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- PDB-5edu: Crystal structure of human histone deacetylase 6 catalytic domain... -

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Basic information

Entry
Database: PDB / ID: 5edu
TitleCrystal structure of human histone deacetylase 6 catalytic domain 2 in complex with trichostatin A
ComponentsMaltose-binding periplasmic protein, Histone deacetylase 6 chimera
KeywordsHYDROLASE/HYDROLASE INHIBITOR / HYDROLASE-HYDROLASE INHIBITOR complex
Function / homology
Function and homology information


negative regulation of hydrogen peroxide metabolic process / cellular response to topologically incorrect protein / polyubiquitinated misfolded protein transport / negative regulation of aggrephagy / positive regulation of cellular response to oxidative stress / erythrocyte enucleation / positive regulation of cholangiocyte proliferation / response to misfolded protein / negative regulation of oxidoreductase activity / regulation of microtubule-based movement ...negative regulation of hydrogen peroxide metabolic process / cellular response to topologically incorrect protein / polyubiquitinated misfolded protein transport / negative regulation of aggrephagy / positive regulation of cellular response to oxidative stress / erythrocyte enucleation / positive regulation of cholangiocyte proliferation / response to misfolded protein / negative regulation of oxidoreductase activity / regulation of microtubule-based movement / parkin-mediated stimulation of mitophagy in response to mitochondrial depolarization / negative regulation of protein-containing complex disassembly / protein-containing complex disassembly / negative regulation of axon extension involved in axon guidance / regulation of establishment of protein localization / positive regulation of tubulin deacetylation / tubulin deacetylation / Cilium Assembly / regulation of autophagy of mitochondrion / peptidyl-lysine deacetylation / tubulin deacetylase activity / collateral sprouting / Transcriptional regulation by RUNX2 / lysosome localization / negative regulation of protein acetylation / misfolded protein binding / negative regulation of microtubule depolymerization / ubiquitin-dependent protein catabolic process via the multivesicular body sorting pathway / protein deacetylation / cilium disassembly / response to growth factor / dendritic spine morphogenesis / histone deacetylase / aggresome assembly / regulation of androgen receptor signaling pathway / protein lysine deacetylase activity / positive regulation of signaling receptor activity / cellular response to misfolded protein / aggresome / cellular response to parathyroid hormone stimulus / positive regulation of dendrite morphogenesis / Hydrolases; Acting on carbon-nitrogen bonds, other than peptide bonds; In linear amides / regulation of fat cell differentiation / microtubule associated complex / negative regulation of gene expression, epigenetic / histone deacetylase activity / response to corticosterone / dynein complex binding / detection of maltose stimulus / axonal transport of mitochondrion / maltose transport complex / Notch-HLH transcription pathway / response to dexamethasone / positive regulation of epithelial cell migration / beta-tubulin binding / cell leading edge / protein quality control for misfolded or incompletely synthesized proteins / RUNX2 regulates osteoblast differentiation / carbohydrate transport / histone deacetylase complex / carbohydrate transmembrane transporter activity / maltose binding / response to immobilization stress / alpha-tubulin binding / maltose transport / maltodextrin transmembrane transport / cilium assembly / polyubiquitin modification-dependent protein binding / HSF1 activation / regulation of macroautophagy / negative regulation of protein-containing complex assembly / ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing / inclusion body / axon cytoplasm / response to amphetamine / ATP-binding cassette (ABC) transporter complex / multivesicular body / positive regulation of synaptic transmission, glutamatergic / cell chemotaxis / transcription corepressor binding / ciliary basal body / ubiquitin binding / regulation of autophagy / caveola / negative regulation of proteolysis / actin filament organization / Late endosomal microautophagy / intracellular protein transport / Hsp90 protein binding / protein destabilization / regulation of protein stability / tau protein binding / NOTCH1 Intracellular Domain Regulates Transcription / beta-catenin binding / Constitutive Signaling by NOTCH1 PEST Domain Mutants / Constitutive Signaling by NOTCH1 HD+PEST Domain Mutants / autophagy / histone deacetylase binding / Aggrephagy / Chaperone Mediated Autophagy
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 family / Histone deacetylase domain / Histone deacetylase domain superfamily / Histone deacetylase domain / Ureohydrolase domain superfamily / Maltose/Cyclodextrin ABC transporter, substrate-binding protein ...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 family / Histone deacetylase domain / Histone deacetylase domain superfamily / Histone deacetylase domain / Ureohydrolase domain superfamily / Maltose/Cyclodextrin ABC transporter, substrate-binding protein / Solute-binding family 1, conserved site / Bacterial extracellular solute-binding proteins, family 1 signature. / Bacterial extracellular solute-binding protein / Bacterial extracellular solute-binding protein / Zinc finger, RING/FYVE/PHD-type
Similarity search - Domain/homology
alpha-maltose / : / TRICHOSTATIN A / Maltose/maltodextrin-binding periplasmic protein / Maltose/maltodextrin-binding periplasmic protein / Histone deacetylase 6
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.79 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)GM 49758 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 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Non-polymer description / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / entity_name_com / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_molecule_features / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_struct_conn_angle / struct_asym / struct_conn / struct_conn_type / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.src_method / _entity.type / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _struct_asym.entity_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Dec 30, 2020Group: Structure summary / Category: audit_author / chem_comp / Item: _audit_author.name / _chem_comp.pdbx_synonyms
Revision 2.2Sep 27, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: Maltose-binding periplasmic protein, Histone deacetylase 6 chimera
A: Maltose-binding periplasmic protein, Histone deacetylase 6 chimera
hetero molecules


