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

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Basic information

Entry
Database: PDB / ID: 5efb
TitleCrystal structure of Danio rerio histone deacetylase 6 catalytic domain 2 in complex with oxamflatin
ComponentsHdac6 protein
KeywordsHYDROLASE/HYDROLASE INHIBITOR / 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
Oxamflatin / : / Protein deacetylase HDAC6 / Protein deacetylase HDAC6
Similarity search - Component
Biological speciesDanio rerio (zebrafish)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.543 Å
AuthorsHai, Y. / Christianson, D.W.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM49758 United States
CitationJournal: Nat.Chem.Biol. / Year: 2016
Title: Histone deacetylase 6 structure and molecular basis of catalysis and inhibition.
Authors: Hai, Y. / Christianson, D.W.
History
DepositionOct 23, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 27, 2016Provider: repository / Type: Initial release
Revision 1.1Aug 10, 2016Group: Database references
Revision 1.2Sep 7, 2016Group: Database references
Revision 1.3Sep 13, 2017Group: Author supporting evidence / Derived calculations / Category: pdbx_audit_support / pdbx_struct_oper_list
Item: _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.4Dec 25, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5Sep 27, 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_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _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

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Assembly

Deposited unit
D: Hdac6 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,7715
Polymers40,2851
Non-polymers4864
Water2,576143
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area230 Å2
ΔGint-0 kcal/mol
Surface area12900 Å2
MethodPISA
Unit cell
Length a, b, c (Å)83.447, 94.431, 51.611
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11D-2193-

HOH

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Components

#1: Protein Hdac6 protein / histone deacetylase 6


Mass: 40285.484 Da / Num. of mol.: 1 / 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, histone deacetylase
#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-5OK / Oxamflatin


Mass: 342.369 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H14N2O4S
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 143 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.52 Å3/Da / Density % sol: 51.26 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop
Details: 0.1 M HEPES, pH 7.5, 10% v/v 2-propanol, 20% PEG4000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 4.2.2 / Wavelength: 1.00003 Å
DetectorType: RDI CMOS_8M / Detector: CMOS / Date: Oct 1, 2015
RadiationMonochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.00003 Å / Relative weight: 1
ReflectionResolution: 2.54→50 Å / Num. obs: 13824 / % possible obs: 98.8 % / Redundancy: 4.9 % / Rmerge(I) obs: 0.137 / Net I/σ(I): 11.6
Reflection shellResolution: 2.54→2.75 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.311 / Mean I/σ(I) obs: 3.1 / % possible all: 92.1

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Processing

Software
NameVersionClassification
PHENIX1.8.3_1479refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 5EEK

5eek


Resolution: 2.543→47.215 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 13.37 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1566 1380 9.98 %
Rwork0.1474 --
obs0.1484 13793 96.03 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.543→47.215 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2772 0 27 143 2942
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0082874
X-RAY DIFFRACTIONf_angle_d1.1083900
X-RAY DIFFRACTIONf_dihedral_angle_d13.641051
X-RAY DIFFRACTIONf_chiral_restr0.04423
X-RAY DIFFRACTIONf_plane_restr0.005508
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5429-2.59180.21391070.1938980X-RAY DIFFRACTION75
2.5918-2.64470.18131270.18221093X-RAY DIFFRACTION87
2.6447-2.70220.16991330.16471221X-RAY DIFFRACTION92
2.7022-2.76510.19371320.1791234X-RAY DIFFRACTION95
2.7651-2.83420.15451350.18041251X-RAY DIFFRACTION97
2.8342-2.91080.18691410.1681256X-RAY DIFFRACTION97
2.9108-2.99650.16771420.16461287X-RAY DIFFRACTION98
2.9965-3.09320.18471450.16721257X-RAY DIFFRACTION98
3.0932-3.20370.14391380.16121279X-RAY DIFFRACTION99
3.2037-3.33190.16561390.14521273X-RAY DIFFRACTION99
3.3319-3.48350.14571360.13741304X-RAY DIFFRACTION99
3.4835-3.66710.13331410.12811273X-RAY DIFFRACTION99
3.6671-3.89680.12411450.12581279X-RAY DIFFRACTION99
3.8968-4.19750.12261430.12511271X-RAY DIFFRACTION99
4.1975-4.61960.14271440.11741293X-RAY DIFFRACTION99
4.6196-5.28730.13041470.13281279X-RAY DIFFRACTION99
5.2873-6.65840.21441400.16561288X-RAY DIFFRACTION99
6.6584-47.22360.17631500.14571287X-RAY DIFFRACTION99

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