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- PDB-8xgz: Crystal structure of a sulfotransferase S4 in complex with PAP -

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Basic information

Entry
Database: PDB / ID: 8xgz
TitleCrystal structure of a sulfotransferase S4 in complex with PAP
ComponentsS4
KeywordsTRANSFERASE / PAP / sulfotransferase
Function / homologyADENOSINE-3'-5'-DIPHOSPHATE
Function and homology information
Biological speciesBambusicola thoracicus (Chinese bamboo-partridge)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.44 Å
AuthorsGao, J. / 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. / Yin, L. / Liu, W.D. / Li, J.S.
History
DepositionDec 16, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 18, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: S4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,5222
Polymers34,0951
Non-polymers4271
Water2,018112
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area790 Å2
ΔGint-6 kcal/mol
Surface area12100 Å2
MethodPISA
Unit cell
Length a, b, c (Å)77.719, 77.719, 141.209
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 S4


Mass: 34094.703 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bambusicola thoracicus (Chinese bamboo-partridge)
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
#2: 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
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 112 / 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: 3.1 Å3/Da / Density % sol: 60.35 %
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
PH range: 6

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17UM / Wavelength: 0.987 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 8, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.987 Å / Relative weight: 1
ReflectionResolution: 2.44→50 Å / Num. obs: 30837 / % possible obs: 99.8 % / Redundancy: 10.5 % / CC1/2: 0.996 / Rrim(I) all: 0.432 / Net I/σ(I): 10.49
Reflection shell
Resolution (Å)Redundancy (%)Num. unique obsCC1/2Diffraction-IDRmerge(I) obsRrim(I) all
2.44-2.583.249080.7111
2.58-2.7647030.85711.734
2.76-2.9843630.93911.273
2.98-3.2640110.97510.8440.862
3.26-3.6536390.99210.4520.462
3.65-4.2131990.99310.2530.259
4.21-5.1427230.99610.1710.174
5.14-7.2221090.99610.1570.16
7.22-5011820.99710.1220.125

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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: 2.44→43.37 Å / SU ML: 0.17 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 18.86 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2185 842 5.01 %
Rwork0.1816 --
obs0.1835 16823 99.78 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.44→43.37 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2419 0 0 112 2531
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0032495
X-RAY DIFFRACTIONf_angle_d0.6663395
X-RAY DIFFRACTIONf_dihedral_angle_d5.032323
X-RAY DIFFRACTIONf_chiral_restr0.046351
X-RAY DIFFRACTIONf_plane_restr0.005437
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.44-2.590.22781340.19662558X-RAY DIFFRACTION99
2.59-2.790.25971380.19192611X-RAY DIFFRACTION100
2.79-3.070.20841390.1652632X-RAY DIFFRACTION100
3.07-3.510.20971390.16922647X-RAY DIFFRACTION100
3.51-4.420.20851420.17022686X-RAY DIFFRACTION100
4.42-43.370.21991500.19892847X-RAY DIFFRACTION100

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