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- PDB-6v79: Crystal structure of Danio rerio histone deacetylase 6 catalytic ... -

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Basic information

Entry
Database: PDB / ID: 6v79
TitleCrystal structure of Danio rerio histone deacetylase 6 catalytic domain 2 (CD2) complexed with NF2376
ComponentsHdac6 protein
KeywordsHYDROLASE / 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 / 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 family / Histone deacetylase domain / Histone deacetylase domain superfamily / Histone deacetylase domain / Ureohydrolase domain superfamily / Zinc finger, RING/FYVE/PHD-type
Similarity search - Domain/homology
: / Chem-QQD / Hdac6 protein / Histone deacetylase 6
Similarity search - Component
Biological speciesDanio rerio (zebrafish)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.03951514036 Å
AuthorsOsko, J.D. / 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: J.Med.Chem. / Year: 2021
Title: Harnessing the Role of HDAC6 in Idiopathic Pulmonary Fibrosis: Design, Synthesis, Structural Analysis, and Biological Evaluation of Potent Inhibitors.
Authors: Campiani, G. / Cavella, C. / Osko, J.D. / Brindisi, M. / Relitti, N. / Brogi, S. / Saraswati, A.P. / Federico, S. / Chemi, G. / Maramai, S. / Carullo, G. / Jaeger, B. / Carleo, A. / ...Authors: Campiani, G. / Cavella, C. / Osko, J.D. / Brindisi, M. / Relitti, N. / Brogi, S. / Saraswati, A.P. / Federico, S. / Chemi, G. / Maramai, S. / Carullo, G. / Jaeger, B. / Carleo, A. / Benedetti, R. / Sarno, F. / Lamponi, S. / Rottoli, P. / Bargagli, E. / Bertucci, C. / Tedesco, D. / Herp, D. / Senger, J. / Ruberti, G. / Saccoccia, F. / Saponara, S. / Gorelli, B. / Valoti, M. / Kennedy, B. / Sundaramurthi, H. / Butini, S. / Jung, M. / Roach, K.M. / Altucci, L. / Bradding, P. / Christianson, D.W. / Gemma, S. / Prasse, A.
History
DepositionDec 8, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 2, 2020Provider: repository / Type: Initial release
Revision 1.1Jul 28, 2021Group: 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.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Aug 4, 2021Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Oct 11, 2023Group: Advisory / Data collection ...Advisory / Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_unobs_or_zero_occ_atoms
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)81,66711
Polymers80,5712
Non-polymers1,0969
Water4,035224
1
A: Hdac6 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,8656
Polymers40,2851
Non-polymers5795
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Hdac6 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,8035
Polymers40,2851
Non-polymers5174
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)48.252, 108.135, 74.345
Angle α, β, γ (deg.)90.000, 90.013, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Hdac6 protein / Histone Deacetylase 6


Mass: 40285.484 Da / Num. of mol.: 2
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 , 5 types, 233 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-QQD / 4-{[(2S)-3,3-dimethyl-2-(pyridin-3-yl)-2,3-dihydro-1H-indol-1-yl]methyl}-N-hydroxybenzamide


Mass: 373.448 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C23H23N3O2 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 224 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 2.41 Å3/Da / Density % sol: 48.9 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop
Details: 10 mg/mL HDAC6 CD2 Protein, 2 mM NF2376 Inhibitor, 0.2 M Ammonium Phosphate Dibasic, 20% peg 3350, 1:1 ratio protein to precipitant

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.98 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 8, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.039→74.4 Å / Num. obs: 46684 / % possible obs: 96.2 % / Redundancy: 3.4 % / Biso Wilson estimate: 22.1643747285 Å2 / CC1/2: 0.982 / Rmerge(I) obs: 0.174 / Rpim(I) all: 0.112 / Net I/σ(I): 5.6
Reflection shellResolution: 2.04→2.11 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.767 / Mean I/σ(I) obs: 1.3 / Num. unique obs: 4751 / CC1/2: 0.662 / Rpim(I) all: 0.498 / % possible all: 95.8

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Processing

Software
NameVersionClassification
PHENIX1.11.1_2575refinement
iMOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 5EEM

5eem


Resolution: 2.03951514036→74.3449980863 Å / SU ML: 0.259158747617 / Cross valid method: FREE R-VALUE / σ(F): 1.36375430773 / Phase error: 24.1165282856
RfactorNum. reflection% reflection
Rfree0.234196557526 2279 4.8817582041 %
Rwork0.194959732075 --
obs0.196922853602 46684 96.1050724638 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 24.0467582879 Å2
Refinement stepCycle: LAST / Resolution: 2.03951514036→74.3449980863 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5477 0 66 224 5767
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.007482673698475690
X-RAY DIFFRACTIONf_angle_d0.9260806631827743
X-RAY DIFFRACTIONf_chiral_restr0.0534327920353846
X-RAY DIFFRACTIONf_plane_restr0.005927433368931010
X-RAY DIFFRACTIONf_dihedral_angle_d10.36473563494573
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.04-2.08390.2999172777921190.2584438278812777X-RAY DIFFRACTION95.1067323481
2.0839-2.13230.3166087579541180.2494339209742854X-RAY DIFFRACTION99.3315508021
2.1323-2.18570.3131410567141410.2341642619952904X-RAY DIFFRACTION99.0243902439
2.1857-2.24480.2775091895461430.2243969876022784X-RAY DIFFRACTION98.9519945909
2.2448-2.31080.2639167849051810.2151626508442799X-RAY DIFFRACTION98.5123966942
2.3108-2.38540.2846509547761480.2098246938742854X-RAY DIFFRACTION98.200850507
2.3854-2.47070.2604380689541560.2146562170632825X-RAY DIFFRACTION98.1237656353
2.4707-2.56960.2486041036171620.2014218454962800X-RAY DIFFRACTION98.0145598941
2.5696-2.68660.2341909007761540.1966844087612884X-RAY DIFFRACTION98.8288874431
2.6866-2.82820.251487835581260.2068018310572797X-RAY DIFFRACTION97.8246318608
2.8282-3.00540.2575612648381350.2108935989372792X-RAY DIFFRACTION96.600660066
3.0054-3.23750.2640024536141430.2103553231712748X-RAY DIFFRACTION95.0986842105
3.2375-3.56330.2326842079311520.1921874764942683X-RAY DIFFRACTION93.410214168
3.5633-4.07880.1893761793611360.1686435481162643X-RAY DIFFRACTION91.2344057781
4.0788-5.13870.1780502550971280.152356579792608X-RAY DIFFRACTION90
5.1387-74.30.1763325637171370.16364664822653X-RAY DIFFRACTION89.7683397683

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