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- PDB-2gh6: Crystal structure of a HDAC-like protein with 9,9,9-trifluoro-8-o... -

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Basic information

Entry
Database: PDB / ID: 2gh6
TitleCrystal structure of a HDAC-like protein with 9,9,9-trifluoro-8-oxo-N-phenylnonan amide bound
ComponentsHistone deacetylase-like amidohydrolase
KeywordsHYDROLASE / Histone deacetylase / zinc-ion / trifluoromethyl ketone
Function / homology
Function and homology information


Hydrolases; Acting on carbon-nitrogen bonds, other than peptide bonds; In linear amides / histone deacetylase activity / negative regulation of transcription by RNA polymerase II / metal ion binding / cytoplasm
Similarity search - Function
Histone deacetylase domain / Arginase; Chain A / Histone deacetylase family / Histone deacetylase domain / Histone deacetylase domain superfamily / Histone deacetylase domain / Ureohydrolase domain superfamily / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
9,9,9-TRIFLUORO-8-OXO-N-PHENYLNONANAMIDE / : / Histone deacetylase-like amidohydrolase
Similarity search - Component
Biological speciesAlcaligenaceae bacterium FB188 (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.203 Å
AuthorsNielsen, T.K. / Hildmann, C. / Riester, D. / Wegener, D. / Schwienhorst, A. / Ficner, R.
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2007
Title: Complex structure of a bacterial class 2 histone deacetylase homologue with a trifluoromethylketone inhibitor.
Authors: Nielsen, T.K. / Hildmann, C. / Riester, D. / Wegener, D. / Schwienhorst, A. / Ficner, R.
History
DepositionMar 26, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 20, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Aug 30, 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_ncs_dom_lim / struct_ref_seq_dif / struct_site
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_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_alt_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_alt_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.pdbx_ptnr2_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 / _struct_conn.ptnr2_label_seq_id / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ref_seq_dif.details / _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: Histone deacetylase-like amidohydrolase
B: Histone deacetylase-like amidohydrolase
C: Histone deacetylase-like amidohydrolase
D: Histone deacetylase-like amidohydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)159,47820
Polymers157,6984
Non-polymers1,78016
Water14,106783
1
A: Histone deacetylase-like amidohydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,8705
Polymers39,4251
Non-polymers4454
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Histone deacetylase-like amidohydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,8705
Polymers39,4251
Non-polymers4454
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Histone deacetylase-like amidohydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,8705
Polymers39,4251
Non-polymers4454
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Histone deacetylase-like amidohydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,8705
Polymers39,4251
Non-polymers4454
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area16050 Å2
ΔGint-195 kcal/mol
Surface area41820 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)68.507, 94.897, 123.301
Angle α, β, γ (deg.)90.00, 104.28, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: ALA / Beg label comp-ID: ALA / End auth comp-ID: ILE / End label comp-ID: ILE / Refine code: 5 / Auth seq-ID: 2 - 368 / Label seq-ID: 2 - 368

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB
3CC
4DD
DetailsProtein is a monomer

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Components

#1: Protein
Histone deacetylase-like amidohydrolase / E.C.3.5.1.- / HDAC-like amidohydrolase / HDAH


Mass: 39424.602 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Alcaligenaceae bacterium FB188 (bacteria)
Strain: DSM 11172
Description: source organism synonym Bordetella sp. (strain FB188)
Gene: hdaH, hdaH1 / Plasmid: pQE / Production host: Escherichia coli (E. coli) / Strain (production host): M15
References: UniProt: Q70I53, Hydrolases; Acting on carbon-nitrogen bonds, other than peptide bonds; In linear amides
#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-CF3 / 9,9,9-TRIFLUORO-8-OXO-N-PHENYLNONANAMIDE


Mass: 301.304 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C15H18F3NO2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 783 / 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: 2.46 Å3/Da / Density % sol: 50.03 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: NaCl, Na-cacodylate, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 Å
DetectorType: RIGAKU / Detector: IMAGE PLATE
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.203→39.84 Å / Num. all: 76561 / Num. obs: 76561
Reflection shellResolution: 2.203→2.26 Å / % possible all: 92.9

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Processing

Software
NameVersionClassification
HKL-2000data reduction
MOLREPphasing
REFMAC5.2refinement
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1ZZ1

1zz1


Resolution: 2.203→39.84 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.931 / SU B: 5.015 / SU ML: 0.129 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.244 / ESU R Free: 0.195 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.21419 3863 5 %RANDOM
Rwork0.15797 ---
all0.16082 ---
obs0.16082 72678 98.91 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 24.778 Å2
Baniso -1Baniso -2Baniso -3
1-0.01 Å20 Å20 Å2
2--0.01 Å20 Å2
3----0.02 Å2
Refinement stepCycle: LAST / Resolution: 2.203→39.84 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10988 0 96 783 11867
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.02111364
X-RAY DIFFRACTIONr_angle_refined_deg1.5591.95315508
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.56451464
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.49323.252492
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.534151632
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.061580
X-RAY DIFFRACTIONr_chiral_restr0.1020.21712
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.028884
X-RAY DIFFRACTIONr_nbd_refined0.220.25745
X-RAY DIFFRACTIONr_nbtor_refined0.2990.27633
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1460.2798
X-RAY DIFFRACTIONr_metal_ion_refined0.2420.235
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1590.231
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.10.27
X-RAY DIFFRACTIONr_mcbond_it0.6511.57264
X-RAY DIFFRACTIONr_mcangle_it1.184211580
X-RAY DIFFRACTIONr_scbond_it2.22534144
X-RAY DIFFRACTIONr_scangle_it3.4914.53928
Refine LS restraints NCS

Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION

Dom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
1A1468medium positional0.220.5
2B1468medium positional0.130.5
3C1468medium positional0.140.5
4D1468medium positional0.150.5
1A1280loose positional0.565
2B1280loose positional0.325
3C1280loose positional0.315
4D1280loose positional0.365
1A1468medium thermal1.152
2B1468medium thermal1.552
3C1468medium thermal0.862
4D1468medium thermal1.712
1A1280loose thermal2.1610
2B1280loose thermal2.4810
3C1280loose thermal1.6210
4D1280loose thermal2.6810
LS refinement shellResolution: 2.203→2.26 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.294 266 -
Rwork0.205 4737 -
obs--88.33 %

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