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- PDB-8xjp: Crystal structure of a sulfotransferase S4 in complex with PAP an... -

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Basic information

Entry
Database: PDB / ID: 8xjp
TitleCrystal structure of a sulfotransferase S4 in complex with PAP and 2-Phe-br
ComponentsSulfotransferase
KeywordsTRANSFERASE / PAP / sulfotransferase
Function / homologyTransferases; Transferring sulfur-containing groups; Sulfotransferases / sulfotransferase activity / Sulfotransferase domain / Sulfotransferase domain / P-loop containing nucleoside triphosphate hydrolase / 2-BROMOPHENOL / ADENOSINE-3'-5'-DIPHOSPHATE / Sulfotransferase
Function and homology information
Biological speciesBambusicola thoracicus (Chinese bamboo-partridge)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 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 in complex with PAP
Authors: Gao, J. / Wang, H. / Chen, Y.Y. / Yang, S.Y. / Yin, L. / Liu, W.D. / Li, J.S.
History
DepositionDec 22, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 25, 2024Provider: 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)34,6953
Polymers34,0951
Non-polymers6002
Water4,846269
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)77.716, 77.716, 139.152
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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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-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
#3: Chemical ChemComp-2BR / 2-BROMOPHENOL / BROMOPHENOL


Mass: 173.007 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H5BrO / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 269 / 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: 3.08 Å3/Da / Density % sol: 60.1 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6
Details: 1.6 M (NH4)2SO4, 0.1 M MES pH6.0, 1% dextran sulfate sodium salt 800

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.987 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Feb 9, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.987 Å / Relative weight: 1
ReflectionResolution: 1.7→50 Å / Num. obs: 47187 / % possible obs: 98.8 % / Redundancy: 26.2 % / CC1/2: 0.998 / Net I/σ(I): 23.3
Reflection shellResolution: 1.7→1.76 Å / Mean I/σ(I) obs: 2.94 / Num. unique obs: 4616 / CC1/2: 0.857

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Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
SAINTdata scaling
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.7→27.81 Å / SU ML: 0.24 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 28.96 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2706 2351 5 %
Rwork0.2462 --
obs0.2475 47021 98.68 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.7→27.81 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2371 0 35 269 2675
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072498
X-RAY DIFFRACTIONf_angle_d0.9433398
X-RAY DIFFRACTIONf_dihedral_angle_d11.428322
X-RAY DIFFRACTIONf_chiral_restr0.057350
X-RAY DIFFRACTIONf_plane_restr0.01437
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7-1.760.382250.32864286X-RAY DIFFRACTION97
1.76-1.830.33422290.32334330X-RAY DIFFRACTION97
1.83-1.910.39152280.33934335X-RAY DIFFRACTION98
1.91-2.020.31822320.30814419X-RAY DIFFRACTION99
2.02-2.140.34292350.28634450X-RAY DIFFRACTION99
2.14-2.310.31142350.27424461X-RAY DIFFRACTION100
2.31-2.540.27812350.25844487X-RAY DIFFRACTION100
2.54-2.910.28892390.25114544X-RAY DIFFRACTION100
2.91-3.660.21972410.21554571X-RAY DIFFRACTION100
3.66-27.810.19032520.17554787X-RAY DIFFRACTION99

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