romier, C. / Sippl, W. / ...Authors: Vogerl, K. / Ong, N. / Senger, J. / Herp, D. / Schmidtkunz, K. / Marek, M. / Muller, M. / Bartel, K. / Shaik, T.B. / Porter, N.J. / Robaa, D. / Christianson, D.W. / Romier, C. / Sippl, W. / Jung, M. / Bracher, F.
History
DepositionJun 15, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 27, 2018Provider: repository / Type: Initial release
Revision 1.1Jul 10, 2019Group: Data collection / 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
Revision 1.2Oct 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_atoms / 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: Histone deacetylase 6
B: Histone deacetylase 6
C: Histone deacetylase 6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)122,33915
Polymers120,8563
Non-polymers1,48212
Water3,999222
1
A: Histone deacetylase 6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,7805
Polymers40,2851
Non-polymers4944
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Histone deacetylase 6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,7805
Polymers40,2851
Non-polymers4944
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Histone deacetylase 6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,7805
Polymers40,2851
Non-polymers4944
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)101.290, 170.940, 151.370
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein Histone deacetylase 6 / HDAC6 / Hdac6 protein


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
#2: Chemical ChemComp-ZN / ZINC ION


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


Mass: 39.098 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: K
#4: Chemical ChemComp-K70 / 10-{[4-(hydroxycarbamoyl)phenyl]methyl}-5lambda~4~-pyrido[3,2-b][1,4]benzothiazin-10-ium


Mass: 350.414 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C19H16N3O2S / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water / 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: 2.71 Å3/Da / Density % sol: 54.63 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / Details: magnesium acetate, HEPES (pH 7.5), PEG 8,000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS-II / Beamline: 17-ID-1 / Wavelength: 0.9793 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 2, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 2.7→87.141 Å / Num. obs: 34541 / % possible obs: 95.5 % / Redundancy: 2.9 % / Net I/σ(I): 5.5

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Processing

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

5eem


Resolution: 2.7→87.141 Å / Cross valid method: FREE R-VALUE / σ(F): 302.31 / Phase error: 22.08
RfactorNum. reflection% reflection
Rfree0.2195 1913 5.54 %
Rwork0.204 --
obs0.2077 34504 94.7 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.7→87.141 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8296 0 84 222 8602
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0038721
X-RAY DIFFRACTIONf_angle_d0.78311883
X-RAY DIFFRACTIONf_dihedral_angle_d19.0115148
X-RAY DIFFRACTIONf_chiral_restr0.0491292
X-RAY DIFFRACTIONf_plane_restr0.0051567
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7008-2.78020.30751510.27812719X-RAY DIFFRACTION91
2.7802-2.86990.30141490.26392653X-RAY DIFFRACTION88
2.8699-2.97250.29021420.25282721X-RAY DIFFRACTION91
2.9725-3.09150.24891150.24252801X-RAY DIFFRACTION93
3.0915-3.23210.25971420.23482764X-RAY DIFFRACTION92
3.2321-3.40250.21741380.21852731X-RAY DIFFRACTION91
3.4025-3.61550.20681420.20122751X-RAY DIFFRACTION91
3.6155-3.89450.23991420.18332733X-RAY DIFFRACTION91
3.8945-4.28620.18081640.17842718X-RAY DIFFRACTION89
4.2862-4.90560.15141560.16362686X-RAY DIFFRACTION88
4.9056-6.17780.24251380.19322690X-RAY DIFFRACTION87
6.1778-43.5760.18541380.18482780X-RAY DIFFRACTION87

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