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- PDB-5g3w: Structure of HDAC like protein from Bordetella Alcaligenes in com... -

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Basic information

Entry
Database: PDB / ID: 5g3w
TitleStructure of HDAC like protein from Bordetella Alcaligenes in complex with the photoswitchable inhibitor CEW65
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 / 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-C65 / : / DI(HYDROXYETHYL)ETHER / Histone deacetylase-like amidohydrolase
Similarity search - Component
Biological speciesBORDETELLA (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 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
DepositionMay 2, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 23, 2016Provider: repository / Type: Initial release
Revision 1.1Mar 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
C: HISTONE DEACETYLASE-LIKE AMIDOHYDROLASE
D: HISTONE DEACETYLASE-LIKE AMIDOHYDROLASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)163,77733
Polymers160,4894
Non-polymers3,28729
Water32,2651791
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area15740 Å2
ΔGint-40.6 kcal/mol
Surface area43410 Å2
MethodPISA
Unit cell
Length a, b, c (Å)92.270, 130.140, 251.130
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222

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Components

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Protein , 1 types, 4 molecules ABCD

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


Mass: 40122.281 Da / Num. of mol.: 4 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) BORDETELLA (bacteria) / Strain: FB188 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): XL1 BLUE / References: UniProt: Q70I53

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Non-polymers , 6 types, 1820 molecules

#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-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: C4H10O3
#5: Chemical
ChemComp-C65 / (2E)-N-hydroxy-3-{4-[(E)-phenyldiazenyl]phenyl}prop-2-enamide


Mass: 267.283 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C15H13N3O2
#6: Chemical ChemComp-1PE / PENTAETHYLENE GLYCOL / PEG400


Mass: 238.278 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H22O6 / Comment: precipitant*YM
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1791 / 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: 2.42 Å3/Da / Density % sol: 49.3 % / Description: NONE
Crystal growpH: 5.25 / Details: PEG 400 MALATE IMIDAZOLE PH 5.25

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1.00002
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 3, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.00002 Å / Relative weight: 1
ReflectionResolution: 1.6→20.67 Å / Num. obs: 197317 / % possible obs: 99.7 % / Observed criterion σ(I): 2.9 / Redundancy: 5.6 % / Rmerge(I) obs: 0.1 / Net I/σ(I): 9.1
Reflection shellResolution: 1.6→1.63 Å / Redundancy: 5.5 % / Rmerge(I) obs: 0.46 / Mean I/σ(I) obs: 2.9 / % possible all: 99.8

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Processing

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

1zz0


Resolution: 1.6→125.57 Å / Cor.coef. Fo:Fc: 0.977 / Cor.coef. Fo:Fc free: 0.962 / SU B: 3.126 / SU ML: 0.048 / Cross valid method: THROUGHOUT / ESU R: 0.089 / ESU R Free: 0.072 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.16662 9836 5 %RANDOM
Rwork0.12496 ---
obs0.12701 187354 99.6 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 15.601 Å2
Baniso -1Baniso -2Baniso -3
1--0.23 Å20 Å20 Å2
2--0.73 Å20 Å2
3----0.5 Å2
Refinement stepCycle: LAST / Resolution: 1.6→125.57 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11096 0 201 1791 13088
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.01911647
X-RAY DIFFRACTIONr_bond_other_d0.0030.0210886
X-RAY DIFFRACTIONr_angle_refined_deg1.5381.95215832
X-RAY DIFFRACTIONr_angle_other_deg1.001324927
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.24151494
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.35123.156507
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.406151671
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.8351584
X-RAY DIFFRACTIONr_chiral_restr0.0860.21725
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.02113508
X-RAY DIFFRACTIONr_gen_planes_other0.0040.022792
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_it1.3731.3065955
X-RAY DIFFRACTIONr_mcbond_other1.3731.3065954
X-RAY DIFFRACTIONr_mcangle_it1.7721.9657453
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.731.5385691
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_restr1.98522531
X-RAY DIFFRACTIONr_sphericity_free34.3845429
X-RAY DIFFRACTIONr_sphericity_bonded8.84823627
LS refinement shellResolution: 1.6→1.642 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.231 725 -
Rwork0.163 13743 -
obs--99.7 %

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