PDB-7qno: Crystal structure of ligand-free Danio rerio HDAC6 CD1 CD2

ID or keywords:

Entry

Database: PDB / ID: 7qno

Title

Crystal structure of ligand-free Danio rerio HDAC6 CD1 CD2

Components

Histone deacetylase 6

Keywords

TRANSPORT PROTEIN / Deacetylase / Histone / Microtuble

Function / homology

Function and homology information

Aggrephagy / negative regulation of cellular component organization / positive regulation of cellular component organization / regulation of biological quality / deacetylase activity / tubulin deacetylase activity / mitochondrion localization / swimming behavior / definitive hemopoiesis / regulation of microtubule-based process ...
Similarity search - Function

Biological species

Danio rerio (zebrafish)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.38 Å

Authors

Kempf, G. / Langousis, G. / Sanchez, J. / Matthias, P.

Funding support

1items

Citation

Journal: Methods Mol.Biol. / Year: 2023
Title: Expression and Crystallization of HDAC6 Tandem Catalytic Domains.
Authors: Langousis, G. / Sanchez, J. / Kempf, G. / Matthias, P.

History

Deposition	Dec 21, 2021	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Feb 9, 2022	Provider: repository / Type: Initial release
Revision 1.1	Nov 23, 2022	Group: Database references / Refinement description / Category: citation / software 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
Revision 1.2	Jan 31, 2024	Group: Data collection / Refinement description Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	7qno.cif.gz	445.2 KB	Display	PDBx/mmCIF format
PDB format	pdb7qno.ent.gz	371 KB	Display	PDB format
PDBx/mmJSON format	7qno.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	7qno_validation.pdf.gz	463.2 KB	Display	wwPDB validaton report
Full document	7qno_full_validation.pdf.gz	470.7 KB	Display
Data in XML	7qno_validation.xml.gz	26.6 KB	Display
Data in CIF	7qno_validation.cif.gz	36.1 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/qn/7qno ftp://data.pdbj.org/pub/pdb/validation_reports/qn/7qno	HTTPS FTP

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Related structure data

Related structure data	5g0hS S: Starting model for refinement
Similar structure data	5g0j-d 4eg4-2 4eg6-2 5j5a-2 4zt3-2 2qs7-d 4mwc-2 4eg5-2 4zt2-2 5tqu-2 Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#7 - Jul 2000 Nucleosome similarity (1) #205 - Jan 2017 Nuclear Pore Complex similarity (1)

Deposited unit

A: Histone deacetylase 6

hetero molecules

92.8 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

Idetical with deposited unit
defined by author
Evidence: gel filtration

Unit cell

Length a, b, c (Å)	186.134, 186.134, 102.442
Angle α, β, γ (deg.)	90.00, 90.00, 120.00
Int Tables number	154
Space group name H-M	P3₂21
Symmetry operation	#1: x,y,z #2: -y,x-y,z+2/3 #3: -x+y,-x,z+1/3 #4: x-y,-y,-z+1/3 #5: -x,-x+y,-z+2/3 #6: y,x,-z

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Protein , 1 types, 1 molecules A

#1: Protein	Histone deacetylase 6 Mass: 91951.164 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Danio rerio (zebrafish) / Gene: hdac6 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: F8W4B7

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Non-polymers , 5 types, 29 molecules

#2: Chemical	ChemComp-PRO / PROLINE Type: L-peptide linking / Mass: 115.130 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₅H₉NO₂
#3: Chemical	ChemComp-K / POTASSIUM ION Mass: 39.098 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: K
#4: Chemical	ChemComp-ZN / ZINC ION Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#5: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL Mass: 92.094 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C₃H₈O₃
#6: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 17 / Source method: isolated from a natural source / Formula: H₂O

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Details

Has ligand of interest	N

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Experiment

Experiment	Method: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

Crystal grow	Temperature: 293 K / Method: vapor diffusion, sitting drop / Details: 2.27 M sodium formate

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1 Å
Detector	Type: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Nov 30, 2020
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1 Å / Relative weight: 1
Reflection	Resolution: 2.377→93.067 Å / Num. obs: 44105 / % possible obs: 95.2 % / Redundancy: 20.4 % / B_iso Wilson estimate: 56.66 Å² / CC_1/2: 0.999 / R_merge(I) obs: 0.153 / R_pim(I) all: 0.035 / Net I/σ(I): 15.7
Reflection shell	Resolution: 2.377→2.683 Å / Redundancy: 19.6 % / R_merge(I) obs: 2.331 / Num. unique obs: 2206 / CC_1/2: 0.488 / R_pim(I) all: 0.533 / % possible all: 73.3

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Processing

Software

Name	Version	Classification
PHENIX	(1.19.1_4122: ???)	refinement
Coot	0.9.6	model building
autoPROC		data reduction
STARANISO		data scaling
PHASER		phasing
ISOLDE		refinement
XDS		data reduction

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 5G0H

5g0h

Resolution: 2.38→63.34 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 28.52 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2278	2216	5.03 %
R_work	0.2124	-	-
obs	0.2132	44087	53.62 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL

