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- PDB-8i09: Crystal structure of serine acetyltransferase from Salmonella typ... -

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Basic information

Entry
Database: PDB / ID: 8i09
TitleCrystal structure of serine acetyltransferase from Salmonella typhimurium complexed with butyl gallate
ComponentsSerine acetyltransferase
KeywordsTRANSFERASE / SALMONELLA / SERINE ACETYLTRANSFERASE / CYSTEINE SYNTHESIS / BETA-HELIX
Function / homology
Function and homology information


serine O-acetyltransferase / serine O-acetyltransferase activity / cysteine biosynthetic process from serine / cytoplasm
Similarity search - Function
Serine O-acetyltransferase / Serine acetyltransferase, N-terminal / Serine acetyltransferase, N-terminal / Serine acetyltransferase, N-terminal / : / Serine acetyltransferase, N-terminal domain superfamily / Serine acetyltransferase, LbH domain / Hexapeptide transferase, conserved site / Hexapeptide-repeat containing-transferases signature. / Hexapeptide repeat ...Serine O-acetyltransferase / Serine acetyltransferase, N-terminal / Serine acetyltransferase, N-terminal / Serine acetyltransferase, N-terminal / : / Serine acetyltransferase, N-terminal domain superfamily / Serine acetyltransferase, LbH domain / Hexapeptide transferase, conserved site / Hexapeptide-repeat containing-transferases signature. / Hexapeptide repeat / Bacterial transferase hexapeptide (six repeats) / Trimeric LpxA-like superfamily
Similarity search - Domain/homology
CYSTEINE / butyl 3,4,5-tris(oxidanyl)benzoate / PHOSPHATE ION / Serine acetyltransferase
Similarity search - Component
Biological speciesSalmonella enterica subsp. enterica serovar Typhimurium (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsToyomoto, T. / Ono, K. / Shiba, T. / Momitani, K. / Zhang, T. / Tsutsuki, H. / Ishikawa, T. / Hoso, K. / Hamada, K. / Rahman, A. ...Toyomoto, T. / Ono, K. / Shiba, T. / Momitani, K. / Zhang, T. / Tsutsuki, H. / Ishikawa, T. / Hoso, K. / Hamada, K. / Rahman, A. / Zhong, H. / Akaike, T. / Yamamoto, K. / Matsuoka, M. / Hanaoka, K. / Niidome, T. / Sawa, T.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Front Microbiol / Year: 2023
Title: Alkyl gallates inhibit serine O -acetyltransferase in bacteria and enhance susceptibility of drug-resistant Gram-negative bacteria to antibiotics.
Authors: Toyomoto, T. / Ono, K. / Shiba, T. / Momitani, K. / Zhang, T. / Tsutsuki, H. / Ishikawa, T. / Hoso, K. / Hamada, K. / Rahman, A. / Wen, L. / Maeda, Y. / Yamamoto, K. / Matsuoka, M. / ...Authors: Toyomoto, T. / Ono, K. / Shiba, T. / Momitani, K. / Zhang, T. / Tsutsuki, H. / Ishikawa, T. / Hoso, K. / Hamada, K. / Rahman, A. / Wen, L. / Maeda, Y. / Yamamoto, K. / Matsuoka, M. / Hanaoka, K. / Niidome, T. / Akaike, T. / Sawa, T.
History
DepositionJan 10, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 22, 2023Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Database references / Category: citation / citation_author
Item: _citation.page_first / _citation.page_last ..._citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
Revision 1.2Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Serine acetyltransferase
B: Serine acetyltransferase
C: Serine acetyltransferase
D: Serine acetyltransferase
E: Serine acetyltransferase
F: Serine acetyltransferase
G: Serine acetyltransferase
H: Serine acetyltransferase
I: Serine acetyltransferase
J: Serine acetyltransferase
K: Serine acetyltransferase
L: Serine acetyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)367,61740
Polymers363,06812
Non-polymers4,54828
Water13,223734
1
A: Serine acetyltransferase
B: Serine acetyltransferase
C: Serine acetyltransferase
hetero molecules

A: Serine acetyltransferase
B: Serine acetyltransferase
C: Serine acetyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)183,80820
Polymers181,5346
Non-polymers2,27414
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_757-x+2,y,-z+21
Buried area21300 Å2
ΔGint-147 kcal/mol
Surface area45040 Å2
MethodPISA
2
D: Serine acetyltransferase
E: Serine acetyltransferase
F: Serine acetyltransferase
hetero molecules

