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- PDB-2vcg: Crystal structure of a HDAC-like protein HDAH from Bordetella sp.... -

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Basic information

Entry
Database: PDB / ID: 2vcg
TitleCrystal structure of a HDAC-like protein HDAH from Bordetella sp. with the bound inhibitor ST-17
ComponentsHISTONE DEACETYLASE-LIKE AMIDOHYDROLASE
KeywordsHYDROLASE / HDAH / INHIBITOR / HDAC-LIKE AMIDOHYDROLASE / HISTONE DEACETYLASE-LIKE AMIDOHYDROLASE
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-S17 / Histone deacetylase-like amidohydrolase
Similarity search - Component
Biological speciesALCALIGENES SP. (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsDickmanns, A. / Strasser, A. / Ficner, R.
CitationJournal: Bioorg.Med.Chem. / Year: 2008
Title: Phenylalanine-Containing Hydroxamic Acids as Selective Inhibitors of Class Iib Histone Deacetylases (Hdacs).
Authors: Schaefer, S. / Saunders, L. / Eliseeva, E. / Velena, A. / Jung, M. / Schwienhorst, A. / Strasser, A. / Dickmanns, A. / Ficner, R. / Schlimme, S. / Sippl, W. / Verdin, E. / Jung, M.
History
DepositionSep 24, 2007Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 8, 2008Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jul 24, 2019Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.4Dec 13, 2023Group: 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
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

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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)163,59124
Polymers161,0144
Non-polymers2,57720
Water30,5171694
1
A: HISTONE DEACETYLASE-LIKE AMIDOHYDROLASE
D: HISTONE DEACETYLASE-LIKE AMIDOHYDROLASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)81,84613
Polymers80,5072
Non-polymers1,33911
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3740 Å2
ΔGint-30.3 kcal/mol
Surface area29030 Å2
MethodPQS
2
B: HISTONE DEACETYLASE-LIKE AMIDOHYDROLASE
C: HISTONE DEACETYLASE-LIKE AMIDOHYDROLASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)81,74511
Polymers80,5072
Non-polymers1,2389
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4510 Å2
ΔGint-20.7 kcal/mol
Surface area28340 Å2
MethodPQS
Unit cell
Length a, b, c (Å)67.664, 93.633, 121.664
Angle α, β, γ (deg.)90.00, 103.99, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 4 molecules ABCD

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


Mass: 40253.480 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) ALCALIGENES SP. (bacteria) / Strain: DSM 11172 / Plasmid: PQE / Production host: ESCHERICHIA COLI (E. coli) / Variant (production host): M15
References: UniProt: Q70I53, Hydrolases; Acting on carbon-nitrogen bonds, other than peptide bonds; In linear amides

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Non-polymers , 6 types, 1714 molecules

#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 5 / 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-S17 / methyl 4-bromo-N-[8-(hydroxyamino)-8-oxooctanoyl]-L-phenylalaninate


Mass: 429.306 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C18H25BrN2O5
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#6: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1694 / Source method: isolated from a natural source / Formula: H2O

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Details

Nonpolymer details(S)-3-(4-BROMO-PHENYL)-2-(7-HYDROXYCARBAMOYL-HEPTANOYLAMINO)- PROPRIONIC ACID METHYL ESTER

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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: 2.5 Å3/Da / Density % sol: 50.8 % / Description: NONE
Crystal growpH: 6.5 / Details: 600 MM NACL 200 MM NA-CACODYLATE 6.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X13 / Wavelength: 0.8015
DetectorType: MARRESEARCH / Detector: CCD / Date: Mar 28, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8015 Å / Relative weight: 1
ReflectionResolution: 1.9→50 Å / Num. obs: 111630 / % possible obs: 96 % / Observed criterion σ(I): 2 / Redundancy: 2.9 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 16.9
Reflection shellResolution: 1.9→1.97 Å / Redundancy: 2.4 % / Rmerge(I) obs: 0.36 / Mean I/σ(I) obs: 4.2 / % possible all: 93.8

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1ZZ0

1zz0


Resolution: 1.9→117.85 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.93 / SU B: 3.014 / SU ML: 0.09 / Cross valid method: THROUGHOUT / ESU R: 0.15 / ESU R Free: 0.141 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.206 5596 5 %RANDOM
Rwork0.156 ---
obs0.159 106011 96 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 16.34 Å2
Baniso -1Baniso -2Baniso -3
1-0.46 Å20 Å2-0.29 Å2
2---0.62 Å20 Å2
3---0.02 Å2
Refinement stepCycle: LAST / Resolution: 1.9→117.85 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11099 0 130 1694 12923
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.02111570
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.3451.94815768
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.22351485
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.9123.033511
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.677151676
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.051588
X-RAY DIFFRACTIONr_chiral_restr0.0880.21733
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.029044
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2260.27879
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.310.28050
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1640.21831
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1910.2199
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1760.292
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.6261.57363
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.103211759
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.83634255
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it2.8814.54005
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.9→1.95 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.285 417
Rwork0.222 7454

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