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- PDB-5g1c: Structure of HDAC like protein from Bordetella Alcaligenes bound ... -

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Basic information

Entry
Database: PDB / ID: 5g1c
TitleStructure of HDAC like protein from Bordetella Alcaligenes bound the photoswitchable pyrazole Inhibitor CEW395
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-9RB / : / DI(HYDROXYETHYL)ETHER / Histone deacetylase-like amidohydrolase
Similarity search - Component
Biological speciesALCALIGENES (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.81 Å
AuthorsKraemer, A. / Meyer-Almes, F.J. / Yildiz, O.
CitationJournal: ACS Infect Dis / Year: 2017
Title: Toward Photopharmacological Antimicrobial Chemotherapy Using Photoswitchable Amidohydrolase Inhibitors.
Authors: Weston, C.E. / Kramer, A. / Colin, F. / Yildiz, O. / Baud, M.G. / Meyer-Almes, F.J. / Fuchter, M.J.
History
DepositionMar 24, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 23, 2016Provider: repository / Type: Initial release
Revision 1.1Dec 28, 2016Group: Atomic model / Derived calculations ...Atomic model / Derived calculations / Non-polymer description / Other
Revision 1.2Mar 15, 2017Group: Database references
Revision 2.0Jan 10, 2024Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Other / Refinement description
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _atom_site.occupancy / _database_2.pdbx_DOI ..._atom_site.occupancy / _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)81,24519
Polymers79,1392
Non-polymers2,10517
Water17,817989
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)162,48938
Polymers158,2794
Non-polymers4,21134
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_565-x,-y+1,z1
Buried area20680 Å2
ΔGint-202.1 kcal/mol
Surface area43750 Å2
MethodPISA
Unit cell
Length a, b, c (Å)101.099, 101.099, 175.057
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
11B-2098-

HOH

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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: 39569.699 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 , 6 types, 1006 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-9RB / (2E)-N-hydroxy-3-{4-[(E)-(1,3,5-trimethyl-1H-pyrazol-4-yl)diazenyl]phenyl}prop-2-enamide


Mass: 299.328 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C15H17N5O2
#5: Chemical ChemComp-1PE / PENTAETHYLENE GLYCOL / PEG400


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


Mass: 106.120 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C4H10O3
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 989 / 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: 57.1 % / 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: 1.00004
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 8, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.00004 Å / Relative weight: 1
ReflectionResolution: 1.81→31.45 Å / Num. obs: 82927 / % possible obs: 99.9 % / Observed criterion σ(I): 5.3 / Redundancy: 20.6 % / Rmerge(I) obs: 0.14 / Net I/σ(I): 15.4
Reflection shellResolution: 1.81→1.85 Å / Redundancy: 21 % / Rmerge(I) obs: 0.69 / Mean I/σ(I) obs: 5.3 / % possible all: 99.3

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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: 1.81→87.55 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.938 / SU B: 5.225 / SU ML: 0.073 / Cross valid method: THROUGHOUT / ESU R: 0.193 / ESU R Free: 0.118 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.21853 4154 5 %RANDOM
Rwork0.17098 ---
obs0.17335 78680 99.81 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 15.603 Å2
Baniso -1Baniso -2Baniso -3
1-0.02 Å20 Å20 Å2
2--0.02 Å20 Å2
3----0.04 Å2
Refinement stepCycle: LAST / Resolution: 1.81→87.55 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5558 0 131 989 6678
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0195888
X-RAY DIFFRACTIONr_bond_other_d0.0050.025517
X-RAY DIFFRACTIONr_angle_refined_deg1.6051.9578005
X-RAY DIFFRACTIONr_angle_other_deg1.174312633
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1645752
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.47723.113257
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.28715839
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.0541543
X-RAY DIFFRACTIONr_chiral_restr0.1230.2867
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0216832
X-RAY DIFFRACTIONr_gen_planes_other0.0040.021403
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_it1.361.3222995
X-RAY DIFFRACTIONr_mcbond_other1.361.3232996
X-RAY DIFFRACTIONr_mcangle_it1.6391.983750
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.3621.5152893
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_restr1.85711405
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.812→1.859 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.232 325 -
Rwork0.176 5675 -
obs--99.45 %

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