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- PDB-9cbk: Crystal Structure of Danio rerio Histone Deacetylase 6 in Complex... -

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Basic information

Entry
Database: PDB / ID: 9cbk
TitleCrystal Structure of Danio rerio Histone Deacetylase 6 in Complex with p-Aminomethyl Phenylthioketone
ComponentsHdac6 protein
KeywordsHYDROLASE/INHIBITOR / Hydrolase / histone deacetylase / inhibitor / metallohydrolase / HYDROLASE-INHIBITOR complex
Function / homology
Function and homology information


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 family / Histone deacetylase domain / Histone deacetylase domain superfamily / Histone deacetylase domain / Ureohydrolase domain superfamily / Zinc finger, RING/FYVE/PHD-type
Similarity search - Domain/homology
: / : / Hdac6 protein
Similarity search - Component
Biological speciesDanio rerio (zebrafish)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.46 Å
AuthorsGoulart Stollmaier, J. / Watson, P.R. / 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: Acs Med.Chem.Lett. / Year: 2024
Title: Design, Synthesis, and Structural Evaluation of Acetylated Phenylthioketone Inhibitors of HDAC10.
Authors: Goulart Stollmaier, J. / Watson, P.R. / Christianson, D.W.
History
DepositionJun 19, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 11, 2024Provider: repository / Type: Initial release
Revision 1.1Oct 30, 2024Group: Database references / Structure summary / Category: citation / citation_author / pdbx_entry_details
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _pdbx_entry_details.has_protein_modification

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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)81,46914
Polymers80,5712
Non-polymers89812
Water9,998555
1
A: Hdac6 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,7347
Polymers40,2851
Non-polymers4496
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Hdac6 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,7347
Polymers40,2851
Non-polymers4496
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)74.701, 91.481, 96.370
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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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 / Fragment: catalytic domain 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Danio rerio (zebrafish) / Gene: hdac6 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A7YT55

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Non-polymers , 5 types, 567 molecules

#2: Chemical ChemComp-A1AVM / 1-[4-(aminomethyl)phenyl]-2-sulfanylethan-1-one


Mass: 181.255 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C9H11NOS / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-ZN / ZINC ION


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


Mass: 39.098 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: K
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 555 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Has protein modificationN

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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: 2.04 Å3/Da / Density % sol: 39.81 % / Description: Single sheet/plate shaped
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop
Details: 10 mg/mL HDAC6, 2 mM inhibitor, 0.2 M DL-malic acid (pH 7.0), 20% (w/v) PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSLS-II / Beamline: 17-ID-2 / Wavelength: 0.98 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jul 10, 2023
Details: Horizontal pre-focus bimorph mirror & KB bimorph mirrors
RadiationMonochromator: Si(111) DCM / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.46→96.37 Å / Num. obs: 114552 / % possible obs: 100 % / Redundancy: 9.5 % / Biso Wilson estimate: 10.37 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.168 / Rpim(I) all: 0.056 / Net I/σ(I): 7.8
Reflection shellResolution: 1.46→1.49 Å / Redundancy: 8.4 % / Rmerge(I) obs: 0.948 / Mean I/σ(I) obs: 2 / Num. unique obs: 5600 / CC1/2: 0.794 / Rpim(I) all: 0.329 / % possible all: 99.6