Refinement step

Cycle: LAST / Resolution: 2.38→63.34 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	5853	0	48	17	5918

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.004	6075
X-RAY DIFFRACTION	f_angle_d	0.72	8240
X-RAY DIFFRACTION	f_dihedral_angle_d	13.156	2219
X-RAY DIFFRACTION	f_chiral_restr	0.043	900
X-RAY DIFFRACTION	f_plane_restr	0.006	1073

LS refinement shell

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Refine-ID	% reflection obs (%)
2.38-2.43	0.5799	4	0.4146	124	X-RAY DIFFRACTION	3
2.43-2.48	0.3101	18	0.3627	282	X-RAY DIFFRACTION	6
2.49-2.55	0.299	23	0.3276	499	X-RAY DIFFRACTION	10
2.55-2.62	0.2692	28	0.32	726	X-RAY DIFFRACTION	15
2.62-2.69	0.308	31	0.3315	621	X-RAY DIFFRACTION	13
2.69-2.78	0.2684	60	0.3173	1204	X-RAY DIFFRACTION	25
2.78-2.88	0.3896	83	0.3015	1407	X-RAY DIFFRACTION	29
2.88-2.99	0.3231	94	0.3101	1832	X-RAY DIFFRACTION	38
2.99-3.13	0.34	125	0.3036	2346	X-RAY DIFFRACTION	49
3.13-3.3	0.2998	167	0.2829	3390	X-RAY DIFFRACTION	69
3.3-3.5	0.2989	251	0.2699	4775	X-RAY DIFFRACTION	98
3.5-3.77	0.2227	270	0.2243	4837	X-RAY DIFFRACTION	100
3.77-4.15	0.2029	251	0.1936	4911	X-RAY DIFFRACTION	100
4.15-4.75	0.1957	275	0.169	4896	X-RAY DIFFRACTION	100
4.75-5.99	0.2007	274	0.1833	4952	X-RAY DIFFRACTION	100
5.99-63.34	0.2055	262	0.1927	5069	X-RAY DIFFRACTION	100

Refinement TLS params.

