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

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Basic information

Entry
Database: PDB / ID: 5efh
TitleCrystal structure of Danio rerio histone deacetylase 6 catalytic domain 2 in complex with trifluoroketone transition state analogue
ComponentsHdac6 protein
KeywordsHYDROLASE
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 domain / Arginase; Chain A / : / Histone deacetylase family / Histone deacetylase domain / Histone deacetylase domain superfamily ...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
BROMIDE ION / Chem-FKS / : / Hdac6 protein / Histone deacetylase 6
Similarity search - Component
Biological speciesDanio rerio (zebrafish)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.162 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 23, 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 / 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
D: Hdac6 protein
A: Hdac6 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)82,08819
Polymers80,5712
Non-polymers1,51717
Water4,522251
1
D: Hdac6 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,9278
Polymers40,2851
Non-polymers6427
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Hdac6 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,16111
Polymers40,2851
Non-polymers87610
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)74.659, 92.414, 96.158
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 2 molecules DA

#1: Protein Hdac6 protein / histone deacetylase 6


Mass: 40285.484 Da / Num. of mol.: 2 / Fragment: catalytic domain 2 (UNP residues 288-646)
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, histone deacetylase

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Non-polymers , 7 types, 268 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-FKS / 7-[(3-aminopropyl)amino]-1,1,1-trifluoroheptane-2,2-diol


Mass: 258.281 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H21F3N2O2
#5: Chemical
ChemComp-BR / BROMIDE ION


Mass: 79.904 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: Br
#6: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#7: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 251 / 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: 2.06 Å3/Da / Density % sol: 40.25 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / Details: 0.2 M sodium bromide, 20% PEG3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 4.2.2 / Wavelength: 1.00003 Å
DetectorType: RDI CMOS_8M / Detector: CMOS / Date: Oct 1, 2015
RadiationMonochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.00003 Å / Relative weight: 1
ReflectionResolution: 2.16→50 Å / Num. obs: 35885 / % possible obs: 98.8 % / Redundancy: 6.6 % / Rmerge(I) obs: 0.148 / Net I/σ(I): 13.5
Reflection shellResolution: 2.16→2.3 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.334 / Mean I/σ(I) obs: 3 / % possible all: 90.3

