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- PDB-5g1b: Bordetella Alcaligenes HDAH native -

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Basic information

Entry
Database: PDB / ID: 5g1b
TitleBordetella Alcaligenes HDAH native
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
: / DI(HYDROXYETHYL)ETHER / Histone deacetylase-like amidohydrolase
Similarity search - Component
Biological speciesALCALIGENES (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 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 24, 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 / 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)80,81616
Polymers79,4162
Non-polymers1,40014
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)161,63232
Polymers158,8314
Non-polymers2,80128
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,-y,z1
Buried area17500 Å2
ΔGint-199.7 kcal/mol
Surface area44760 Å2
MethodPISA
Unit cell
Length a, b, c (Å)100.660, 100.660, 175.110
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number94
Space group name H-MP42212

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Components

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Protein , 1 types, 2 molecules AB

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


Mass: 39707.844 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

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Non-polymers , 5 types, 929 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-1PE / PENTAETHYLENE GLYCOL / PEG400


Mass: 238.278 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H22O6 / Comment: precipitant*YM
#5: Chemical
ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C4H10O3
#6: 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: 2.9 Å3/Da / Density % sol: 57.7 % / Description: NONE
Crystal growpH: 5.25 / Details: pH 5.25

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.99988
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 7, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99988 Å / Relative weight: 1
ReflectionResolution: 1.7→27.6 Å / Num. obs: 99299 / % possible obs: 100 % / Observed criterion σ(I): 2.3 / Redundancy: 8 % / Rmerge(I) obs: 0.13 / Net I/σ(I): 8.4
Reflection shellResolution: 1.7→1.73 Å / Redundancy: 8.2 % / Rmerge(I) obs: 0.85 / Mean I/σ(I) obs: 2.3 / % 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: PDB ENTRY 5G0X

5g0x


Resolution: 1.7→87.56 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.957 / SU B: 4.348 / SU ML: 0.062 / Cross valid method: THROUGHOUT / ESU R: 0.114 / ESU R Free: 0.088 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.19147 4899 4.9 %RANDOM
Rwork0.15174 ---
obs0.15371 94197 99.8 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 18.786 Å2
Baniso -1Baniso -2Baniso -3
1-0.65 Å2-0 Å2-0 Å2
2--0.65 Å2-0 Å2
3----1.29 Å2
Refinement stepCycle: LAST / Resolution: 1.7→87.56 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5568 0 80 915 6563
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0195809
X-RAY DIFFRACTIONr_bond_other_d0.0040.025447
X-RAY DIFFRACTIONr_angle_refined_deg1.5081.9487893
X-RAY DIFFRACTIONr_angle_other_deg1.106312480
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2345745
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.25223.164256
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.76815831
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.4321542
X-RAY DIFFRACTIONr_chiral_restr0.0840.2862
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0216713
X-RAY DIFFRACTIONr_gen_planes_other0.0030.021371
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_it1.9641.6022977
X-RAY DIFFRACTIONr_mcbond_other1.9611.6012976
X-RAY DIFFRACTIONr_mcangle_it2.4862.4073723
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.5861.8652832
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_restr2.92511256
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.7→1.744 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.256 347 -
Rwork0.211 6869 -
obs--99.9 %

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