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- PDB-8i04: Crystal structure of serine acetyltransferase from Salmonella typ... -

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Basic information

Entry
Database: PDB / ID: 8i04
TitleCrystal structure of serine acetyltransferase from Salmonella typhimurium complexed with serine
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
PHOSPHATE ION / SERINE / Serine acetyltransferase
Similarity search - Component
Biological speciesSalmonella enterica subsp. enterica serovar Typhimurium (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 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

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)91,1777
Polymers90,7673
Non-polymers4104
Water1,24369
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)182,35514
Polymers181,5346
Non-polymers8208
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_554-x,-x+y,-z-1/31
Buried area22800 Å2
ΔGint-153 kcal/mol
Surface area46640 Å2
MethodPISA
Unit cell
Length a, b, c (Å)122.157, 122.157, 128.184
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein Serine acetyltransferase


Mass: 30255.689 Da / Num. of mol.: 3
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-SER / SERINE


Type: L-peptide linking / Mass: 105.093 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Formula: C3H7NO3 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 69 / 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: 3.33 Å3/Da / Density % sol: 63.07 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: 100 MM HEPES, 100 MM SODIUM CHLORIDE, 6% MPD

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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: Apr 12, 2019
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 2.3→50 Å / Num. obs: 47207 / % possible obs: 99.8 % / Redundancy: 15.6 % / CC1/2: 0.999 / Rmerge(I) obs: 0.096 / Rpim(I) all: 0.103 / Net I/σ(I): 14.4
Reflection shellResolution: 2.3→2.44 Å / Rmerge(I) obs: 0.763 / Mean I/σ(I) obs: 2.7 / Num. unique obs: 7555 / CC1/2: 0.876 / % possible all: 99

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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: 2.3→19.99 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.953 / SU B: 5.717 / SU ML: 0.137 / Cross valid method: THROUGHOUT / ESU R: 0.204 / ESU R Free: 0.176 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21019 2489 5.1 %RANDOM
Rwork0.17196 ---
obs0.17392 46601 99.67 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 56.857 Å2
Baniso -1Baniso -2Baniso -3
1-0.01 Å20 Å20 Å2
2--0.01 Å2-0 Å2
3----0.03 Å2
Refinement stepCycle: 1 / Resolution: 2.3→19.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5800 0 26 69 5895
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0195945
X-RAY DIFFRACTIONr_bond_other_d0.0020.025841
X-RAY DIFFRACTIONr_angle_refined_deg1.4451.9628064
X-RAY DIFFRACTIONr_angle_other_deg0.974313427
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3115771
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.38723.896231
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.58315990
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.1381536
X-RAY DIFFRACTIONr_chiral_restr0.0850.2922
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0216720
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021278
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_it3.1575.3463099
X-RAY DIFFRACTIONr_mcbond_other3.1565.3463098
X-RAY DIFFRACTIONr_mcangle_it4.5758.0083865
X-RAY DIFFRACTIONr_mcangle_other4.5758.0073866
X-RAY DIFFRACTIONr_scbond_it4.2386.0112846
X-RAY DIFFRACTIONr_scbond_other4.2276.012841
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other6.8228.7754193
X-RAY DIFFRACTIONr_long_range_B_refined8.39342.5786420
X-RAY DIFFRACTIONr_long_range_B_other8.39442.5766413
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.304→2.363 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.291 179 -
Rwork0.242 3298 -
obs--98.19 %

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