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

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Basic information

Entry
Database: PDB / ID: 5eem
TitleCrystal structure of Danio rerio histone deacetylase 6 catalytic domain 2
ComponentsHdac6 protein
KeywordsHYDROLASE
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
FORMIC ACID / : / Hdac6 protein / Histone deacetylase 6
Similarity search - Component
Biological speciesDanio rerio (zebrafish)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsHai, Y. / Christianson, D.W.
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 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_oper_list / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation / _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

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Assembly

Deposited unit
B: Hdac6 protein
A: Hdac6 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)80,92710
Polymers80,5712
Non-polymers3568
Water5,531307
1
B: Hdac6 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,4986
Polymers40,2851
Non-polymers2135
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Hdac6 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,4294
Polymers40,2851
Non-polymers1443
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)48.485, 55.400, 74.183
Angle α, β, γ (deg.)73.58, 89.84, 82.64
Int Tables number1
Space group name H-MP1

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Components

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Protein , 1 types, 2 molecules BA

#1: Protein Hdac6 protein / histone deacetylase 6


Mass: 40285.484 Da / Num. of mol.: 2 / 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

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Non-polymers , 5 types, 315 molecules

#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#3: Chemical
ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: K
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#5: Chemical ChemComp-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CH2O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 307 / 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: 2.35 Å3/Da / Density % sol: 47.69 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop
Details: 0.1 M sodium acetate, 0.1 M sodium formate, 20% PEG3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.97918 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Aug 15, 2015
RadiationMonochromator: single crystal Si(220) side bounce / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. obs: 47957 / % possible obs: 97 % / Redundancy: 1.9 % / Rmerge(I) obs: 0.162 / Net I/σ(I): 6.4
Reflection shellResolution: 2→2.15 Å / Redundancy: 1.9 % / Rmerge(I) obs: 0.501 / Mean I/σ(I) obs: 1.8 / % possible all: 96.6

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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→15.91 Å / SU ML: 0.28 / Cross valid method: FREE R-VALUE / σ(F): 1.98 / Phase error: 29.19 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2727 2416 5.04 %
Rwork0.2236 --
obs0.226 47934 96.71 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2→15.91 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5496 0 10 307 5813
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0055693
X-RAY DIFFRACTIONf_angle_d0.8787740
X-RAY DIFFRACTIONf_dihedral_angle_d12.4882075
X-RAY DIFFRACTIONf_chiral_restr0.033850
X-RAY DIFFRACTIONf_plane_restr0.0041010
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9994-2.04020.32131520.27412446X-RAY DIFFRACTION89
2.0402-2.08440.34131320.27042676X-RAY DIFFRACTION96
2.0844-2.13280.3391340.2642720X-RAY DIFFRACTION97
2.1328-2.1860.35261440.25492660X-RAY DIFFRACTION96
2.186-2.2450.31441480.24432654X-RAY DIFFRACTION97
2.245-2.31080.33121410.23352728X-RAY DIFFRACTION97
2.3108-2.38520.29381410.24012670X-RAY DIFFRACTION97
2.3852-2.47010.28911340.2442696X-RAY DIFFRACTION97
2.4701-2.56860.30011290.23782693X-RAY DIFFRACTION97
2.5686-2.6850.31021660.23642673X-RAY DIFFRACTION97
2.685-2.82580.28091380.23762700X-RAY DIFFRACTION98
2.8258-3.00180.2831450.22422706X-RAY DIFFRACTION98
3.0018-3.23180.26511390.22332715X-RAY DIFFRACTION98
3.2318-3.55370.22741640.19792685X-RAY DIFFRACTION98
3.5537-4.06050.23451420.18892732X-RAY DIFFRACTION98
4.0605-5.08780.19851220.18842713X-RAY DIFFRACTION98
5.0878-15.91080.24041450.21322651X-RAY DIFFRACTION96

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