D: Serine acetyltransferase
E: Serine acetyltransferase
F: Serine acetyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)183,80820
Polymers181,5346
Non-polymers2,27414
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_858-x+3,y,-z+31
Buried area21640 Å2
ΔGint-151 kcal/mol
Surface area44650 Å2
MethodPISA
3
G: Serine acetyltransferase
H: Serine acetyltransferase
I: Serine acetyltransferase
J: Serine acetyltransferase
K: Serine acetyltransferase
L: Serine acetyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)183,80820
Polymers181,5346
Non-polymers2,27414
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area21620 Å2
ΔGint-152 kcal/mol
Surface area44970 Å2
MethodPISA
Unit cell
Length a, b, c (Å)177.363, 102.649, 158.715
Angle α, β, γ (deg.)90.00, 111.85, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein
Serine acetyltransferase


Mass: 30255.689 Da / Num. of mol.: 12
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Salmonella enterica subsp. enterica serovar Typhimurium (bacteria)
Gene: cysE / Production host: Escherichia coli (E. coli) / References: UniProt: A0A0D6I3Y9, serine O-acetyltransferase
#2: Chemical
ChemComp-CYS / CYSTEINE


Type: L-peptide linking / Mass: 121.158 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C3H7NO2S
#3: Chemical
ChemComp-NF0 / butyl 3,4,5-tris(oxidanyl)benzoate / butyl gallate


Mass: 226.226 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C11H14O5 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Formula: PO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 734 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

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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: 2.13 Å3/Da / Density % sol: 42.2 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 100 MM HEPES, 100 MM SODIUM CHLORIDE, 15% MPD, 5 MM DTT, 5 MM butyl gallate
PH range: 7.0-7.4

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 0.9 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Oct 27, 2020
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 1.8→50 Å / Num. obs: 233218 / % possible obs: 99.3 % / Redundancy: 3.7 % / CC1/2: 0.995 / Rpim(I) all: 0.102 / Net I/σ(I): 7.2
Reflection shellResolution: 1.8→1.9 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.86 / Mean I/σ(I) obs: 1.2 / Num. unique obs: 38709 / CC1/2: 0.813 / % possible all: 97.8

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Processing

Software
NameVersionClassification
REFMAC5.8.0103refinement
XDSdata reduction
XDSdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7E3Y

7e3y


Resolution: 1.8→19.96 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.955 / SU B: 4.927 / SU ML: 0.139 / Cross valid method: THROUGHOUT / ESU R: 0.152 / ESU R Free: 0.14 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24112 12032 4.9 %RANDOM
Rwork0.20352 ---
obs0.20539 231739 99.31 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 38.969 Å2
Baniso -1Baniso -2Baniso -3
1--0 Å2-0 Å20.01 Å2
2---0 Å20 Å2
3---0 Å2
Refinement stepCycle: 1 / Resolution: 1.8→19.96 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms22113 0 296 734 23143
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.01922886
X-RAY DIFFRACTIONr_bond_other_d0.0030.0222589
X-RAY DIFFRACTIONr_angle_refined_deg1.4911.97131071
X-RAY DIFFRACTIONr_angle_other_deg1.0583.00251888
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.07952951
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.65123.662852
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.141153762
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.80915144
X-RAY DIFFRACTIONr_chiral_restr0.0890.23569
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.02125709
X-RAY DIFFRACTIONr_gen_planes_other0.0020.024859
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_it2.0463.71311858
X-RAY DIFFRACTIONr_mcbond_other2.0463.71311857
X-RAY DIFFRACTIONr_mcangle_it3.0415.54114791
X-RAY DIFFRACTIONr_mcangle_other3.0415.54114792
X-RAY DIFFRACTIONr_scbond_it2.6574.09611028
X-RAY DIFFRACTIONr_scbond_other2.6574.08711013
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.1995.99716256
X-RAY DIFFRACTIONr_long_range_B_refined5.85829.47525722
X-RAY DIFFRACTIONr_long_range_B_other5.86929.43725384
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.8→1.843 Å
RfactorNum. reflection% reflection
Rfree0.461 893 -
Rwork0.437 16316 -
obs--96.14 %

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