Theoretical massNumber of molelcules
Total (without water)164,61512
Polymers163,0392
Non-polymers1,57710
Water1,04558
1
B: Maltose-binding periplasmic protein, Histone deacetylase 6 chimera
hetero molecules


Theoretical massNumber of molelcules
Total (without water)82,3086
Polymers81,5191
Non-polymers7885
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Maltose-binding periplasmic protein, Histone deacetylase 6 chimera
hetero molecules


Theoretical massNumber of molelcules
Total (without water)82,3086
Polymers81,5191
Non-polymers7885
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)49.262, 149.032, 216.333
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 / Sugars , 2 types, 4 molecules BA

#1: Protein Maltose-binding periplasmic protein, Histone deacetylase 6 chimera / MBP / MMBP / Maltodextrin-binding protein / HD6


Mass: 81519.352 Da / Num. of mol.: 2
Fragment: MBP + HD6 catalytic domain 2 (UNP residues 479-835)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli), (gene. exp.) Homo sapiens (human)
Gene: malE, Z5632, ECs5017, HDAC6, KIAA0901, JM21 / Plasmid: pET28lic / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)RIL
References: UniProt: P0AEY0, UniProt: Q9UBN7, UniProt: P0AEX9*PLUS, histone deacetylase
#2: Polysaccharide alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose / alpha-maltose


Type: oligosaccharide, Oligosaccharide / Class: Nutrient / Mass: 342.297 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: oligosaccharide / References: alpha-maltose
DescriptorTypeProgram
DGlcpa1-4DGlcpa1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1a_1-5]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[][a-D-Glcp]{[(4+1)][a-D-Glcp]{}}LINUCSPDB-CARE

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Non-polymers , 4 types, 66 molecules

#3: Chemical ChemComp-TSN / TRICHOSTATIN A / 7-[4-(DIMETHYLAMINO)PHENYL]-N-HYDROXY-4,6-DIMETHYL-7-OXO-2,4-HEPTADIENAMIDE


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


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#5: Chemical
ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: K
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 58 / 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: 2.44 Å3/Da / Density % sol: 49.49 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / Details: 0.2 M potassium sodium tartrate, 20% PEG3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.9798 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Aug 15, 2015
RadiationMonochromator: single crystal Si(220) side bounce / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9798 Å / Relative weight: 1
ReflectionResolution: 2.79→149 Å / Num. obs: 40864 / % possible obs: 100 % / Redundancy: 11 % / Rmerge(I) obs: 0.204 / Net I/σ(I): 12.9
Reflection shellHighest resolution: 2.79 Å / Redundancy: 11.3 % / Rmerge(I) obs: 1.853 / Mean I/σ(I) obs: 1.9 / % possible all: 100

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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 4CBT

