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

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Basic information

Entry
Database: PDB / ID: 5efk
TitleCrystal structure of Danio rerio histone deacetylase 6 catalytic domain 2 (Y745F mutant) in complex with alpha tubulin K40 tripeptide substrate
Components
  • Hdac6 protein
  • alpha tubulin K40 tripeptide
KeywordsHYDROLASE
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
: / 7-AMINO-4-METHYL-CHROMEN-2-ONE / NITRATE ION / DI(HYDROXYETHYL)ETHER / Protein deacetylase HDAC6 / Protein deacetylase HDAC6
Similarity search - Component
Biological speciesDanio rerio (zebrafish)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.82 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_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_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 1.6Nov 15, 2023Group: Data collection / Derived calculations / Category: chem_comp_atom / chem_comp_bond / struct_conn
Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2 / _struct_conn.pdbx_leaving_atom_flag

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: Hdac6 protein
A: alpha tubulin K40 tripeptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,30110
Polymers40,6602
Non-polymers6418
Water5,170287
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1890 Å2
ΔGint-37 kcal/mol
Surface area13160 Å2
MethodPISA
Unit cell
Length a, b, c (Å)83.277, 94.667, 51.622
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
11B-2006-

NO3

21B-2006-

NO3

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Components

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Protein / Protein/peptide , 2 types, 2 molecules BA

#1: Protein Hdac6 protein / histone deacetylase 6


Mass: 40269.484 Da / Num. of mol.: 1 / Fragment: catalytic domain 2 (UNP residues 288-646) / Mutation: Y745F
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: Protein/peptide alpha tubulin K40 tripeptide


Mass: 390.390 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Danio rerio (zebrafish) / Production host: Escherichia coli (E. coli)

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Non-polymers , 8 types, 295 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-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#7: Chemical ChemComp-NO3 / NITRATE ION


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


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#9: Chemical ChemComp-MCM / 7-AMINO-4-METHYL-CHROMEN-2-ONE / 7-AMINO-4-METHYLCOUMARIN


Mass: 175.184 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H9NO2
#10: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 287 / 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: 2.5 Å3/Da / Density % sol: 50.84 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 9
Details: 0.1 M Bicine, pH 9.0, 2% v/v 1,4-dioxane, 10% PEG20000

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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: 1.82→50 Å / Num. obs: 37390 / % possible obs: 94.1 % / Redundancy: 11 % / Rmerge(I) obs: 0.164 / Net I/σ(I): 0.655
Reflection shellResolution: 1.82→1.95 Å / Redundancy: 4.1 % / Rmerge(I) obs: 0.655 / Mean I/σ(I) obs: 1.1 / % possible all: 94.1