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Processing

Software
NameVersionClassification
PHENIX1.21rc1_5156refinement
iMOSFLM7.4.0data reduction
Aimless0.7.13data scaling
PHASER2.8.3phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.46→48.19 Å / SU ML: 0.1592 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 23.1119
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.194 2008 1.76 %
Rwork0.1776 216334 -
obs0.1778 114335 99.76 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 13.76 Å2
Refinement stepCycle: LAST / Resolution: 1.46→48.19 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5490 0 46 555 6091
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00775709
X-RAY DIFFRACTIONf_angle_d0.94617756
X-RAY DIFFRACTIONf_chiral_restr0.0837850
X-RAY DIFFRACTIONf_plane_restr0.01091015
X-RAY DIFFRACTIONf_dihedral_angle_d12.20622038
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.46-1.480.31491500.31357689X-RAY DIFFRACTION98.77
1.48-1.50.33411420.29927638X-RAY DIFFRACTION99.16
1.5-1.520.2971310.28367718X-RAY DIFFRACTION99.73
1.52-1.540.29841350.27827752X-RAY DIFFRACTION99.7
1.54-1.560.27331400.26327718X-RAY DIFFRACTION99.77
1.56-1.580.36131260.25787715X-RAY DIFFRACTION99.81
1.58-1.610.23871380.24867688X-RAY DIFFRACTION99.76
1.61-1.640.25281570.24667818X-RAY DIFFRACTION99.81
1.64-1.660.27221180.23377717X-RAY DIFFRACTION99.83
1.66-1.690.2381550.22567788X-RAY DIFFRACTION99.86
1.69-1.730.21451350.21397646X-RAY DIFFRACTION99.77
1.73-1.760.19661300.19637725X-RAY DIFFRACTION99.78
1.76-1.80.18971390.1847711X-RAY DIFFRACTION99.83
1.8-1.840.18471440.17997720X-RAY DIFFRACTION99.87
1.84-1.890.20031480.17367724X-RAY DIFFRACTION99.75
1.89-1.940.20991230.17017757X-RAY DIFFRACTION99.77
1.94-20.18221380.17227752X-RAY DIFFRACTION99.95
2-2.060.2141390.1567730X-RAY DIFFRACTION99.9
2.06-2.130.14831350.15147783X-RAY DIFFRACTION99.97
2.13-2.220.17271360.1467703X-RAY DIFFRACTION99.91
2.22-2.320.15121460.15417703X-RAY DIFFRACTION99.85
2.32-2.440.16751240.15097753X-RAY DIFFRACTION99.91
2.44-2.60.16921400.15997738X-RAY DIFFRACTION99.87
2.6-2.80.2261460.16027708X-RAY DIFFRACTION99.85
2.8-3.080.20971280.16477744X-RAY DIFFRACTION99.91
3.08-3.520.16471370.15787745X-RAY DIFFRACTION99.9
3.52-4.440.13921370.13497753X-RAY DIFFRACTION99.92
4.44-48.190.14681480.15037698X-RAY DIFFRACTION99.44
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.0591577872839-0.09328866743840.01057604799370.105993673013-0.0145652945940.0159390158517-0.001815844339070.0953473430888-0.04725760999470.001591476402960.005191155050090.0437399332680.0176722941164-0.0564332994522-0.001813967759410.0737491352636-0.0158509620365-0.003070181887850.0941145818275-0.006971282835990.09071750643-29.6400038653-9.01143736724-6.90275056444
20.212935732721-0.02081754416940.002564597151820.1771874710470.1058767698970.07503323753130.01231362538920.0374687261091-0.1014910610910.0167106252309-0.008185577832760.006208770366130.05752806176460.00694638459540.003064772758770.1083645048920.006792075623530.004178500835270.0785291032810.006370879477380.122845190488-21.1092062657-15.99358143560.98697345611
30.316977379233-0.07539989605390.183178612210.26374497784-0.1040825127650.289620027921-0.0378740756821-0.009202487342180.003736070189350.05110345654090.0141917069087-0.0390348549086-0.0281635945220.01038833648475.64914428117E-100.05773657182150.00156340428035-0.003746502910970.0597403496265-0.0007181041638650.0588129704107-16.49074753521.247304196094.48907144763
40.122364401647-0.1196424953230.06544443302470.177528138563-0.1588079004030.165414119562-0.04162865158930.03166100592150.05850288165810.02802490241340.0122596239871-0.02106378619-0.0756516869597-0.021485112286-0.0179785505540.08851759709-0.000827296031456-0.008593633664260.07448720233960.002359615297040.0858612065945-20.021767351711.167006304-1.33557642834
50.05875599299150.07350994348970.02482900363030.07248067049350.006370383580120.03705566168980.0125964819607-0.01315829707690.03341736203870.01487966438740.0221516323951-0.06167001708290.01529584678810.002657115621140.001789164262120.07803651100390.006937609062290.005605093417190.07456884740890.003326517046760.0914406788355-45.8611410094-11.7380915543-17.6127390301
60.1578888886350.00422623887809-0.05971398328230.180008717882-0.005228584529980.0695121699856-0.00626751065373-0.0269876460977-0.0445869465520.016338399977-0.01033933520430.001641252062910.0358027951650.00129545639588-0.02131575169390.0690025561171-0.009911291385530.006788768511870.0713951130354-0.008290211924870.0721986967351-52.9762781986-13.237235755-20.0397738273
70.02676070203790.0362641130486-0.02568053540410.0422940606066-0.01831699891110.0151590098669-0.0276889510026-0.01825023233510.0115125678487-0.004663390718270.01579596936870.02894197723910.01789150665970.02367656458890.0002328372059540.0699405653962-0.003004453932350.003663476916540.0870396315987-0.004131409345740.0817210830187-57.9247219559-4.85872845725-18.8621568529
80.2099226049590.06189092408030.1614088714490.2166148562090.1599347214450.386667504902-0.06760534963330.0291673956870.0368149358222-0.07306644255710.02050978901280.0403897953382-0.0776522387515-0.0237945591875-0.05106675124870.0793022786033-0.00604937316842-0.01419751306530.06699953813170.001711669053970.0682993547293-58.1209256073.71861513455-29.3264648411
90.07274787292610.03378036593590.0528706939080.03200623860070.03529798296070.126647874347-0.0238543615783-0.004720135476790.03400280312240.0101053092873-0.00589296600380.0134309524108-0.05400746096110.00913447535887-0.01742637510310.0789117943748-0.00764170524716-0.003397459464090.0680033382793-0.01063808168340.0804987982859-51.67332794088.91782696489-15.9052009659
100.05529071172390.0188834561856-0.01728886998150.0477688715301-0.00755157230370.00344689277549-0.09753502345410.02086422398530.0812202597666-0.108271403973-0.0572985250958-0.00877842544181-0.184276421337-0.0327309478597-0.2133158772890.277536482945-0.00559701447447-0.134576315703-0.0900705633460.1436896590320.124555137013-61.439834734916.8260638052-35.4972696562
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 442 through 479 )AA442 - 4791 - 38
22chain 'A' and (resid 480 through 537 )AA480 - 53739 - 96
33chain 'A' and (resid 538 through 718 )AA538 - 71897 - 277
44chain 'A' and (resid 719 through 798 )AA719 - 798278 - 357
55chain 'B' and (resid 442 through 466 )BE442 - 4661 - 25
66chain 'B' and (resid 467 through 557 )BE467 - 55726 - 116
77chain 'B' and (resid 558 through 577 )BE558 - 577117 - 136
88chain 'B' and (resid 578 through 718 )BE578 - 718137 - 277
99chain 'B' and (resid 719 through 776 )BE719 - 776278 - 335
1010chain 'B' and (resid 777 through 797 )BE777 - 797336 - 356

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