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- PDB-5g0i: Crystal structure of Danio rerio HDAC6 CD1 and CD2 (linker cleave... -

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Basic information

Entry
Database: PDB / ID: 5g0i
TitleCrystal structure of Danio rerio HDAC6 CD1 and CD2 (linker cleaved) in complex with Nexturastat 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 / 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 / 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
: / NEXTURASTAT A / Histone deacetylase 6
Similarity search - Component
Biological speciesDANIO RERIO (zebrafish)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.99 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
Revision 1.3Jan 10, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _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.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_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.pdbx_dist_value / _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_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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: HDAC6
B: HDAC6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)180,79521
Polymers178,6952
Non-polymers2,10019
Water11,349630
1
A: HDAC6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)90,41511
Polymers89,3481
Non-polymers1,06810
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: HDAC6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)90,38010
Polymers89,3481
Non-polymers1,0329
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)162.560, 52.830, 186.420
Angle α, β, γ (deg.)90.00, 108.92, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11B-2148-

HOH

Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (0.8189, 0.5739, -0.004035), (0.5733, -0.8184, -0.03993), (-0.02621, 0.03038, -0.9992)
Vector: -29.21, -46.92, 87.38)

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein HDAC6


Mass: 89347.539 Da / Num. of mol.: 2 / Fragment: CATALYTIC DOMAIN 1 AND 2, UNP RESIDUES 25-831
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 , 6 types, 649 molecules

#2: Chemical
ChemComp-ZN / ZINC ION


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


Mass: 39.098 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: K
#4: Chemical
ChemComp-N4R / NEXTURASTAT A


Mass: 341.404 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C19H23N3O3
#5: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#6: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 630 / 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: 2.1 Å3/Da / Density % sol: 42 % / Description: NONE
Crystal growDetails: 23% PEG 3350, 0.1M KCL

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Details: MIRRORS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.99→50 Å / Num. obs: 101593 / % possible obs: 98.8 % / Observed criterion σ(I): -3 / Redundancy: 3.2 % / Biso Wilson estimate: 45.35 Å2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 10.3
Reflection shellResolution: 1.99→2.05 Å / Redundancy: 2.9 % / Rmerge(I) obs: 1.22 / Mean I/σ(I) obs: 0.9 / % possible all: 94.2

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Processing

Software
NameVersionClassification
BUSTER2.11.5refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRIES 5G0G AND 5G0H

5g0g

5g0h


Resolution: 1.99→45.58 Å / Cor.coef. Fo:Fc: 0.9596 / Cor.coef. Fo:Fc free: 0.954 / SU R Cruickshank DPI: 0.165 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.165 / SU Rfree Blow DPI: 0.137 / SU Rfree Cruickshank DPI: 0.137
Details: ADDUCT OF CYS581 COULD NOT BE IDENTIFIED AND HAS NOT BEEN MODELED. CHAIN A IS MORE ORDERED AND DISPLAYS HIGHER QUALITY ELECTRON DENSITY. NCS RESTRAINTS HAVE BEEN USED
RfactorNum. reflection% reflectionSelection details
Rfree0.2003 5080 5 %RANDOM
Rwork0.1739 ---
obs0.1752 101593 98.19 %-
Displacement parametersBiso mean: 55.28 Å2
Baniso -1Baniso -2Baniso -3
1--3.0534 Å20 Å2-1.7433 Å2
2---5.1435 Å20 Å2
3---8.1969 Å2
Refine analyzeLuzzati coordinate error obs: 0.328 Å
Refinement stepCycle: LAST / Resolution: 1.99→45.58 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11227 0 121 630 11978
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0111672HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.0415831HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d3983SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes262HARMONIC2
X-RAY DIFFRACTIONt_gen_planes1793HARMONIC5
X-RAY DIFFRACTIONt_it11672HARMONIC20
X-RAY DIFFRACTIONt_nbd4SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion3.32
X-RAY DIFFRACTIONt_other_torsion16.78
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion1471SEMIHARMONIC5
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_contact13968SEMIHARMONIC4
LS refinement shellResolution: 1.99→2.04 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.3407 323 5 %
Rwork0.3094 6138 -
all0.311 6461 -
obs--98.19 %
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)
10.86650.27990.28480.65510.31871.48490.0085-0.00730.02460.054-0.03320.06130.184-0.21590.0246-0.0144-0.02360.021-0.10950.0098-0.0351-18.7749-32.339459.2712
20.94560.12620.09810.91890.07561.6598-0.0224-0.01220.04890.08080.0171-0.09380.04260.3370.0053-0.08390.0063-0.0183-0.0740.0135-0.053414.7968-14.051371.2405
33.98241.0512-1.8080.9315-0.17611.1507-0.43471.50330.1712-0.25290.5260.16680.1752-0.7214-0.0913-0.2422-0.247-0.07210.27790.1089-0.3874-63.4868-33.544927.815
42.76730.2566-1.78810.8648-0.13712.6236-0.11690.6892-0.0637-0.31660.0885-0.17670.2432-0.50940.0284-0.1096-0.12140.08340.009-0.04-0.276-25.4408-29.848615.4213
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{A|58 - 419}
2X-RAY DIFFRACTION2{A|442 - 801}
3X-RAY DIFFRACTION3{B|59 - 418}
4X-RAY DIFFRACTION4{B|442 - 801}

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