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- PDB-8szu: Structure of Kdac1-Citarinostat complex from Acinetobacter baumannii -

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Basic information

Entry
Database: PDB / ID: 8szu
TitleStructure of Kdac1-Citarinostat complex from Acinetobacter baumannii
ComponentsHistone deacetylase domain-containing protein
KeywordsHYDROLASE / histone deacetylase / metallohydrolase
Function / homology
Function and homology information


histone deacetylase activity / epigenetic regulation of gene expression / metal ion binding / cytoplasm
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
: / Citarinostat / Histone deacetylase domain-containing protein
Similarity search - Component
Biological speciesAcinetobacter baumannii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 Å
AuthorsWatson, P.R. / Christianson, D.W.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM49758 United States
CitationJournal: Biochemistry / Year: 2023
Title: Structure and Function of Kdac1, a Class II Deacetylase from the Multidrug-Resistant Pathogen Acinetobacter baumannii .
Authors: Watson, P.R. / Christianson, D.W.
History
DepositionMay 30, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 6, 2023Provider: repository / Type: Initial release
Revision 1.1Oct 4, 2023Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation_author.identifier_ORCID
Revision 1.2Nov 8, 2023Group: Derived calculations / Structure summary / Category: chem_comp / entity / pdbx_entity_nonpoly
Item: _chem_comp.name / _chem_comp.pdbx_synonyms ..._chem_comp.name / _chem_comp.pdbx_synonyms / _entity.pdbx_description / _pdbx_entity_nonpoly.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Histone deacetylase domain-containing protein
B: Histone deacetylase domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)83,03912
Polymers80,8802
Non-polymers2,15910
Water5,981332
1
A: Histone deacetylase domain-containing protein
B: Histone deacetylase domain-containing protein
hetero molecules

A: Histone deacetylase domain-containing protein
B: Histone deacetylase domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)166,07824
Polymers161,7604
Non-polymers4,31820
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_555-y,-x,-z+1/21
Buried area13610 Å2
ΔGint-56 kcal/mol
Surface area43180 Å2
MethodPISA
Unit cell
Length a, b, c (Å)80.594, 80.594, 204.645
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212
Space group name HallP4abw2nw
Symmetry operation#1: x,y,z
#2: -y+1/2,x+1/2,z+1/4
#3: y+1/2,-x+1/2,z+3/4
#4: x+1/2,-y+1/2,-z+3/4
#5: -x+1/2,y+1/2,-z+1/4
#6: -x,-y,z+1/2
#7: y,x,-z
#8: -y,-x,-z+1/2
Components on special symmetry positions
IDModelComponents
11B-637-

HOH

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Components

#1: Protein Histone deacetylase domain-containing protein


Mass: 40439.953 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Acinetobacter baumannii (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: R8YPJ7
#2: Chemical
ChemComp-X4U / Citarinostat / 2-[(2-chlorophenyl)(phenyl)amino]-N-[7-(hydroxyamino)-7-oxoheptyl]pyrimidine-5-carboxamide


Mass: 467.948 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C24H26ClN5O3 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#4: Chemical
ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: K
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 332 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.06 Å3/Da / Density % sol: 40.2 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop
Details: 10mg/mL Kdac1 0.2 M magnesium chloride hexahydrate and 20% PEG 3,350 (w/v) seeded

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSLS-II / Beamline: 17-ID-2 / Wavelength: 0.98 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Mar 3, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.75→43.73 Å / Num. obs: 783129 / % possible obs: 100 % / Redundancy: 11.4 % / Biso Wilson estimate: 18.68 Å2 / CC1/2: 0.98 / Net I/σ(I): 16.9
Reflection shellResolution: 1.75→1.78 Å / Mean I/σ(I) obs: 4.6 / Num. unique obs: 67310 / CC1/2: 0.818

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
Zanudadata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.75→43.73 Å / SU ML: 0.1581 / Cross valid method: FREE R-VALUE / σ(F): 2.1 / Phase error: 18.2055
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2113 3513 5.08 %
Rwork0.1833 65641 -
obs0.1847 69154 99.76 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 19.78 Å2
Refinement stepCycle: LAST / Resolution: 1.75→43.73 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5298 0 120 332 5750
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00695544
X-RAY DIFFRACTIONf_angle_d0.94877540
X-RAY DIFFRACTIONf_chiral_restr0.0568832
X-RAY DIFFRACTIONf_plane_restr0.0069975
X-RAY DIFFRACTIONf_dihedral_angle_d11.4034772
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.75-1.770.26981270.22222440X-RAY DIFFRACTION94.76
1.77-1.80.2461260.21522605X-RAY DIFFRACTION100
1.8-1.820.28111330.20612574X-RAY DIFFRACTION100
1.82-1.850.24241480.19592578X-RAY DIFFRACTION100
1.85-1.880.25661480.19512596X-RAY DIFFRACTION100
1.88-1.910.21541240.18642604X-RAY DIFFRACTION100
1.91-1.950.20521410.17512577X-RAY DIFFRACTION100
1.95-1.990.22361290.17642604X-RAY DIFFRACTION100
1.99-2.030.20991430.17532602X-RAY DIFFRACTION100
2.03-2.070.22041280.17982631X-RAY DIFFRACTION100
2.07-2.120.21761310.17442610X-RAY DIFFRACTION100
2.12-2.170.19651400.17522599X-RAY DIFFRACTION99.96
2.17-2.230.21271360.17632609X-RAY DIFFRACTION100
2.23-2.30.16661350.18152622X-RAY DIFFRACTION100
2.3-2.370.24021530.1792614X-RAY DIFFRACTION99.96
2.37-2.450.17691420.18292594X-RAY DIFFRACTION100
2.45-2.550.20751520.19342618X-RAY DIFFRACTION99.96
2.55-2.670.20391470.19042617X-RAY DIFFRACTION99.96
2.67-2.810.22331270.2052641X-RAY DIFFRACTION99.93
2.81-2.990.22931680.20242641X-RAY DIFFRACTION99.96
2.99-3.220.26121350.20572671X-RAY DIFFRACTION100
3.22-3.540.23051500.19072667X-RAY DIFFRACTION100
3.54-4.050.19331560.17352682X-RAY DIFFRACTION100
4.05-5.10.16671480.14632742X-RAY DIFFRACTION99.97
5.1-43.730.19711460.18092903X-RAY DIFFRACTION99.51

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