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

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Basic information

Entry
Database: PDB / ID: 5efj
TitleCrystal structure of Danio rerio histone deacetylase 6 catalytic domain 2 in complex with HC toxin
Components
  • HC toxin
  • Hdac6 protein
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 / potassium ion binding / histone deacetylase complex / hematopoietic progenitor cell differentiation / epigenetic regulation of gene expression ...Aggrephagy / 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 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
HC Toxin / : / NITRATE ION / polypeptide(D) / Protein deacetylase HDAC6 / Protein deacetylase HDAC6
Similarity search - Component
Biological speciesDanio rerio (zebrafish)
Bipolaris zeicola (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.73 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 / struct_conn_type
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.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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 / _struct_conn.ptnr2_label_seq_id / _struct_conn_type.id
Revision 2.0Nov 15, 2023Group: Atomic model / Data collection / Derived calculations
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / pdbx_validate_rmsd_bond / struct_conn
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_1 / _chem_comp_bond.atom_id_2 / _struct_conn.ptnr1_label_atom_id
Revision 2.1Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
D: Hdac6 protein
F: HC toxin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,30411
Polymers40,7582
Non-polymers5469
Water5,278293
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1980 Å2
ΔGint-38 kcal/mol
Surface area13370 Å2
MethodPISA
Unit cell
Length a, b, c (Å)83.530, 94.144, 51.476
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11D-2005-

NO3

21D-2005-

NO3

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Components

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Protein / Polypeptide(D) , 2 types, 2 molecules DF

#1: Protein Hdac6 protein / histone deacetylase 6


Mass: 40285.484 Da / Num. of mol.: 1 / 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
#2: Polypeptide(D) HC toxin / Toxin I


Type: Peptide-like / Class: Inhibitor / Mass: 472.532 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bipolaris zeicola (fungus) / References: HC Toxin

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Non-polymers , 6 types, 302 molecules

#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#4: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: K
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#6: Chemical ChemComp-NO3 / NITRATE ION


Mass: 62.005 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: NO3
#7: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 293 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.48 Å3/Da / Density % sol: 50.46 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / Details: 0.2 M sodium nitrate, 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: 1.73→50 Å / Num. obs: 42871 / % possible obs: 98.7 % / Redundancy: 6.6 % / Rmerge(I) obs: 0.151 / Net I/σ(I): 14
Reflection shellResolution: 1.73→1.85 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.442 / Mean I/σ(I) obs: 1.6 / % possible all: 90.6

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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: 1.73→47.072 Å / SU ML: 0.15 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 15.27 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1731 2163 5.05 %
Rwork0.1519 --
obs0.153 42818 98.48 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.73→47.072 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2809 0 29 293 3131
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0112952
X-RAY DIFFRACTIONf_angle_d1.3083999
X-RAY DIFFRACTIONf_dihedral_angle_d13.2311081
X-RAY DIFFRACTIONf_chiral_restr0.062435
X-RAY DIFFRACTIONf_plane_restr0.007521
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7254-1.76550.26881060.23272304X-RAY DIFFRACTION85
1.7655-1.80960.20231440.19822612X-RAY DIFFRACTION96
1.8096-1.85860.21561380.17192669X-RAY DIFFRACTION99
1.8586-1.91330.18341750.1572698X-RAY DIFFRACTION99
1.9133-1.9750.17791210.14592713X-RAY DIFFRACTION100
1.975-2.04560.18821370.14712698X-RAY DIFFRACTION99
2.0456-2.12750.16191440.14582724X-RAY DIFFRACTION100
2.1275-2.22430.14841520.13792713X-RAY DIFFRACTION100
2.2243-2.34160.16841570.13872736X-RAY DIFFRACTION100
2.3416-2.48830.15671440.14652720X-RAY DIFFRACTION100
2.4883-2.68040.1771390.14772779X-RAY DIFFRACTION100
2.6804-2.95010.15751510.14942744X-RAY DIFFRACTION100
2.9501-3.37690.19731620.14872776X-RAY DIFFRACTION100
3.3769-4.25410.14931490.13562815X-RAY DIFFRACTION100
4.2541-47.08950.17061440.16382954X-RAY DIFFRACTION100
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)
13.88472.54440.38134.31090.11411.356-0.21560.2970.1794-0.24990.1435-0.0629-0.16750.05980.02890.128-0.00710.02520.08090.0240.0534-12.735229.9363-17.592
21.410.21220.09991.1126-0.08420.8487-0.04160.05320.2847-0.10120.02690.0473-0.1564-0.04090.00080.10110.0112-0.01440.07870.0180.1122-17.966533.1578-12.2348
31.1959-0.01290.24810.666-0.31431.26230.0006-0.16890.06680.07050.01290.0179-0.0964-0.1139-0.0120.07170.00520.00590.0827-0.01350.0744-17.620324.91821.5048
42.1821-0.8195-0.52942.58350.91822.74670.0052-0.184-0.0570.07880.0622-0.0880.19170.0623-0.03460.0747-0.0094-0.01830.08370.03370.0565-11.527212.80455.6542
51.45420.258-0.25691.0152-0.24381.43830.0125-0.0313-0.0776-0.02710.03310.0130.1451-0.0602-0.02860.0833-0.0121-0.0180.0707-0.00320.0676-16.544713.7927-4.4011
60.0828-0.10020.08380.4559-0.34190.83290.03640.0435-0.3074-0.09810.0059-0.11610.25470.1302-0.04030.16820.0046-0.0150.1057-0.01620.1469-13.11398.3044-12.0532
73.863-0.9869-0.65181.43350.63972.23650.0192-0.3481-0.31480.1736-0.0243-0.00290.328-0.0753-0.02270.1545-0.0334-0.03470.13340.0490.0803-13.08389.799414.281
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'D' and (resid 442 through 466 )
2X-RAY DIFFRACTION2chain 'D' and (resid 467 through 557 )
3X-RAY DIFFRACTION3chain 'D' and (resid 558 through 656 )
4X-RAY DIFFRACTION4chain 'D' and (resid 657 through 684 )
5X-RAY DIFFRACTION5chain 'D' and (resid 685 through 746 )
6X-RAY DIFFRACTION6chain 'D' and (resid 747 through 776 )
7X-RAY DIFFRACTION7chain 'D' and (resid 777 through 798 )

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