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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: 1.82→45.322 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 17.01 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1834 1868 5 %
Rwork0.1569 --
obs0.1583 37329 98.96 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.82→45.322 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2792 0 37 287 3116
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072895
X-RAY DIFFRACTIONf_angle_d1.113909
X-RAY DIFFRACTIONf_dihedral_angle_d14.5551044
X-RAY DIFFRACTIONf_chiral_restr0.047423
X-RAY DIFFRACTIONf_plane_restr0.005509
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8139-1.86290.26851210.26732395X-RAY DIFFRACTION88
1.8629-1.91770.25541510.2092676X-RAY DIFFRACTION99
1.9177-1.97960.18571430.16612702X-RAY DIFFRACTION100
1.9796-2.05040.19221340.15632713X-RAY DIFFRACTION100
2.0504-2.13250.21431480.16482738X-RAY DIFFRACTION100
2.1325-2.22950.21241280.15042728X-RAY DIFFRACTION100
2.2295-2.34710.19211310.14722766X-RAY DIFFRACTION100
2.3471-2.49410.17691550.15112717X-RAY DIFFRACTION100
2.4941-2.68660.17541500.15322746X-RAY DIFFRACTION100
2.6866-2.9570.19361460.15482758X-RAY DIFFRACTION100
2.957-3.38470.1511400.15332789X-RAY DIFFRACTION100
3.3847-4.26390.16451560.13662805X-RAY DIFFRACTION100
4.2639-45.33580.17181650.15632928X-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)
10.0012-0.0016-0.00330.00440.00150.00350.00290.02330.0096-0.0433-0.0391-0.0116-0.0061-0.002100.085-0.02120.00520.08160.02650.0853-11.936830.7852-17.418
20.0040.0066-0.0010.0022-0.00780.0091-0.00810.07990.1003-0.05980.01340.07120.010.0096-00.0675-0.0182-0.00830.05890.0357-0.0716-19.676521.0626-20.4966
30.0034-0.00260.00150.0018-0.00220.0016-0.0267-0.01660.04440.01820.0065-0.0029-0.0176-0.03300.07150.0436-0.0092-0.0323-0.05020.2404-20.914642.0464-4.2912
40.0062-0.0082-0.00070.0036-0.00140.00080.01430.02070.0593-0.02050.0015-0.0198-0.0566-0.173-00.0255-0.0883-0.0056-0.13360.02760.1064-14.927137.7782-9.9287
50.0021-0.0035-00.00510.00030.0038-0.0121-0.0030.0326-0.00110.0354-0.0136-0.0142-0.01600.0485-0.0016-0.00420.05480.00130.049-21.409324.6607-8.2723
60.0032-0.00260.0006-0.0008-0.0030.0072-0.0349-0.03420.03840.00440.0421-0.04750.0166-0.0392-00.02290.00730.00530.0257-0.00280.04-21.476926.6254-0.4864
70.0035-0.00230.00340.0025-0.00140.00780.0106-0.03960.01580.0177-0.0324-0.0051-0.0218-0.00200.0488-0.0044-0.0060.0706-0.01470.0436-11.956323.48888.1027
8-0.0007-0.00130.0020.0018-0.00350.00510.0416-0.0394-0.0101-0.0008-0.0002-0.00670.06150.022600.03470.02050.02080.06160.0029-0.0103-11.505412.82685.6604
90.00760.00470.00870.006100.01990.0022-0.01910.0251-0.01410.0084-0.00570.03340.001400.0455-0.0097-0.00440.0355-0.00070.0337-16.546613.8616-4.324
100.00470-0.00470.00320.010.0055-0.0132-0.0133-0.0649-0.0224-0.0084-0.02740.04340.0647-00.06960.00720.0010.0643-0.00850.065-13.05698.3622-11.6455
110.0012-0.00120.0013-0.0001-0.00190.0020.0204-0.034-0.00220.0399-0.02350.00090.0258-0.0165-00.0522-0.0052-0.03690.09050.0505-0.0342-13.13369.844614.176
121.4129-0.1617-0.52213.8717-8.14932-0.01120.01830.00550.0019-0.00420.0069-0.19440.01860.01740.3438-0.0187-0.01480.3482-0.00590.40.664831.9792-1.6871
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'B' and (resid 443 through 466 )
2X-RAY DIFFRACTION2chain 'B' and (resid 467 through 495 )
3X-RAY DIFFRACTION3chain 'B' and (resid 496 through 516 )
4X-RAY DIFFRACTION4chain 'B' and (resid 517 through 557 )
5X-RAY DIFFRACTION5chain 'B' and (resid 558 through 577 )
6X-RAY DIFFRACTION6chain 'B' and (resid 578 through 616 )
7X-RAY DIFFRACTION7chain 'B' and (resid 617 through 656 )
8X-RAY DIFFRACTION8chain 'B' and (resid 657 through 684 )
9X-RAY DIFFRACTION9chain 'B' and (resid 685 through 746 )
10X-RAY DIFFRACTION10chain 'B' and (resid 747 through 776 )
11X-RAY DIFFRACTION11chain 'B' and (resid 777 through 798 )
12X-RAY DIFFRACTION12chain 'A' and (resid 2 through 3 )

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