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- PDB-8xu3: Crystal structure of a sulfotransferase S4 from in complex with P... -

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Basic information

Entry
Database: PDB / ID: 8xu3
TitleCrystal structure of a sulfotransferase S4 from in complex with PAP and PNP
ComponentsSulfotransferase
KeywordsTRANSFERASE / PAP / sulfotransferase
Function / homologyTransferases; Transferring sulfur-containing groups; Sulfotransferases / sulfotransferase activity / Sulfotransferase domain / Sulfotransferase domain / P-loop containing nucleoside triphosphate hydrolase / ADENOSINE-3'-5'-DIPHOSPHATE / P-NITROPHENOL / Sulfotransferase
Function and homology information
Biological speciesBambusicola thoracicus (Chinese bamboo-partridge)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.82 Å
AuthorsGao, J. / Wang, H. / Chen, Y.Y. / Yang, S.Y. / Yin, L. / Liu, W.D. / Li, J.S.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: To Be Published
Title: Crystal structure of a sulfotransferase S4 from in complex with PAP and PNP
Authors: Gao, J. / Wang, H. / Chen, Y.Y. / Yang, S.Y. / Yin, L. / Liu, W.D. / Li, J.S.
History
DepositionJan 12, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 15, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Sulfotransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,6613
Polymers34,0951
Non-polymers5662
Water5,278293
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)77.957, 77.957, 140.570
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
Components on special symmetry positions
IDModelComponents
11A-681-

HOH

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Components

#1: Protein Sulfotransferase


Mass: 34094.703 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bambusicola thoracicus (Chinese bamboo-partridge)
Gene: CIB84_007067
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: A0A2P4SYK2, Transferases; Transferring sulfur-containing groups; Sulfotransferases
#2: Chemical ChemComp-NPO / P-NITROPHENOL


Mass: 139.109 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H5NO3 / 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: obtained synthetically / Formula: C10H15N5O10P2 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 293 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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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: 3.14 Å3/Da / Density % sol: 60.88 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop
Details: 1.6 M (NH4)2SO4, 0.1 M MES pH 6.0, 1% dextran sulfate sodium salt 8000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL10U2 / Wavelength: 0.9785 Å
DetectorType: DECTRIS PILATUS 12M / Detector: PIXEL / Date: Jul 18, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9785 Å / Relative weight: 1
ReflectionResolution: 1.82→43.37 Å / Num. obs: 39722 / % possible obs: 100 % / Redundancy: 28.6 % / CC1/2: 1 / Rmerge(I) obs: 0.078 / Rpim(I) all: 0.015 / Rrim(I) all: 0.079 / Χ2: 0.99 / Net I/σ(I): 33.8 / Num. measured all: 1135627
Reflection shellResolution: 1.82→1.86 Å / % possible obs: 100 % / Redundancy: 27.5 % / Rmerge(I) obs: 0.832 / Num. measured all: 64116 / Num. unique obs: 2331 / CC1/2: 0.946 / Rpim(I) all: 0.16 / Rrim(I) all: 0.847 / Χ2: 0.96 / Net I/σ(I) obs: 4.7

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Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
XDSdata scaling
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.82→37.56 Å / SU ML: 0.15 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 17.84 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2009 1981 5 %
Rwork0.1736 --
obs0.1749 39645 99.99 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.82→37.56 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2429 0 0 293 2722
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072505
X-RAY DIFFRACTIONf_angle_d0.923408
X-RAY DIFFRACTIONf_dihedral_angle_d5.52330
X-RAY DIFFRACTIONf_chiral_restr0.056351
X-RAY DIFFRACTIONf_plane_restr0.008439
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.82-1.890.21881930.22313679X-RAY DIFFRACTION100
1.89-1.960.21291960.19043720X-RAY DIFFRACTION100
1.96-2.050.20381950.1833698X-RAY DIFFRACTION100
2.05-2.160.22351930.19033702X-RAY DIFFRACTION100
2.16-2.290.20911980.183754X-RAY DIFFRACTION100
2.29-2.470.21811960.1763708X-RAY DIFFRACTION100
2.47-2.720.21981970.17853747X-RAY DIFFRACTION100
2.72-3.110.20072000.18013803X-RAY DIFFRACTION100
3.11-3.920.18712010.15913826X-RAY DIFFRACTION100
3.92-37.560.18772120.16384027X-RAY DIFFRACTION100

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