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- PDB-7yq0: Crystal structure of adenosine 5'-phosphosulfate kinase from Arch... -

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Basic information

Entry
Database: PDB / ID: 7yq0
TitleCrystal structure of adenosine 5'-phosphosulfate kinase from Archaeoglobus fulgidus in complex with ADP
ComponentsAdenylyl-sulfate kinase
KeywordsTRANSFERASE / APS kinase / archaea
Function / homology
Function and homology information


sulfate assimilation via adenylyl sulfate reduction / sulfate assimilation, phosphoadenylyl sulfate reduction by phosphoadenylyl-sulfate reductase (thioredoxin) / adenylyl-sulfate kinase / adenylylsulfate kinase activity / sulfate adenylyltransferase (ATP) activity / hydrogen sulfide biosynthetic process / ATP binding / metal ion binding / cytoplasm
Similarity search - Function
: / Adenylyl-sulfate kinase / Adenylylsulphate kinase / 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 / Adenylyl-sulfate kinase
Similarity search - Component
Biological speciesArchaeoglobus fulgidus (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.58 Å
AuthorsKawakami, T. / Teramoto, T. / Kakuta, Y.
Funding support Japan, 1items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)21K05384 Japan
CitationJournal: Biochem.Biophys.Res.Commun. / Year: 2022
Title: Crystal structure of adenosine 5'-phosphosulfate kinase isolated from Archaeoglobus fulgidus.
Authors: Kawakami, T. / Teramoto, T. / Kakuta, Y.
History
DepositionAug 5, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 18, 2023Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Adenylyl-sulfate kinase
B: Adenylyl-sulfate kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,80113
Polymers40,1862
Non-polymers1,61411
Water6,467359
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5620 Å2
ΔGint-25 kcal/mol
Surface area16070 Å2
MethodPISA
Unit cell
Length a, b, c (Å)65.080, 74.320, 109.870
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Adenylyl-sulfate kinase / APS kinase / ATP adenosine-5'-phosphosulfate 3'-phosphotransferase / Adenosine-5'-phosphosulfate kinase


Mass: 20093.211 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Archaeoglobus fulgidus (archaea) / Gene: cysC, XD40_0245, XD48_1780 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A101DF63, adenylyl-sulfate kinase
#2: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: ADP, energy-carrying molecule*YM
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C3H8O3 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 359 / 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: 3.31 Å3/Da / Density % sol: 62.79 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 5
Details: 0.1 M Malonic Acid/imidazole/boric acid buffer pH 5.0, 25% (w/v) PEG 1500

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL45XU / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Nov 17, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.58→50 Å / Num. obs: 73723 / % possible obs: 100 % / Redundancy: 10 % / CC1/2: 0.99 / Net I/σ(I): 13.2
Reflection shellResolution: 1.58→1.67 Å / Num. unique obs: 12233 / CC1/2: 0.584

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Processing

Software
NameVersionClassification
PHENIX(1.19.2_4158: ???)refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5CB6

5cb6


Resolution: 1.58→44.72 Å / SU ML: 0.29 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 25.14 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.204 1999 2.71 %
Rwork0.1866 --
obs0.1871 73642 99.98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.58→44.72 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2794 0 103 359 3256
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.013107
X-RAY DIFFRACTIONf_angle_d1.1674217
X-RAY DIFFRACTIONf_dihedral_angle_d16.8591266
X-RAY DIFFRACTIONf_chiral_restr0.073452
X-RAY DIFFRACTIONf_plane_restr0.01527
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.58-1.620.42871410.40955037X-RAY DIFFRACTION100
1.62-1.660.3771410.37395057X-RAY DIFFRACTION100
1.66-1.710.32761400.34135053X-RAY DIFFRACTION100
1.71-1.770.33431410.31055062X-RAY DIFFRACTION100
1.77-1.830.30191420.27445060X-RAY DIFFRACTION100
1.83-1.90.22531420.22845086X-RAY DIFFRACTION100
1.9-1.990.25891410.20195051X-RAY DIFFRACTION100
1.99-2.10.21491420.18635097X-RAY DIFFRACTION100
2.1-2.230.22541420.17685104X-RAY DIFFRACTION100
2.23-2.40.19761440.16945134X-RAY DIFFRACTION100
2.4-2.640.16951430.16935120X-RAY DIFFRACTION100
2.64-3.020.18251440.16795153X-RAY DIFFRACTION100
3.02-3.810.17871450.14795226X-RAY DIFFRACTION100
3.81-44.720.15291510.14985403X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: -7.7752 Å / Origin y: -24.0125 Å / Origin z: 30.765 Å
111213212223313233
T0.1031 Å20.0063 Å2-0.0102 Å2-0.1413 Å20.0017 Å2--0.1702 Å2
L0.2581 °20.058 °2-0.15 °2-0.9785 °2-0.4218 °2--1.7058 °2
S-0.0397 Å °0.0221 Å °0.028 Å °0.0328 Å °0.0527 Å °0.0788 Å °0.0204 Å °-0.157 Å °-0.0173 Å °
Refinement TLS groupSelection details: all

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