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- PDB-7bw9: Crystal structure of Serine acetyltransferase isoform 3 in comple... -

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Basic information

Entry
Database: PDB / ID: 7bw9
TitleCrystal structure of Serine acetyltransferase isoform 3 in complex with cysteine from Entamoeba histolytica
ComponentsSerine acetyltransferase 1, putative
KeywordsTRANSFERASE / Left handed beta-helical (LBH) domain / serine acetyltransferase / Cysteine biosynthesis / Cysteine synthase Complex.
Function / homology
Function and homology information


serine O-acetyltransferase / serine O-acetyltransferase activity / amino acid biosynthetic process
Similarity search - Function
serine acetyltransferase, domain 1 / serine acetyltransferase, domain 1 / : / Serine acetyltransferase, N-terminal domain superfamily / Serine acetyltransferase, LbH domain / Hexapeptide repeat / Bacterial transferase hexapeptide (six repeats) / Trimeric LpxA-like superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
CYSTEINE / serine O-acetyltransferase
Similarity search - Component
Biological speciesEntamoeba histolytica (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.131 Å
AuthorsDharavath, S. / Kumar, S. / Gourinath, S.
Funding support India, 1items
OrganizationGrant numberCountry
Science and Engineering Research Board (SERB) India
CitationJournal: To Be Published
Title: Crystal structure of Serine acetyltransferase isoform 3 in complex with cysteine from Entamoeba histolytica
Authors: Dharavath, S. / Kumar, S.
History
DepositionApr 14, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 14, 2021Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Serine acetyltransferase 1, putative
B: Serine acetyltransferase 1, putative
C: Serine acetyltransferase 1, putative
hetero molecules


Theoretical massNumber of molelcules
Total (without water)113,5806
Polymers113,2173
Non-polymers3633
Water6,413356
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12710 Å2
ΔGint-64 kcal/mol
Surface area29730 Å2
MethodPISA
Unit cell
Length a, b, c (Å)120.323, 76.307, 96.726
Angle α, β, γ (deg.)90.000, 95.520, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11C-504-

HOH

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Components

#1: Protein Serine acetyltransferase 1, putative / Serine acetyltransferase isoform 3


Mass: 37738.914 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Entamoeba histolytica (eukaryote) / Gene: KM1_023830 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: M7WGH7
#2: Chemical ChemComp-CYS / CYSTEINE


Type: L-peptide linking / Mass: 121.158 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H7NO2S / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 356 / 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: 1.99 Å3/Da / Density % sol: 38.2 %
Crystal growTemperature: 289.15 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.1 M Hepes pH 7.5, 0.2 M KSCN, 0.2 M KBr, 25 % PEG 3350
PH range: 7.2 - 8.5

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Data collection

DiffractionMean temperature: 193 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 1 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Apr 28, 2014
RadiationMonochromator: Si(111) monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.13→50 Å / Num. obs: 48708 / % possible obs: 99.9 % / Redundancy: 5.2 % / CC1/2: 0.95 / CC star: 0.98 / Rpim(I) all: 0.053 / Χ2: 1.054 / Net I/σ(I): 15.3
Reflection shellResolution: 2.13→2.17 Å / Redundancy: 4.6 % / Mean I/σ(I) obs: 2.2 / Num. unique obs: 2424 / CC1/2: 0.82 / CC star: 0.95 / Rpim(I) all: 0.28 / Χ2: 0.767 / % possible all: 99.5

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Processing

Software
NameVersionClassification
PHENIXdev_3352refinement
PDB_EXTRACT3.25data extraction
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3p47

3p47


Resolution: 2.131→39.54 Å / SU ML: 0.26 / Cross valid method: THROUGHOUT / σ(F): 1.38 / Phase error: 23.26 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2226 998 2.05 %
Rwork0.1741 47676 -
obs0.1751 48674 99.6 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 84.28 Å2 / Biso mean: 27.8204 Å2 / Biso min: 8.12 Å2
Refinement stepCycle: final / Resolution: 2.131→39.54 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6573 0 0 356 6929
Biso mean---31.71 -
Num. residues----836
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.131-2.24320.27591390.222666498
2.2432-2.38370.26831420.20236769100
2.3837-2.56770.26481430.18486802100
2.5677-2.82610.29581440.19096841100
2.8261-3.23480.23441420.17666826100
3.2348-4.07490.16731440.1566823100
4.0749-39.540.21440.15826951100

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