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

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Basic information

Entry
Database: PDB / ID: 5eef
TitleCrystal structure of Danio rerio histone deacetylase 6 catalytic domain 1 in complex with trichostatin A
ComponentsHDAC6
KeywordsHYDROLASE/HYDROLASE INHIBITOR / 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
AMMONIUM ION / TRICHOSTATIN A / Histone deacetylase 6
Similarity search - Component
Biological speciesDanio rerio (zebrafish)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.151 Å
AuthorsHai, Y. / 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: 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 22, 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 13, 2017Group: Author supporting evidence / Derived calculations / Category: pdbx_audit_support / pdbx_struct_oper_list
Item: _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.4Dec 25, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5Sep 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 / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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
B: HDAC6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)81,61713
Polymers80,5892
Non-polymers1,02811
Water2,954164
1
A: HDAC6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,8577
Polymers40,2951
Non-polymers5626
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: HDAC6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,7616
Polymers40,2951
Non-polymers4665
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)52.876, 123.717, 55.186
Angle α, β, γ (deg.)90.00, 113.85, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein HDAC6 /


Mass: 40294.594 Da / Num. of mol.: 2 / Fragment: catalytic domain 1 (UNP residues 60-419)
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: F8W4B7

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Non-polymers , 6 types, 175 molecules

#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-TSN / TRICHOSTATIN A / 7-[4-(DIMETHYLAMINO)PHENYL]-N-HYDROXY-4,6-DIMETHYL-7-OXO-2,4-HEPTADIENAMIDE / Trichostatin A


Mass: 302.368 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C17H22N2O3 / Comment: antifungal, antibiotic*YM
#4: Chemical
ChemComp-NH4 / AMMONIUM ION / Ammonium


Mass: 18.038 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: H4N
#5: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#6: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 164 / 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: 2.05 Å3/Da / Density % sol: 39.96 % / Description: plates
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.2 M ammonium sulfate, 0.1 M MES, pH 6.5, 25% PEG5000 MME

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL14-1 / Wavelength: 1.28184 Å
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Jul 23, 2015
RadiationMonochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.28184 Å / Relative weight: 1
ReflectionResolution: 2.15→45.04 Å / Num. obs: 34861 / % possible obs: 99 % / Redundancy: 3.1 % / Rmerge(I) obs: 0.178 / Net I/σ(I): 10.6
Reflection shellResolution: 2.15→2.6 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.701 / Mean I/σ(I) obs: 2 / % possible all: 95.9

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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: 2.151→45.04 Å / SU ML: 0.26 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 26.82 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2548 1752 5.04 %
Rwork0.2106 --
obs0.2128 34749 98.64 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.151→45.04 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5518 0 63 164 5745
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0045750
X-RAY DIFFRACTIONf_angle_d0.7887808
X-RAY DIFFRACTIONf_dihedral_angle_d15.9162080
X-RAY DIFFRACTIONf_chiral_restr0.03858
X-RAY DIFFRACTIONf_plane_restr0.0031014
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1508-2.2090.33361190.28432447X-RAY DIFFRACTION93
2.209-2.2740.32811190.28562444X-RAY DIFFRACTION96
2.274-2.34730.32091320.26792496X-RAY DIFFRACTION98
2.3473-2.43120.28971240.27182541X-RAY DIFFRACTION98
2.4312-2.52860.31681320.26432548X-RAY DIFFRACTION100
2.5286-2.64360.31151190.25392600X-RAY DIFFRACTION100
2.6436-2.7830.32421510.24592534X-RAY DIFFRACTION100
2.783-2.95730.27591460.23292566X-RAY DIFFRACTION100
2.9573-3.18560.28791370.2292538X-RAY DIFFRACTION100
3.1856-3.50610.23651500.19812578X-RAY DIFFRACTION100
3.5061-4.01310.21821430.17582563X-RAY DIFFRACTION100
4.0131-5.05510.18381180.16132593X-RAY DIFFRACTION100
5.0551-45.040.22851620.17132549X-RAY DIFFRACTION99
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)
10.188-0.0572-0.08010.0443-0.01590.08480.1384-0.0890.01140.1866-0.17490.18610.20740.358400.27760.0442-0.01370.18040.00650.2606-5.5565-35.4768-0.5096
20.0241-0.01660.11660.2050.06010.18290.0278-0.149-0.14090.088-0.0466-0.01060.0101-0.034900.2149-0.01640.00780.21210.02590.2109-19.1551-31.80255.8159
30.38640.08860.13320.3269-0.03020.43220.0651-0.0049-0.05470.02420.02560.00310.0715-0.0424-00.1321-0.0004-0.01620.0728-0.00750.1136-22.0055-30.9056-4.9485
40.40840.2718-0.08230.25360.00230.5485-0.01290.1164-0.026-0.0339-0.0229-0.0037-0.03840.087700.10320.02610.00050.0842-0.00740.0777-13.2546-22.4491-17.041
50.08370.08360.00630.02320.07290.18960.0456-0.1944-0.02090.1191-0.1972-0.0992-0.22460.3009-00.2757-0.0207-0.02380.2454-0.01760.21217.520812.298-12.5135
60.0290.06970.16250.18330.17440.0609-0.0662-0.18860.04881.57620.4811-0.80330.21390.6533-0-1.1127-0.38780.35430.4220.10680.111216.14347.179-23.2107
7-0.24260.15990.45810.0950.0970.453-0.08480.0461-0.1572-0.01220.05160.0113-0.16580.168100.0964-0.02020.00730.12360.02610.10559.26846.5237-25.7138
8-0.0101-0.02350.1330.0222-0.02050.16-0.22420.0518-0.3378-0.17220.22690.0792-0.2145-0.0056-00.17080.0478-0.02430.12060.05970.0832-5.30514.0095-34.2181
90.04380.0434-0.01170.094-0.08920.27010.7415-0.6516-0.583-0.0716-0.09230.07190.7167-0.69480-0.41880.34840.29230.0102-0.1166-0.0256-8.1551-1.2813-24.1048
100.01730.03030.08810.0657-0.09460.24670.1282-0.0412-0.01660.0141-0.1313-0.0674-0.0569-0.1167-00.11210.00590.01040.19060.00870.16-4.4756-1.0215-12.656
110.0148-0.0059-0.0226-0.002-0.02160.02920.10470.0352-0.2055-0.08640.09360.11490.2521-0.418200.1855-0.0153-0.0510.29180.03970.2945-14.8494-7.7574-33.2146
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 59 through 98 )
2X-RAY DIFFRACTION2chain 'A' and (resid 99 through 134 )
3X-RAY DIFFRACTION3chain 'A' and (resid 135 through 274 )
4X-RAY DIFFRACTION4chain 'A' and (resid 275 through 417 )
5X-RAY DIFFRACTION5chain 'B' and (resid 58 through 98 )
6X-RAY DIFFRACTION6chain 'B' and (resid 99 through 135 )
7X-RAY DIFFRACTION7chain 'B' and (resid 136 through 240 )
8X-RAY DIFFRACTION8chain 'B' and (resid 241 through 274 )
9X-RAY DIFFRACTION9chain 'B' and (resid 275 through 336 )
10X-RAY DIFFRACTION10chain 'B' and (resid 337 through 394 )
11X-RAY DIFFRACTION11chain 'B' and (resid 395 through 417 )

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