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- PDB-8y9p: Crystal structure of bacterial activating sulfotransferase SgdX2 -

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Basic information

Entry
Database: PDB / ID: 8y9p
TitleCrystal structure of bacterial activating sulfotransferase SgdX2
ComponentsSgdX2
KeywordsTRANSFERASE / sulfotransferase / SgdX2
Function / homologySulfotransferase, S. mansonii-type / Sulfotransferase domain / P-loop containing nucleoside triphosphate hydrolase / ADENOSINE-3'-5'-DIPHOSPHATE / SgdX2
Function and homology information
Biological speciesMicromonospora sp. (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.64 Å
AuthorsMori, T. / Teramoto, T. / Kakuta, Y.
Funding support Japan, 1items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS) Japan
CitationJournal: Biochem.Biophys.Res.Commun. / Year: 2024
Title: Crystal structure of activating sulfotransferase SgdX2 involved in biosynthesis of secondary metabolite sungeidine.
Authors: Mori, T. / Teramoto, T. / Kakuta, Y.
History
DepositionFeb 7, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 15, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: SgdX2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,7654
Polymers29,1531
Non-polymers6113
Water3,117173
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)86.760, 86.760, 63.740
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number170
Space group name H-MP65

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Components

#1: Protein SgdX2


Mass: 29153.277 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Micromonospora sp. (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: A0A6G7MAL8
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-A3P / ADENOSINE-3'-5'-DIPHOSPHATE


Type: RNA linking / Mass: 427.201 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C10H15N5O10P2 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 173 / 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: 2.38 Å3/Da / Density % sol: 48.22 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.2 M Sodium chloride, 0.1 M Bis-Tris, pH 5.5, 25% (w/v) PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL45XU / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jun 4, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.64→48.61 Å / Num. obs: 33523 / % possible obs: 100 % / Redundancy: 14.3 % / CC1/2: 0.999 / Rrim(I) all: 0.06 / Net I/σ(I): 28.62
Reflection shellResolution: 1.64→1.73 Å / Mean I/σ(I) obs: 4.06 / Num. unique obs: 5400 / CC1/2: 0.857 / Rrim(I) all: 0.803

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Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.64→48.61 Å / SU ML: 0.16 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 20.03 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1867 2009 6 %
Rwork0.1646 --
obs0.166 33493 99.97 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.64→48.61 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1572 0 39 173 1784
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.013
X-RAY DIFFRACTIONf_angle_d1.311
X-RAY DIFFRACTIONf_dihedral_angle_d13.692584
X-RAY DIFFRACTIONf_chiral_restr0.077232
X-RAY DIFFRACTIONf_plane_restr0.012289
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.64-1.680.27031400.2422234X-RAY DIFFRACTION100
1.68-1.730.2411400.21652232X-RAY DIFFRACTION100
1.73-1.780.21741420.20382251X-RAY DIFFRACTION100
1.78-1.830.22251420.18392232X-RAY DIFFRACTION100
1.83-1.90.22561450.2032232X-RAY DIFFRACTION100
1.9-1.980.20411440.17782236X-RAY DIFFRACTION100
1.98-2.070.19421460.16482250X-RAY DIFFRACTION100
2.07-2.180.18991430.15442235X-RAY DIFFRACTION100
2.18-2.310.18391390.16022246X-RAY DIFFRACTION100
2.31-2.490.22081400.18032255X-RAY DIFFRACTION100
2.49-2.740.18661450.16832255X-RAY DIFFRACTION100
2.74-3.140.1871440.16692252X-RAY DIFFRACTION100
3.14-3.950.15431450.15362283X-RAY DIFFRACTION100
3.95-48.610.17561540.14672291X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: 30.8886 Å / Origin y: 13.1264 Å / Origin z: -0.7865 Å
111213212223313233
T0.1346 Å2-0.0022 Å20.0113 Å2-0.1259 Å20.0017 Å2--0.1422 Å2
L1.6011 °20.2521 °2-0.7049 °2-3.3163 °20.2214 °2--2.3387 °2
S-0.0212 Å °-0.061 Å °-0.0132 Å °0.1493 Å °-0.0023 Å °-0.0157 Å °0.04 Å °0.0179 Å °0.0115 Å °
Refinement TLS groupSelection details: all

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