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- PDB-5g17: Bordetella Alcaligenes HDAH (T101A) bound to 9,9,9-trifluoro-8,8-... -

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Basic information

Entry
Database: PDB / ID: 5g17
TitleBordetella Alcaligenes HDAH (T101A) bound to 9,9,9-trifluoro-8,8- dihydroxy-N-phenylnonanamide.
ComponentsHISTONE DEACETYLASE-LIKE AMIDOHYDROLASE
KeywordsHYDROLASE / HDAH / HDAC / HDLP
Function / homology
Function and homology information


Hydrolases; Acting on carbon-nitrogen bonds, other than peptide bonds; In linear amides / histone deacetylase activity / epigenetic regulation of gene expression / hydrolase activity / metal ion binding
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
Chem-6DK / : / Histone deacetylase-like amidohydrolase
Similarity search - Component
Biological speciesALCALIGENES (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.51 Å
AuthorsKraemer, A. / Meyer-Almes, F.J. / Yildiz, O.
CitationJournal: Biochim. Biophys. Acta / Year: 2017
Title: The thermodynamic signature of ligand binding to histone deacetylase-like amidohydrolases is most sensitive to the flexibility in the L2-loop lining the active site pocket.
Authors: Meyners, C. / Kramer, A. / Yildiz, O. / Meyer-Almes, F.J.
History
DepositionMar 23, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 12, 2017Provider: repository / Type: Initial release
Revision 1.1Apr 19, 2017Group: Database references
Revision 1.2Jul 5, 2017Group: Database references / Category: citation
Item: _citation.country / _citation.journal_id_ASTM ..._citation.country / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_volume / _citation.page_first / _citation.page_last
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 / pdbx_struct_special_symmetry / 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: HISTONE DEACETYLASE-LIKE AMIDOHYDROLASE
B: HISTONE DEACETYLASE-LIKE AMIDOHYDROLASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)79,72910
Polymers78,8032
Non-polymers9268
Water16,484915
1
A: HISTONE DEACETYLASE-LIKE AMIDOHYDROLASE
B: HISTONE DEACETYLASE-LIKE AMIDOHYDROLASE
hetero molecules

A: HISTONE DEACETYLASE-LIKE AMIDOHYDROLASE
B: HISTONE DEACETYLASE-LIKE AMIDOHYDROLASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)159,45820
Polymers157,6064
Non-polymers1,85216
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_565-x,-y+1,z1
Buried area13040 Å2
ΔGint-66.6 kcal/mol
Surface area42720 Å2
MethodPISA
Unit cell
Length a, b, c (Å)101.270, 101.270, 175.220
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number94
Space group name H-MP42212
Components on special symmetry positions
IDModelComponents
11A-2087-

HOH

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Components

#1: Protein HISTONE DEACETYLASE-LIKE AMIDOHYDROLASE / HDAC-LIKE AMIDOHYDROLASE / HDAH / HDAH


Mass: 39401.527 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) ALCALIGENES (bacteria) / Strain: FB188 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): XL1 BLUE / References: UniProt: Q70I53, amidase
#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-6DK / 9,9,9-tris(fluoranyl)-8,8-bis(oxidanyl)-~{N}-phenyl-nonanamide


Mass: 319.319 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C15H20F3NO3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 915 / 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: 2.87 Å3/Da / Density % sol: 57 % / Description: NONE
Crystal growpH: 7.5 / Details: pH 7.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1.03895
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 21, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.03895 Å / Relative weight: 1
ReflectionResolution: 1.51→25 Å / Num. obs: 142442 / % possible obs: 100 % / Observed criterion σ(I): 2.7 / Redundancy: 11.9 % / Rmerge(I) obs: 0.12 / Net I/σ(I): 11.5
Reflection shellResolution: 1.51→1.54 Å / Redundancy: 12.2 % / Rmerge(I) obs: 1.02 / Mean I/σ(I) obs: 2.7 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0103refinement
MOSFLMdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1ZZ0

1zz0


Resolution: 1.51→87.68 Å / Cor.coef. Fo:Fc: 0.979 / Cor.coef. Fo:Fc free: 0.97 / SU B: 2.113 / SU ML: 0.034 / Cross valid method: THROUGHOUT / ESU R: 0.058 / ESU R Free: 0.053 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.15793 7092 5 %RANDOM
Rwork0.12971 ---
obs0.13112 135251 99.95 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 16.226 Å2
Baniso -1Baniso -2Baniso -3
1-0.24 Å20 Å2-0 Å2
2--0.24 Å2-0 Å2
3----0.48 Å2
Refinement stepCycle: LAST / Resolution: 1.51→87.68 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5524 0 50 915 6489
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0195757
X-RAY DIFFRACTIONr_bond_other_d0.0050.025347
X-RAY DIFFRACTIONr_angle_refined_deg1.5091.9497804
X-RAY DIFFRACTIONr_angle_other_deg1.109312235
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1865739
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.81623.16250
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.89115825
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.9361542
X-RAY DIFFRACTIONr_chiral_restr0.0910.2859
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0216649
X-RAY DIFFRACTIONr_gen_planes_other0.0040.021363
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.3171.382958
X-RAY DIFFRACTIONr_mcbond_other1.3171.382959
X-RAY DIFFRACTIONr_mcangle_it1.6112.0763695
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.5021.562799
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr2.21711104
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.511→1.55 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.22 525 -
Rwork0.2 9821 -
obs--99.99 %

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