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- PDB-8i1m: Crystal structure of oxidated APSK1 domain from human PAPSS1 in c... -

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Basic information

Entry
Database: PDB / ID: 8i1m
TitleCrystal structure of oxidated APSK1 domain from human PAPSS1 in complex with APS and ADP
ComponentsPAPSS1 protein
KeywordsBIOSYNTHETIC PROTEIN / 5'-phosphosulfate kinase 1 / APSK1 / human PAPSS1
Function / homology
Function and homology information


3'-phosphoadenosine 5'-phosphosulfate biosynthetic process / adenylylsulfate kinase activity / sulfate adenylyltransferase (ATP) activity / sulfate assimilation / ATP binding
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 nucleoside triphosphate hydrolase
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / ADENOSINE-5'-PHOSPHOSULFATE / PHOSPHATE ION / PAPSS1 protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.699 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 1.2Nov 6, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature
Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: PAPSS1 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,4104
Polymers22,4601
Non-polymers9493
Water2,810156
1
A: PAPSS1 protein
hetero molecules

A: PAPSS1 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,8208
Polymers44,9212
Non-polymers1,8996
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area5620 Å2
ΔGint-65 kcal/mol
Surface area16000 Å2
MethodPISA
Unit cell
Length a, b, c (Å)114.352, 51.361, 32.397
Angle α, β, γ (deg.)90.00, 91.94, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-402-

HOH

21A-553-

HOH

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Components

#1: Protein PAPSS1 protein


Mass: 22460.309 Da / Num. of mol.: 1 / Fragment: APSK1 domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PAPSS1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q05BW9
#2: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 1 / 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.: 1 / Source method: obtained synthetically / Formula: C10H14N5O10PS / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 156 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

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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: 2.23 Å3/Da / Density % sol: 44.8 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: 2.0 M Ammonium sulfate, 0.1 M HEPES, pH7.5 and 2% w/v PEG4000

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Data collection

DiffractionMean temperature: 180 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.9785 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jan 18, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9785 Å / Relative weight: 1
ReflectionResolution: 1.699→50 Å / Num. obs: 18780 / % possible obs: 90.3 % / Redundancy: 5.9 % / Rmerge(I) obs: 1.004 / Χ2: 0.029 / Net I/σ(I): 7.7
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsΧ2Diffraction-ID% possible all
1.7-1.764.20.46211490.946156.7
1.76-1.834.40.38414301.01168.4
1.83-1.915.20.42717860.995186.4
1.91-2.025.50.3320000.976196.9
2.02-2.145.90.24120241.002198.3
2.14-2.316.30.17820661.02198.8
2.31-2.546.80.1320691.009199.5
2.54-2.916.40.08520501.003198.4
2.91-3.666.90.04920980.923199.8
3.66-506.50.03621081.612198.7

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Processing

Software
NameVersionClassification
HKL-3000data scaling
PHENIX1.17.1refinement
DENZOdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2OFX

2ofx


Resolution: 1.699→46.848 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 25.6 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2299 815 5.09 %
Rwork0.1823 --
obs0.1847 15998 77.01 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.699→46.848 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1495 0 59 156 1710
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0061587
X-RAY DIFFRACTIONf_angle_d1.0352159
X-RAY DIFFRACTIONf_dihedral_angle_d18.377962
X-RAY DIFFRACTIONf_chiral_restr0.054237
X-RAY DIFFRACTIONf_plane_restr0.006277
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6995-1.8060.3337660.22551043X-RAY DIFFRACTION33
1.806-1.94540.29131130.21551816X-RAY DIFFRACTION56
1.9454-2.14120.27021230.20162572X-RAY DIFFRACTION78
2.1412-2.4510.26281830.19083143X-RAY DIFFRACTION96
2.451-3.08790.23341590.18923278X-RAY DIFFRACTION99
3.0879-46.8480.1851710.16163331X-RAY DIFFRACTION99

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