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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: 2.162→49.712 Å / SU ML: 0.23 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 26.11 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2418 1782 4.98 %
Rwork0.1962 --
obs0.1985 35769 98.6 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.162→49.712 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5566 0 57 251 5874
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0055766
X-RAY DIFFRACTIONf_angle_d0.9657826
X-RAY DIFFRACTIONf_dihedral_angle_d13.4692126
X-RAY DIFFRACTIONf_chiral_restr0.036849
X-RAY DIFFRACTIONf_plane_restr0.0041019
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1623-2.22080.2561160.22322307X-RAY DIFFRACTION88
2.2208-2.28610.281380.222521X-RAY DIFFRACTION97
2.2861-2.35990.29891380.22062554X-RAY DIFFRACTION99
2.3599-2.44430.2251410.20412629X-RAY DIFFRACTION100
2.4443-2.54210.26081410.20912630X-RAY DIFFRACTION100
2.5421-2.65780.3151390.21172616X-RAY DIFFRACTION100
2.6578-2.79790.25311390.21542601X-RAY DIFFRACTION100
2.7979-2.97320.28461320.21412671X-RAY DIFFRACTION100
2.9732-3.20270.24941250.20922643X-RAY DIFFRACTION100
3.2027-3.52490.251290.19382654X-RAY DIFFRACTION100
3.5249-4.03480.23231380.17752677X-RAY DIFFRACTION100
4.0348-5.08260.19161570.16722676X-RAY DIFFRACTION100
5.0826-49.72520.19371490.17112808X-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)
14.742-2.04472.33994.09-1.59813.4013-0.1576-0.34020.32760.24740.22770.2259-0.3359-0.3238-0.05340.1313-0.02840.05750.16650.00440.139882.5337196.8157148.7668
23.39010.28550.51072.10480.12361.34530.0719-0.5850.0590.4206-0.04060.0267-0.0197-0.3428-0.0450.18010.00970.01820.1910.01260.089885.0058187.6269159.5577
30.67540.1643-0.16380.8565-0.57780.9136-0.01340.07530.3470.0511-0.0947-0.042-0.33250.11330.04020.2705-0.1203-0.07370.18850.11210.288697.3098204.0605141.3421
42.75080.3336-0.71613.96161.24354.955-0.130.60460.6474-0.5924-0.03630.3052-0.9376-0.39690.16550.241-0.0441-0.08260.32910.14070.318382.2978205.6552135.1781
50.8337-0.8130.09582.0096-0.74210.9325-0.2348-0.01920.30930.31920.0092-0.2874-0.32280.1410.22650.1719-0.0384-0.07640.1056-0.00280.199697.7897195.9879150.5372
61.465-0.076-0.70652.1574-0.14762.6244-0.0818-0.01310.17890.12230.0311-0.3206-0.04140.2940.03980.1257-0.0695-0.04840.14870.03370.172494.5709189.7912147.4967
71.5504-0.2818-0.02581.4506-0.27871.7391-0.16390.40980.0535-0.23540.0647-0.20040.01230.16920.07470.1518-0.07980.03380.17520.00540.138297.1008185.7258135.826
81.80250.2402-0.28512.0073-0.88832.522-0.02090.2847-0.4293-0.32240.074-0.14530.3673-0.0194-0.05290.2419-0.0460.06190.1704-0.07050.181893.5384172.8778136.1233
93.5546-0.62520.44881.841-0.17221.726-0.18820.0136-0.256-0.04050.119-0.0280.1208-0.04910.06110.1272-0.05890.0250.1020.01340.102992.5539177.1167143.2148
103.9517-1.25540.3733.0172-0.65151.7882-0.1418-0.1799-0.16720.13540.0264-0.29660.0880.0620.11280.12250.0017-0.00140.0980.02490.093592.8285178.3513149.7162
111.9092-0.5514-0.06050.25040.19211.3489-0.0443-0.0994-0.3989-0.15630.06010.12320.2769-0.1872-0.0280.2235-0.0836-0.0120.17480.02710.171385.6109173.4903152.231
123.4076-0.59240.04860.6475-0.71351.39530.12970.7726-0.8045-0.46150.0244-0.1190.35530.1903-0.13240.4059-0.06280.08930.3104-0.1570.309599.189167.7643131.0997
134.8218-0.42371.01163.2598-0.40153.0375-0.0808-0.2990.37090.09850.09450.2741-0.3406-0.28630.00090.0962-0.00970.05330.13470.00140.1782.6009242.8659173.9844
142.47170.7731-0.05812.4823-0.25751.65440.0028-0.60030.05140.444-0.0544-0.0467-0.2240.04990.03790.15630.0038-0.01110.2578-0.02650.115587.4275235.8127183.5718
153.3129-1.48250.64333.3949-1.13612.1259-0.20030.17040.58910.03570.0463-0.1351-0.33620.18710.14820.1744-0.0539-0.0180.16960.03220.302197.4807250.8383164.0462
162.2891-0.1941-0.05082.6074-0.51932.01320.00940.01490.2352-0.04460.12080.1544-0.2608-0.0193-0.08090.0937-0.02370.01090.19030.02840.156389.2434247.5028167.0788
172.97940.5041-0.02692.10970.02192.1216-0.0738-0.2736-0.07720.1708-0.1572-0.1271-0.04240.19770.18920.0681-0.0166-0.02010.14310.01580.12795.2833235.6752173.3071
181.93630.5804-0.66522.0348-0.25091.9061-0.27310.2815-0.1933-0.34280.1533-0.21880.21840.13510.11380.17-0.02660.05250.18-0.00180.15597.2287231.6585161.0686
190.86990.3718-0.9911.3595-1.0051.8281-0.37260.1505-0.3123-0.3024-0.0006-0.12340.4878-0.17070.29690.4305-0.14190.3930.1766-0.0410.356493.5213218.8198161.1988
203.245-0.24-0.21561.58410.06071.316-0.3158-0.0815-0.533-0.13270.0285-0.15940.49850.16630.23550.23420.01250.11750.15720.03160.251192.5185223.0833168.3807
213.0792-0.5663-0.43782.2215-0.41111.0742-0.3575-0.2077-0.4611-0.01360.094-0.21040.36280.17340.22240.18810.0620.10230.15510.00360.232992.757224.2957174.9228
223.26080.76650.37641.8463-0.7181.3752-0.1355-0.1148-0.7465-0.24370.1301-0.16860.6509-0.06370.07650.2778-0.0020.06050.27420.03250.265385.2497219.6392177.2211
231.45270.1639-0.44970.65330.24641.0385-0.15670.187-0.5209-0.21950.0964-0.15920.42790.01950.12710.6886-0.04360.47510.2138-0.21180.603199.1063213.6992156.2582
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'D' and (resid 443 through 466 )
2X-RAY DIFFRACTION2chain 'D' and (resid 467 through 489 )
3X-RAY DIFFRACTION3chain 'D' and (resid 490 through 516 )
4X-RAY DIFFRACTION4chain 'D' and (resid 517 through 537 )
5X-RAY DIFFRACTION5chain 'D' and (resid 538 through 558 )
6X-RAY DIFFRACTION6chain 'D' and (resid 559 through 577 )
7X-RAY DIFFRACTION7chain 'D' and (resid 578 through 656 )
8X-RAY DIFFRACTION8chain 'D' and (resid 657 through 684 )
9X-RAY DIFFRACTION9chain 'D' and (resid 685 through 718 )
10X-RAY DIFFRACTION10chain 'D' and (resid 719 through 746 )
11X-RAY DIFFRACTION11chain 'D' and (resid 747 through 776 )
12X-RAY DIFFRACTION12chain 'D' and (resid 777 through 798 )
13X-RAY DIFFRACTION13chain 'A' and (resid 443 through 466 )
14X-RAY DIFFRACTION14chain 'A' and (resid 467 through 495 )
15X-RAY DIFFRACTION15chain 'A' and (resid 496 through 516 )
16X-RAY DIFFRACTION16chain 'A' and (resid 517 through 557 )
17X-RAY DIFFRACTION17chain 'A' and (resid 558 through 577 )
18X-RAY DIFFRACTION18chain 'A' and (resid 578 through 656 )
19X-RAY DIFFRACTION19chain 'A' and (resid 657 through 684 )
20X-RAY DIFFRACTION20chain 'A' and (resid 685 through 718 )
21X-RAY DIFFRACTION21chain 'A' and (resid 719 through 746 )
22X-RAY DIFFRACTION22chain 'A' and (resid 747 through 776 )
23X-RAY DIFFRACTION23chain 'A' and (resid 777 through 798 )

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