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

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Basic information

Entry
Database: PDB / ID: 6csp
TitleCrystal structure of Danio rerio histone deacetylase 6 catalytic domain 2 in complex with cyclohexenylhydroxamate
ComponentsHdac6 protein
KeywordsHYDROLASE / Zinc hydrolase / tubulin 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
N-hydroxycyclohex-1-ene-1-carboxamide / : / DI(HYDROXYETHYL)ETHER / Hdac6 protein / Histone deacetylase 6
Similarity search - Component
Biological speciesDanio rerio (zebrafish)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.237 Å
AuthorsPorter, N.J. / 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: Biochemistry / Year: 2018
Title: Entropy as a Driver of Selectivity for Inhibitor Binding to Histone Deacetylase 6.
Authors: Porter, N.J. / Wagner, F.F. / Christianson, D.W.
History
DepositionMar 21, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 30, 2018Provider: repository / Type: Initial release
Revision 1.1Jul 11, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Mar 13, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_ptnr1_label_alt_id / _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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Hdac6 protein
B: Hdac6 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)82,75437
Polymers80,5712
Non-polymers2,18335
Water16,520917
1
A: Hdac6 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,29718
Polymers40,2851
Non-polymers1,01217
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1860 Å2
ΔGint2 kcal/mol
Surface area13250 Å2
MethodPISA
2
B: Hdac6 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,45719
Polymers40,2851
Non-polymers1,17118
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2500 Å2
ΔGint12 kcal/mol
Surface area13950 Å2
MethodPISA
Unit cell
Length a, b, c (Å)74.700, 91.830, 96.549
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Hdac6 protein /


Mass: 40285.484 Da / Num. of mol.: 2
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

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Non-polymers , 7 types, 952 molecules

#2: Chemical ChemComp-ZN / ZINC ION


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


Mass: 39.098 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: K
#4: Chemical
ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#5: Chemical ChemComp-FBM / N-hydroxycyclohex-1-ene-1-carboxamide / cyclohexenylhydroxamate


Mass: 141.168 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C7H11NO2 / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical...
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 22 / Source method: obtained synthetically / Formula: C2H6O2
#7: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#8: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 917 / 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: 2.08 Å3/Da / Density % sol: 40.85 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / Details: 0.2 M ammonium chloride 20% Peg 3,350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.97946 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 16, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97946 Å / Relative weight: 1
ReflectionResolution: 1.24→59.08 Å / Num. obs: 188513 / % possible obs: 99.7 % / Redundancy: 6.1 % / Biso Wilson estimate: 7.27 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.101 / Rpim(I) all: 0.044 / Rrim(I) all: 0.11 / Net I/σ(I): 10 / Num. measured all: 1156727 / Scaling rejects: 73
Reflection shell

Diffraction-ID: 1 / % possible all: 99.9

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs
1.24-1.266.20.5935764592840.8710.2570.6483
6.78-59.086.70.048883013210.9920.0210.05326.9

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Processing

Software
NameVersionClassification
Aimless0.5.32data scaling
PHENIX1.12_2829refinement
PDB_EXTRACT3.24data extraction
MOSFLMdata reduction
PHASERphasing
RefinementResolution: 1.237→48.275 Å / SU ML: 0.1 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 15.27 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1533 9414 5 %
Rwork0.1272 178945 -
obs0.1285 188359 99.64 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 47.7 Å2 / Biso mean: 11.5608 Å2 / Biso min: 3.44 Å2
Refinement stepCycle: final / Resolution: 1.237→48.275 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5546 0 289 935 6770
Biso mean--23.27 23.87 -
Num. residues----714
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0086105
X-RAY DIFFRACTIONf_angle_d1.0548283
X-RAY DIFFRACTIONf_chiral_restr0.107886
X-RAY DIFFRACTIONf_plane_restr0.0081100
X-RAY DIFFRACTIONf_dihedral_angle_d24.7662241
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.237-1.25110.25293200.186858976217100
1.2511-1.26580.22043060.174659296235100
1.2658-1.28120.19263470.169758846231100
1.2812-1.29740.20573220.164858956217100
1.2974-1.31450.20723530.159958676220100
1.3145-1.33250.18823100.16115899620999
1.3325-1.35160.20063050.15785877618299
1.3516-1.37170.20152890.15459486237100
1.3717-1.39320.17763110.143459096220100
1.3932-1.4160.17993030.134459746277100
1.416-1.44040.162970.125359696266100
1.4404-1.46660.15932960.118859186214100
1.4666-1.49480.16192940.115759756269100
1.4948-1.52540.15282850.110359716256100
1.5254-1.55850.13722680.1085960622899
1.5585-1.59480.16143130.1115870618399
1.5948-1.63470.13843200.106159216241100
1.6347-1.67890.13632890.107459876276100
1.6789-1.72830.14442900.111160146304100
1.7283-1.78410.143440.107559136257100
1.7841-1.84780.14393040.108560126316100
1.8478-1.92180.12983410.10975890623199
1.9218-2.00930.14083330.11495959629299
2.0093-2.11520.13643270.110660056332100
2.1152-2.24770.13362880.109960346322100
2.2477-2.42130.13273120.110860156327100
2.4213-2.66490.14483200.121760466366100
2.6649-3.05050.14643290.12986029635899
3.0505-3.8430.14953470.13226067641499
3.843-48.31150.14443510.15286311666299

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