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

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Basic information

Entry
Database: PDB / ID: 8xjq
TitleCrystal structure of a sulfotransferase S4 in complex with PAP and PNPS
ComponentsSulfotransferase
KeywordsTRANSFERASE / PAP / sulfotransferase
Function / homologyTransferases; Transferring sulfur-containing groups; Sulfotransferases / sulfotransferase activity / Sulfotransferase domain / Sulfotransferase domain / P-loop containing nucleoside triphosphate hydrolase / 4-nitrophenyl sulfate / P-NITROPHENOL / 3'-PHOSPHATE-ADENOSINE-5'-PHOSPHATE SULFATE / Sulfotransferase
Function and homology information
Biological speciesBambusicola thoracicus (Chinese bamboo-partridge)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.78 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 and PNPS
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)35,0995
Polymers34,0951
Non-polymers1,0054
Water5,260292
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area850 Å2
ΔGint-4 kcal/mol
Surface area12270 Å2
MethodPISA
Unit cell
Length a, b, c (Å)78.045, 78.045, 140.124
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-684-

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.: 2 / Source method: obtained synthetically / Formula: C6H5NO3 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-PPS / 3'-PHOSPHATE-ADENOSINE-5'-PHOSPHATE SULFATE


Mass: 507.264 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O13P2S / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-4NS / 4-nitrophenyl sulfate / 4-nitrophenyl hydrogen sulfate


Mass: 219.172 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H5NO6S / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 292 / 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: 3.07 Å3/Da / Density % sol: 59.99 %
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: BL17UM / Wavelength: 0.9785 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 20, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9785 Å / Relative weight: 1
ReflectionResolution: 1.78→43.35 Å / Num. obs: 42303 / % possible obs: 100 % / Redundancy: 27.7 % / CC1/2: 1 / Rmerge(I) obs: 0.073 / Rpim(I) all: 0.014 / Rrim(I) all: 0.075 / Χ2: 0.99 / Net I/σ(I): 33 / Num. measured all: 1169870
Reflection shellResolution: 1.78→1.82 Å / % possible obs: 99.3 % / Redundancy: 16.2 % / Rmerge(I) obs: 0.97 / Num. measured all: 37959 / Num. unique obs: 2339 / CC1/2: 0.878 / Rpim(I) all: 0.241 / Rrim(I) all: 1.001 / Χ2: 0.92 / Net I/σ(I) obs: 2.8

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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: 1.78→43.35 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 20.51 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2043 2112 5 %
Rwork0.1777 --
obs0.1791 42216 99.93 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.78→43.35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2442 0 0 292 2734
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0132518
X-RAY DIFFRACTIONf_angle_d1.1573429
X-RAY DIFFRACTIONf_dihedral_angle_d7.405366
X-RAY DIFFRACTIONf_chiral_restr0.078354
X-RAY DIFFRACTIONf_plane_restr0.012440
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.78-1.840.29442060.24983900X-RAY DIFFRACTION99
1.84-1.920.25342080.20793934X-RAY DIFFRACTION100
1.92-20.24022080.19973965X-RAY DIFFRACTION100
2-2.110.19942080.18873953X-RAY DIFFRACTION100
2.11-2.240.22052080.1833948X-RAY DIFFRACTION100
2.24-2.420.22542100.17983988X-RAY DIFFRACTION100
2.42-2.660.23132100.18194000X-RAY DIFFRACTION100
2.66-3.040.20352130.18174029X-RAY DIFFRACTION100
3.04-3.830.16492150.1654089X-RAY DIFFRACTION100
3.84-43.350.19512260.16564298X-RAY DIFFRACTION100

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