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- PDB-6mr5: Crystal Structure of Danio rerio histone deacetylase 6 catalytic ... -

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Basic information

Entry
Database: PDB / ID: 6mr5
TitleCrystal Structure of Danio rerio histone deacetylase 6 catalytic domain 2 in complex with a mercaptoacetamide-based inhibitor
ComponentsHdac6 protein
KeywordsHYDROLASE/HYDROLASE INHIBITOR / histone deacetylase / zinc hydrolase / 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 / 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
CITRATE ANION / : / DI(HYDROXYETHYL)ETHER / Chem-W45 / Hdac6 protein / Histone deacetylase 6
Similarity search - Component
Biological speciesDanio rerio (zebrafish)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.85 Å
AuthorsPorter, N.J. / Christianson, D.W.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI)GM49758 United States
CitationJournal: ACS Med Chem Lett / Year: 2018
Title: Molecular Basis for the Selective Inhibition of Histone Deacetylase 6 by a Mercaptoacetamide Inhibitor.
Authors: Porter, N.J. / Shen, S. / Barinka, C. / Kozikowski, A.P. / Christianson, D.W.
History
DepositionOct 11, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 5, 2018Provider: repository / Type: Initial release
Revision 1.1Jan 23, 2019Group: Data collection / Database references / Category: citation
Item: _citation.journal_abbrev / _citation.journal_volume ..._citation.journal_abbrev / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Dec 18, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Mar 13, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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_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: Hdac6 protein
B: Hdac6 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)82,01214
Polymers80,5712
Non-polymers1,44112
Water5,819323
1
A: Hdac6 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,8806
Polymers40,2851
Non-polymers5955
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Hdac6 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,1328
Polymers40,2851
Non-polymers8467
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)159.010, 46.460, 96.400
Angle α, β, γ (deg.)90.000, 119.190, 90.000
Int Tables number5
Space group name H-MC121

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Hdac6 protein /


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 , 7 types, 335 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-W45 / N-[5-(5,6-dichloro-1H-indol-1-yl)pentyl]-2-sulfanylacetamide


Mass: 345.287 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C15H18Cl2N2OS / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3
#6: Chemical ChemComp-FLC / CITRATE ANION / Citric acid


Mass: 189.100 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H5O7
#7: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


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


Mass: 18.015 Da / Num. of mol.: 323 / 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: 1.95 Å3/Da / Density % sol: 36.99 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop
Details: 0.04 M citrate / 0.06 M Bis-Tris propane (pH 6.4) 20% Peg 3,350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.97917 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 5, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97917 Å / Relative weight: 1
ReflectionResolution: 1.85→84.16 Å / Num. obs: 52293 / % possible obs: 98.9 % / Redundancy: 3.2 % / Biso Wilson estimate: 22.48 Å2 / CC1/2: 0.991 / Rmerge(I) obs: 0.1 / Net I/σ(I): 7.5 / Num. measured all: 168669 / Scaling rejects: 19
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Diffraction-ID% possible all
1.85-1.893.30.69232250.642199.6
9.06-84.1630.0485040.992199.8

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Processing

Software
NameVersionClassification
Aimless0.5.32data scaling
PHENIX1.12_2829refinement
PDB_EXTRACT3.24data extraction
iMOSFLMdata reduction
PHASERphasing
RefinementResolution: 1.85→47.762 Å / SU ML: 0.23 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 23.47 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2259 2613 5 %
Rwork0.1899 49669 -
obs0.1916 52282 98.74 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 65.4 Å2 / Biso mean: 24.6679 Å2 / Biso min: 9.83 Å2
Refinement stepCycle: final / Resolution: 1.85→47.762 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5472 0 79 324 5875
Biso mean--33.95 29.43 -
Num. residues----711
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0035760
X-RAY DIFFRACTIONf_angle_d0.6637832
X-RAY DIFFRACTIONf_chiral_restr0.045849
X-RAY DIFFRACTIONf_plane_restr0.0041026
X-RAY DIFFRACTIONf_dihedral_angle_d18.2033415
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 19

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.85-1.88370.31991300.288526252755100
1.8837-1.91990.33331660.270725832749100
1.9199-1.95910.36781250.26526022727100
1.9591-2.00170.31371420.253326202762100
2.0017-2.04820.27031310.234526002731100
2.0482-2.09950.30431420.23412634277699
2.0995-2.15620.24421540.22482577273199
2.1562-2.21970.26581470.21082577272499
2.2197-2.29130.26541300.2062587271798
2.2913-2.37320.28681400.20282604274498
2.3732-2.46820.23081310.20812548267997
2.4682-2.58060.26091320.20512558269096
2.5806-2.71660.23141330.19722609274299
2.7166-2.88680.23061220.19582647276999
2.8868-3.10960.20671360.19532651278799
3.1096-3.42250.22061500.18362607275799
3.4225-3.91750.18371360.15782663279999
3.9175-4.93490.15221290.1412594272396
4.9349-47.77750.17161370.154227832920100

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