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- PDB-5g0j: Crystal structure of Danio rerio HDAC6 CD1 and CD2 (linker intact... -

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Basic information

Entry
Database: PDB / ID: 5g0j
TitleCrystal structure of Danio rerio HDAC6 CD1 and CD2 (linker intact) in complex with Nexturastat A
ComponentsHDAC6
KeywordsCELL CYCLE / HISTONE / HISTONE DEACETYLASE
Function / homology
Function and homology information


Aggrephagy / tubulin deacetylase activity / swimming behavior / definitive hemopoiesis / protein lysine deacetylase activity / regulation of tubulin deacetylation / histone deacetylase activity / potassium ion binding / histone deacetylase complex / hematopoietic progenitor cell differentiation ...Aggrephagy / tubulin deacetylase activity / swimming behavior / definitive hemopoiesis / protein lysine deacetylase activity / regulation of tubulin deacetylation / histone deacetylase activity / 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
: / NEXTURASTAT A / Histone deacetylase 6
Similarity search - Component
Biological speciesDANIO RERIO (zebrafish)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.88 Å
AuthorsMiyake, Y. / Keusch, J.J. / Wang, L. / Saito, M. / Hess, D. / Wang, X. / Melancon, B.J. / Helquist, P. / Gut, H. / Matthias, P.
CitationJournal: Nat.Chem.Biol. / Year: 2016
Title: Structural Insights Into Hdac6 Tubulin Deacetylation and its Selective Inhibition
Authors: Miyake, Y. / Keusch, J.J. / Wang, L. / Saito, M. / Hess, D. / Wang, X. / Melancon, B.J. / Helquist, P. / Gut, H. / Matthias, P.
History
DepositionMar 18, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 27, 2016Provider: repository / Type: Initial release
Revision 1.1Aug 10, 2016Group: Database references
Revision 1.2Sep 28, 2016Group: Database references
Revision 1.3Jan 10, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _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.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_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.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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_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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: HDAC6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)88,18810
Polymers87,5141
Non-polymers6739
Water2,918162
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)187.224, 187.224, 102.718
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

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Protein , 1 types, 1 molecules A

#1: Protein HDAC6


Mass: 87514.406 Da / Num. of mol.: 1 / Fragment: CATALYTIC DOMAIN 1 AND 2, UNP RESIDUES 40-831
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) DANIO RERIO (zebrafish) / Cell line (production host): SF9 / Production host: SPODOPTERA FRUGIPERDA (fall armyworm) / References: UniProt: F8W4B7

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Non-polymers , 5 types, 171 molecules

#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#4: Chemical
ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: K
#5: Chemical ChemComp-N4R / NEXTURASTAT A


Mass: 341.404 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C19H23N3O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 162 / 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: 5.6 Å3/Da / Density % sol: 78 % / Description: NONE
Crystal growDetails: 3.3M SODIUM FORMATE, 17% GLYCEROL, 0.1M TRIS PH 7.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Details: MIRRORS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.88→162.14 Å / Num. obs: 47289 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 11.2 % / Biso Wilson estimate: 88.96 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 20.4
Reflection shellResolution: 2.88→2.89 Å / Redundancy: 11.3 % / Rmerge(I) obs: 0.79 / Mean I/σ(I) obs: 2.4 / % possible all: 100

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Processing

Software
NameVersionClassification
BUSTER2.11.5refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRIES 5G0G AND 5G0H

5g0g

5g0h


Resolution: 2.88→50 Å / Cor.coef. Fo:Fc: 0.898 / Cor.coef. Fo:Fc free: 0.8705 / SU R Cruickshank DPI: 0.259 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.254 / SU Rfree Blow DPI: 0.216 / SU Rfree Cruickshank DPI: 0.22
Details: DIFFRACTION DATA ARE ANISOTROPIC. STRUCTURAL MODELING WAS CARRIED OUT USING MAP SHARPENING
RfactorNum. reflection% reflectionSelection details
Rfree0.2141 2382 5.06 %RANDOM
Rwork0.1756 ---
obs0.1775 47112 99.96 %-
Displacement parametersBiso mean: 90.06 Å2
Baniso -1Baniso -2Baniso -3
1--21.9843 Å20 Å20 Å2
2---21.9843 Å20 Å2
3---43.9685 Å2
Refine analyzeLuzzati coordinate error obs: 0.383 Å
Refinement stepCycle: LAST / Resolution: 2.88→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5860 0 33 162 6055
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.016038HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.228196HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d2053SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes135HARMONIC2
X-RAY DIFFRACTIONt_gen_planes909HARMONIC5
X-RAY DIFFRACTIONt_it6038HARMONIC20
X-RAY DIFFRACTIONt_nbd5SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion2.99
X-RAY DIFFRACTIONt_other_torsion19.99
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion765SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies1HARMONIC1
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact7316SEMIHARMONIC4
LS refinement shellResolution: 2.88→2.96 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2708 183 5.31 %
Rwork0.245 3264 -
all0.2463 3447 -
obs--99.96 %

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