4cbt


Resolution: 2.79→87.54 Å / SU ML: 0.45 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 29.31 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2754 2055 5.04 %RANDOM
Rwork0.2126 ---
obs0.2157 40774 99.95 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.79→87.54 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11010 0 96 58 11164
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00311395
X-RAY DIFFRACTIONf_angle_d0.73815529
X-RAY DIFFRACTIONf_dihedral_angle_d14.6184063
X-RAY DIFFRACTIONf_chiral_restr0.0261720
X-RAY DIFFRACTIONf_plane_restr0.0032028
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.79-2.85490.38541500.31572518X-RAY DIFFRACTION100
2.8549-2.92630.35741410.30022548X-RAY DIFFRACTION100
2.9263-3.00540.38681470.29582489X-RAY DIFFRACTION100
3.0054-3.09390.36341170.30182594X-RAY DIFFRACTION100
3.0939-3.19380.38691230.28292499X-RAY DIFFRACTION100
3.1938-3.30790.32171320.2822597X-RAY DIFFRACTION100
3.3079-3.44040.31931300.26012531X-RAY DIFFRACTION100
3.4404-3.59690.33231120.24042589X-RAY DIFFRACTION100
3.5969-3.78660.26841440.2162571X-RAY DIFFRACTION100
3.7866-4.02380.27641510.20212531X-RAY DIFFRACTION100
4.0238-4.33450.23321400.17952582X-RAY DIFFRACTION100
4.3345-4.77070.20371300.16182610X-RAY DIFFRACTION100
4.7707-5.46090.25441220.17162647X-RAY DIFFRACTION100
5.4609-6.87970.24061490.19282631X-RAY DIFFRACTION100
6.8797-87.58280.22991670.16992782X-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)
11.05430.51360.5452.29750.641.74950.01960.0517-0.20820.12110.04620.10430.3235-0.046-0.20380.5032-0.0309-0.00270.38530.03430.4002-22.5061-35.656732.6609
21.15080.6211-0.17321.8997-0.25161.13330.09790.0689-0.08470.0306-0.0706-0.17820.01690.07610.00430.32320.017-0.03240.3660.01360.3841-5.1763-3.398715.4311
31.00760.4461-0.02780.4448-0.61831.74960.2391-0.74350.41640.37920.027-0.3376-0.37280.61250.06160.6987-0.13790.06590.8252-0.26950.62021.44361.214386.1916
40.3771-0.3163-0.40850.97310.05521.28170.1582-0.09050.3375-0.3222-0.08760.2946-0.4321-0.07080.01180.56870.0027-0.04090.4893-0.05150.54580.6298-7.224564.4875
50.8374-0.066-0.03560.4696-0.52570.86340.1812-0.2710.58010.0067-0.0952-0.0654-0.51450.23230.06170.7207-0.07930.06080.5656-0.09520.55479.5768-1.156564.6434
60.592-0.1-0.20290.2846-0.28540.78670.2256-0.09620.3988-0.1773-0.08830.1967-0.64170.10070.02420.73850.00060.03710.5982-0.05640.6362-2.45620.666170.0573
70.82380.02930.430.6834-0.36750.93220.0557-0.20020.0595-0.09990.02840.08460.02980.0898-0.04160.2791-0.0003-0.00150.3447-0.02310.36687.8888-41.614682.3394
80.8067-0.2640.21620.98020.2010.96280.01790.0110.07880.01550.0111-0.25460.01810.14610.04320.2234-0.00830.0160.33880.01720.370718.8811-34.377391.2284
90.6715-0.17150.31820.41260.07311.31370.06520.01610.1880.1044-0.0075-0.181-0.0373-0.13760.01260.2890.0096-0.00730.35170.0330.41467.281-25.170395.8614
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'B' and (resid 111 through 473 )
2X-RAY DIFFRACTION2chain 'B' and (resid 474 through 835 )
3X-RAY DIFFRACTION3chain 'A' and (resid 114 through 166 )
4X-RAY DIFFRACTION4chain 'A' and (resid 167 through 308 )
5X-RAY DIFFRACTION5chain 'A' and (resid 309 through 380 )
6X-RAY DIFFRACTION6chain 'A' and (resid 381 through 460 )
7X-RAY DIFFRACTION7chain 'A' and (resid 461 through 516 )
8X-RAY DIFFRACTION8chain 'A' and (resid 517 through 755 )
9X-RAY DIFFRACTION9chain 'A' and (resid 756 through 835 )

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