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- PDB-8i1o: Crystal structure of APSK2 domain from human PAPSS2 in complex wi... -

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Basic information

Entry
Database: PDB / ID: 8i1o
TitleCrystal structure of APSK2 domain from human PAPSS2 in complex with exogenous APS and ADP
ComponentsBifunctional 3'-phosphoadenosine 5'-phosphosulfate synthase 2
KeywordsBIOSYNTHETIC PROTEIN / 5'-phosphosulfate kinase 2 domain / APSK2 / human papss2
Function / homology
Function and homology information


Defective PAPSS2 causes SEMD-PA / 3'-phosphoadenosine 5'-phosphosulfate biosynthetic process / Transport and metabolism of PAPS / adenylyl-sulfate kinase / sulfate adenylyltransferase / adenylylsulfate kinase activity / sulfate adenylyltransferase (ATP) activity / Metabolism of ingested H2SeO4 and H2SeO3 into H2Se / sulfate assimilation / hormone metabolic process ...Defective PAPSS2 causes SEMD-PA / 3'-phosphoadenosine 5'-phosphosulfate biosynthetic process / Transport and metabolism of PAPS / adenylyl-sulfate kinase / sulfate adenylyltransferase / adenylylsulfate kinase activity / sulfate adenylyltransferase (ATP) activity / Metabolism of ingested H2SeO4 and H2SeO3 into H2Se / sulfate assimilation / hormone metabolic process / nucleotidyltransferase activity / ATP binding / nucleus / cytosol
Similarity search - Function
Sulphate adenylyltransferase / Sulphate adenylyltransferase catalytic domain / ATP-sulfurylase PUA-like domain / ATP-sulfurylase / PUA-like domain / Adenylyl-sulfate kinase / Adenylylsulphate kinase / PUA-like superfamily / Rossmann-like alpha/beta/alpha sandwich fold / P-loop containing nucleotide triphosphate hydrolases ...Sulphate adenylyltransferase / Sulphate adenylyltransferase catalytic domain / ATP-sulfurylase PUA-like domain / ATP-sulfurylase / PUA-like domain / Adenylyl-sulfate kinase / Adenylylsulphate kinase / PUA-like superfamily / Rossmann-like alpha/beta/alpha sandwich fold / P-loop containing nucleotide triphosphate hydrolases / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / ADENOSINE-5'-PHOSPHOSULFATE / Bifunctional 3'-phosphoadenosine 5'-phosphosulfate synthase 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsZhang, L. / Song, W.Y. / Zhang, L.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: Structure / Year: 2023
Title: Redox switching mechanism of the adenosine 5'-phosphosulfate kinase domain (APSK2) of human PAPS synthase 2.
Authors: Zhang, L. / Song, W. / Li, T. / Mu, Y. / Zhang, P. / Hu, J. / Lin, H. / Zhang, J. / Gao, H. / Zhang, L.
History
DepositionJan 13, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 28, 2023Provider: repository / Type: Initial release
Revision 1.1Jul 19, 2023Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2May 29, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Bifunctional 3'-phosphoadenosine 5'-phosphosulfate synthase 2
B: Bifunctional 3'-phosphoadenosine 5'-phosphosulfate synthase 2
C: Bifunctional 3'-phosphoadenosine 5'-phosphosulfate synthase 2
D: Bifunctional 3'-phosphoadenosine 5'-phosphosulfate synthase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)93,47612
Polymers90,0584
Non-polymers3,4188
Water2,738152
1
A: Bifunctional 3'-phosphoadenosine 5'-phosphosulfate synthase 2
B: Bifunctional 3'-phosphoadenosine 5'-phosphosulfate synthase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,7386
Polymers45,0292
Non-polymers1,7094
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5800 Å2
ΔGint-55 kcal/mol
Surface area15930 Å2
MethodPISA
2
C: Bifunctional 3'-phosphoadenosine 5'-phosphosulfate synthase 2
D: Bifunctional 3'-phosphoadenosine 5'-phosphosulfate synthase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,7386
Polymers45,0292
Non-polymers1,7094
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5920 Å2
ΔGint-48 kcal/mol
Surface area16160 Å2
MethodPISA
Unit cell
Length a, b, c (Å)64.725, 53.035, 130.639
Angle α, β, γ (deg.)90.00, 102.44, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Bifunctional 3'-phosphoadenosine 5'-phosphosulfate synthase 2 / PAPS synthase 2 / PAPSS 2 / Sulfurylase kinase 2 / SK 2 / SK2


Mass: 22514.451 Da / Num. of mol.: 4 / Fragment: APSK2 domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PAPSS2, ATPSK2 / Production host: Escherichia coli (E. coli)
References: UniProt: O95340, sulfate adenylyltransferase, adenylyl-sulfate kinase
#2: Chemical
ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#3: Chemical
ChemComp-ADX / ADENOSINE-5'-PHOSPHOSULFATE


Type: RNA linking / Mass: 427.284 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H14N5O10PS / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 152 / 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: 2.43 Å3/Da / Density % sol: 49.41 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: 0.2 M Ammonium citrate dihydrate, pH7.0 and 20% w/v PEG3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.9875 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: May 6, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9875 Å / Relative weight: 1
ReflectionResolution: 2.4→50 Å / Num. obs: 31651 / % possible obs: 92.2 % / Redundancy: 3.8 % / Rmerge(I) obs: 0.156 / Χ2: 0.163 / Net I/σ(I): 6.2 / Num. measured all: 121780
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsΧ2Diffraction-ID% possible all
2.4-2.493.80.35530960.949191.5
2.49-2.593.80.29630970.977191.4
2.59-2.73.70.25531411.157191.7
2.7-2.853.60.21131140.996191.9
2.85-3.023.90.19631381.048192.4
3.02-3.263.90.17132031.2193.1
3.26-3.583.80.12332111.21193.5
3.58-4.140.09931991.31192.8
4.1-5.1740.08331681.145192
5.17-5040.10732843.016192

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Processing

Software
NameVersionClassification
HKL-3000data scaling
PHENIX1.2refinement
HKL-3000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2OFX

2ofx


Resolution: 2.4→48.972 Å / SU ML: 0.26 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 25.08 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2298 1385 5.12 %
Rwork0.1915 --
obs0.1935 27060 78.8 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.4→48.972 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6088 0 216 152 6456
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0126437
X-RAY DIFFRACTIONf_angle_d1.788743
X-RAY DIFFRACTIONf_dihedral_angle_d23.1463895
X-RAY DIFFRACTIONf_chiral_restr0.116957
X-RAY DIFFRACTIONf_plane_restr0.0131120
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4-2.48410.25821090.2152089X-RAY DIFFRACTION65
2.4841-2.58360.24851270.22562160X-RAY DIFFRACTION68
2.5836-2.70120.3351160.23242313X-RAY DIFFRACTION71
2.7012-2.84360.25951140.22992387X-RAY DIFFRACTION74
2.8436-3.02170.29281290.23112602X-RAY DIFFRACTION80
3.0217-3.2550.27081550.2252689X-RAY DIFFRACTION83
3.255-3.58240.25541400.19542774X-RAY DIFFRACTION85
3.5824-4.10060.19951580.16942871X-RAY DIFFRACTION88
4.1006-5.16540.18291570.15192876X-RAY DIFFRACTION88
5.1654-48.9720.21211800.18582914X-RAY DIFFRACTION87

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