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- PDB-5li3: Crystal structure of HDAC-like protein from P. aeruginosa in comp... -

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Basic information

Entry
Database: PDB / ID: 5li3
TitleCrystal structure of HDAC-like protein from P. aeruginosa in complex with a photo-switchable inhibitor.
ComponentsAcetoin utilization protein
KeywordsSIGNALING PROTEIN / Histone deacetylase / Histone Deacetylase Inhibitors / HDAH
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 / : / Acetoin utilization protein / Histone deacetylase-like amidohydrolase
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsKraemer, A. / Meyer-Almes, F.J. / Yildiz, O.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research FoundationME 3122/2-1 Germany
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
DepositionJul 14, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 23, 2016Provider: repository / Type: Initial release
Revision 1.1Feb 22, 2017Group: Database references
Revision 1.2Sep 6, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Jan 10, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _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_asym_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_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Acetoin utilization protein
B: Acetoin utilization protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)83,08310
Polymers82,1972
Non-polymers8868
Water2,756153
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4760 Å2
ΔGint-27 kcal/mol
Surface area24690 Å2
MethodPISA
Unit cell
Length a, b, c (Å)82.190, 82.190, 217.030
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: ARG / Beg label comp-ID: ARG / End auth comp-ID: GLY / End label comp-ID: GLY / Refine code: _ / Auth seq-ID: 3 - 369 / Label seq-ID: 3 - 369

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

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Components

#1: Protein Acetoin utilization protein


Mass: 41098.438 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Gene: AO946_14160 / Plasmid: pET21a / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A0D6GAJ7, UniProt: Q9HXM1*PLUS
#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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 153 / 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: 2.23 Å3/Da / Density % sol: 44.83 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.5M potassium hydrogen phosphate 0.5M sodium hydrogen phosphate 0.1M ammonium sulphate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1.0002 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 4, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0002 Å / Relative weight: 1
ReflectionResolution: 2.1→32 Å / Num. obs: 41043 / % possible obs: 100 % / Observed criterion σ(F): 2.5 / Redundancy: 11.1 % / CC1/2: 0.988 / Rmerge(I) obs: 0.24 / Net I/σ(I): 6.5
Reflection shellResolution: 2.1→2.16 Å / Redundancy: 11.8 % / Rmerge(I) obs: 0.92 / Mean I/σ(I) obs: 2.5 / CC1/2: 0.84 / % 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: 5g0x

5g0x


Resolution: 2.4→32 Å / Cor.coef. Fo:Fc: 0.934 / Cor.coef. Fo:Fc free: 0.906 / SU B: 12.055 / SU ML: 0.269 / Cross valid method: THROUGHOUT / ESU R: 0.583 / ESU R Free: 0.298 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.27013 1424 4.7 %RANDOM
Rwork0.22473 ---
obs0.22698 28611 99.96 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 46.624 Å2
Baniso -1Baniso -2Baniso -3
1-1.44 Å2-0 Å2-0 Å2
2--1.44 Å2-0 Å2
3----2.87 Å2
Refinement stepCycle: 1 / Resolution: 2.4→32 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5654 0 50 153 5857
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0195852
X-RAY DIFFRACTIONr_bond_other_d0.0030.025488
X-RAY DIFFRACTIONr_angle_refined_deg1.3911.9627928
X-RAY DIFFRACTIONr_angle_other_deg1.111312544
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0245740
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.92522.598281
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.08715861
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.9191560
X-RAY DIFFRACTIONr_chiral_restr0.0670.2837
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0216820
X-RAY DIFFRACTIONr_gen_planes_other0.0030.021440
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_it2.0654.5032968
X-RAY DIFFRACTIONr_mcbond_other2.0654.5042969
X-RAY DIFFRACTIONr_mcangle_it3.3686.7433704
X-RAY DIFFRACTIONr_mcangle_other3.3686.7453705
X-RAY DIFFRACTIONr_scbond_it2.3534.8622884
X-RAY DIFFRACTIONr_scbond_other2.3534.8642885
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.8417.1754225
X-RAY DIFFRACTIONr_long_range_B_refined6.33336.1056510
X-RAY DIFFRACTIONr_long_range_B_other6.31936.1136503
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Number: 44166 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.07 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 2.4→2.462 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.378 107 -
Rwork0.325 2059 -
obs--99.95 %

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