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

ID	L11 (°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)
1	4.1992	1.9456	-2.3754	2.7024	-0.6448	4.8301	-0.4375	0.246	-0.1124	-0.2225	0.2167	0.2566	0.6576	-0.3459	0.1457	0.5057	0.0132	-0.0908	0.2191	-0.005	0.3889	-97.1364	46.839	-9.1878
2	2.4105	0.7425	-0.7027	5.2582	1.7762	4.0868	-0.0041	0.4903	-0.0516	-0.4537	0.0688	0.4465	0.09	-0.1011	-0.0899	0.3798	0.0153	-0.0572	0.2569	-0.0011	0.2207	-92.8639	52.9452	-13.928
3	4.0389	0.6261	-1.1785	1.1132	0.1377	1.401	-0.3117	0.3507	-0.6013	0.0107	0.2182	0.272	0.9226	-0.4044	0.2006	1.3267	-0.163	0.0327	0.4963	-0.1637	0.7613	-99.358	26.3049	-14.0845
4	2.9821	-1.132	-0.1111	4.0903	1.2487	6.9427	-0.4225	0.0845	-0.6676	0.1153	0.0698	0.5243	1.5195	-0.7966	0.3919	1.3498	-0.2235	0.0374	0.596	-0.0023	1.1034	-109.9456	26.1156	-2.5333
5	1.8424	0.371	0.0791	1.9698	0.4074	1.5141	-0.2082	0.2474	-0.715	-0.2003	0.226	-0.027	0.9467	0.019	0.0795	0.7528	0.0301	-0.0125	0.2653	-0.0693	0.4133	-92.2967	36.8665	-10.6549
6	6.5595	0.1058	2.8128	6.3746	0.6776	8.3423	-0.428	0.799	-0.6889	-0.5945	0.4164	-0.3561	0.9172	0.9329	0.0075	0.9491	0.0731	0.3662	0.717	-0.2933	0.5884	-78.182	33.772	-21.5038
7	1.164	0.2123	-0.4238	0.4396	0.4797	0.9429	-0.2759	-0.2731	-0.7486	-0.0632	0.216	-0.2053	1.1823	0.4477	0.0937	0.8647	0.5031	0.0562	0.5309	0.0299	0.6219	-81.0338	34.3153	3.6512
8	2.21	0.254	1.6587	0.5955	-0.0714	1.3601	-0.2522	-0.2941	-0.3235	0.016	0.2798	-0.4334	0.6164	0.9713	-0.1168	0.6876	0.3907	0.027	0.7643	-0.1151	0.5485	-70.4599	40.558	-4.5635
9	2.684	0.8672	-1.0369	2.2043	0.7269	4.3941	-0.2346	-0.2338	-0.2311	-0.0758	0.2381	-0.244	0.4923	0.7047	-0.0237	0.4264	0.1062	-0.0071	0.4146	0.0035	0.4204	-84.2172	47.5663	-0.3064
10	2.7298	2.2455	1.0749	3.0686	0.3537	0.6559	-0.0975	-0.3008	0.2977	-0.0323	0.1138	0.2449	-0.0287	0.4573	-0.1233	0.2709	0.0313	-0.0217	0.331	-0.078	0.1945	-86.2444	56.1223	-0.8773
11	3.4002	-0.2437	-0.7829	5.1882	-0.032	4.0913	-0.1616	-0.6822	-0.4214	0.3947	0.2315	-0.2202	0.7831	0.9558	-0.0486	0.6779	0.4304	-0.0004	0.997	-0.0144	0.4196	-74.2112	43.1183	14.8049
12	1.6176	0.0059	-0.6676	1.3632	0.9681	0.9684	-0.1012	-0.6659	-0.3588	0.1813	0.3079	-0.4828	0.548	1.066	-0.1802	0.6353	0.413	-0.0271	1.2177	-0.1212	0.6422	-67.2883	42.9521	10.4626
13	0.8086	0.6219	0.367	0.6353	0.2483	0.3034	-0.0052	-0.4802	0.4251	-0.238	0.4447	-0.2688	-0.0796	0.9816	-0.2153	0.6691	-0.7243	0.0637	1.5353	-0.8039	0.7607	-52.0859	74.3053	-7.9408
14	1.2212	1.812	0.9448	3.0996	1.5005	0.7538	-0.027	-0.0691	0.169	-0.1963	0.2633	-0.3942	-0.319	0.8316	-0.2374	0.7805	-0.3629	-0.0653	2.4873	-0.7376	1.2932	-34.3234	73.5473	2.8973
15	0.4491	0.2775	0.3865	0.4883	0.3599	0.3756	0.015	-0.0285	0.1081	-0.2192	0.2404	-0.2859	-0.2337	0.6743	-0.2587	0.5038	-0.9044	-0.0615	1.4671	-1.0338	0.5109	-55.5899	73.6571	-3.0453
16	0.5629	0.3211	0.252	0.516	0.2702	0.1551	-0.0706	0.0255	0.1668	-0.2541	0.3681	-0.4754	-0.215	0.9823	-0.3499	0.3584	-0.3388	-0.0551	1.6473	-0.7007	0.6098	-56.7875	68.8773	5.2246
17	3.2044	-0.3814	-0.7556	0.8054	0.441	1.9845	-0.012	-0.1107	-0.0782	0.0765	0.1134	-0.384	0.2061	0.7949	-0.2344	0.2601	0.1673	-0.1647	1.93	-0.4842	0.7108	-52.3608	60.0667	9.7426
18	0.5072	0.0234	-0.3577	0.6552	0.8306	1.3347	-0.0591	-0.1886	-0.1031	0.0475	0.1732	-0.4512	0.1168	0.8483	-0.2692	0.3683	0.3578	-0.1765	2.0265	-0.4115	0.775	-50.627	54.7553	10.9334
19	0.9256	0.088	-0.2996	0.6289	0.6148	1.0357	-0.142	-0.4129	-0.2928	-0.1557	0.6471	-0.6167	0.3096	1.3912	-0.0224	0.0233	0.191	0.1196	1.5487	-0.4603	0.537	-60.1313	52.9249	-1.2727
20	3.826	-1.3619	-3.1778	1.3302	0.7143	3.7168	0.0713	0.5527	-0.8205	-0.4247	-0.5743	-0.6371	0.515	0.3883	0.491	1.4164	0.8062	-0.0791	1.9996	0.1866	1.3663	-58.7124	28.8939	11.5496

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	(chain A and resid 55:93)
2	X-RAY DIFFRACTION	2	(chain A and resid 94:114)
3	X-RAY DIFFRACTION	3	(chain A and resid 115:138)
4	X-RAY DIFFRACTION	4	(chain A and resid 139:146)
5	X-RAY DIFFRACTION	5	(chain A and resid 147:215)
6	X-RAY DIFFRACTION	6	(chain A and resid 216:222)
7	X-RAY DIFFRACTION	7	(chain A and resid 223:300)
8	X-RAY DIFFRACTION	8	(chain A and resid 301:317)
9	X-RAY DIFFRACTION	9	(chain A and resid 318:363)
10	X-RAY DIFFRACTION	10	(chain A and resid 364:389)
11	X-RAY DIFFRACTION	11	(chain A and resid 390:403)
12	X-RAY DIFFRACTION	12	(chain A and resid 404:437)
13	X-RAY DIFFRACTION	13	(chain A and resid 438:523)
14	X-RAY DIFFRACTION	14	(chain A and resid 524:530)
15	X-RAY DIFFRACTION	15	(chain A and resid 531:577)
16	X-RAY DIFFRACTION	16	(chain A and resid 578:616)
17	X-RAY DIFFRACTION	17	(chain A and resid 617:641)
18	X-RAY DIFFRACTION	18	(chain A and resid 642:673)
19	X-RAY DIFFRACTION	19	(chain A and resid 674:802)
20	X-RAY DIFFRACTION	20	(chain A and resid 803:809)

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