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- PDB-5g0h: Crystal structure of Danio rerio HDAC6 CD2 in complex with (S)- t... -

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Basic information

Entry
Database: PDB / ID: 5g0h
TitleCrystal structure of Danio rerio HDAC6 CD2 in complex with (S)- trichostatin A
ComponentsHDAC6
KeywordsCELL CYCLE / HISTONE / HISTONE DEACETYLASE
Function / homology
Function and homology information


: / Aggrephagy / : / tubulin deacetylase activity / swimming behavior / definitive hemopoiesis / protein lysine deacetylase activity / histone deacetylase activity / regulation of tubulin deacetylation / potassium ion binding ...: / Aggrephagy / : / tubulin deacetylase activity / swimming behavior / definitive hemopoiesis / protein lysine deacetylase activity / histone deacetylase activity / regulation of tubulin deacetylation / potassium ion binding / histone deacetylase complex / hematopoietic progenitor cell differentiation / angiogenesis / negative regulation of transcription by RNA polymerase II / 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 / Histone deacetylase domain ...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
S-Trichostatin A / : / Histone deacetylase 6
Similarity search - Component
Biological speciesDANIO RERIO (zebrafish)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsMiyake, Y. / Keusch, J.J. / Wang, L. / Saito, M. / Hess, D. / Wang, X. / Melancon, B.J. / Helquist, P. / Gut, H. / Matthias, P.
CitationJournal: Nat.Chem.Biol. / Year: 2016
Title: Structural Insights Into Hdac6 Tubulin Deacetylation and its Selective Inhibition
Authors: Miyake, Y. / Keusch, J.J. / Wang, L. / Saito, M. / Hess, D. / Wang, X. / Melancon, B.J. / Helquist, P. / Gut, H. / Matthias, P.
History
DepositionMar 18, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 27, 2016Provider: repository / Type: Initial release
Revision 1.1Aug 10, 2016Group: Database references
Revision 1.2Sep 28, 2016Group: Database references

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: HDAC6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)88,58115
Polymers87,5141
Non-polymers1,06714
Water6,323351
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)49.980, 48.230, 73.780
Angle α, β, γ (deg.)90.00, 103.22, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 1 molecules A

#1: Protein HDAC6 /


Mass: 87514.406 Da / Num. of mol.: 1 / Fragment: CATALYTIC DOMAIN 2, UNP RESIDUES 40-831
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) DANIO RERIO (zebrafish) / Plasmid: POPINF / Cell line (production host): SF9 / Production host: SPODOPTERA FRUGIPERDA (fall armyworm) / References: UniProt: F8W4B7

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Non-polymers , 5 types, 365 molecules

#2: Chemical ChemComp-E1Z / S-Trichostatin A


Mass: 302.368 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H22N2O3
#3: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 2 / 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-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C2H6O2
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 351 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 1.8 Å3/Da / Density % sol: 32 % / Description: NONE
Crystal growDetails: 15% PEG 3350, 0.1M KCL

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Details: MIRRORS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.6→50 Å / Num. obs: 44152 / % possible obs: 96.7 % / Observed criterion σ(I): -3 / Redundancy: 3.2 % / Biso Wilson estimate: 18.31 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 10.2
Reflection shellResolution: 1.6→1.64 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.71 / Mean I/σ(I) obs: 1.6 / % possible all: 83.8

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Processing

Software
NameVersionClassification
BUSTER2.11.5refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: HOMOLOGY MODEL

Resolution: 1.6→23.43 Å / Cor.coef. Fo:Fc: 0.9525 / Cor.coef. Fo:Fc free: 0.9439 / SU R Cruickshank DPI: 0.078 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.082 / SU Rfree Blow DPI: 0.078 / SU Rfree Cruickshank DPI: 0.076
RfactorNum. reflection% reflectionSelection details
Rfree0.1741 2204 5 %RANDOM
Rwork0.1502 ---
obs0.1515 44079 97.22 %-
Displacement parametersBiso mean: 20.62 Å2
Baniso -1Baniso -2Baniso -3
1--7.0782 Å20 Å2-3.2574 Å2
2--3.2915 Å20 Å2
3---3.7866 Å2
Refine analyzeLuzzati coordinate error obs: 0.157 Å
Refinement stepCycle: LAST / Resolution: 1.6→23.43 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2810 0 65 351 3226
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.012961HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.994000HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1007SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes64HARMONIC2
X-RAY DIFFRACTIONt_gen_planes443HARMONIC5
X-RAY DIFFRACTIONt_it2961HARMONIC20
X-RAY DIFFRACTIONt_nbd1SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion3.87
X-RAY DIFFRACTIONt_other_torsion14.85
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion376SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies7HARMONIC1
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact3965SEMIHARMONIC4
LS refinement shellResolution: 1.6→1.64 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2708 149 5.01 %
Rwork0.2303 2823 -
all0.2324 2972 -
obs--97.22 %
Refinement TLS params.Method: refined / Origin x: -16.8724 Å / Origin y: 4.772 Å / Origin z: -16.2349 Å
111213212223313233
T-0.0185 Å2-0.0021 Å20.0101 Å2--0.0127 Å20.0004 Å2---0.0352 Å2
L0.3036 °2-0.0271 °2-0.058 °2-0.3793 °20.0022 °2--0.3473 °2
S0.0073 Å °-0.0068 Å °-0.0041 Å °-0.0048 Å °-0.0082 Å °-0.0277 Å °-0.0055 Å °0.0097 Å °0.0009 Å °
Refinement TLS groupSelection details: { A|* }

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