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- PDB-7r0u: Structure of a cytosolic sulfotransferase of Anopheles gambiae (A... -

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Basic information

Entry
Database: PDB / ID: 7r0u
TitleStructure of a cytosolic sulfotransferase of Anopheles gambiae (AGAP001425) in complex with 3'-phosphoadenosine 5-phosphate and vanillin.
ComponentsAGAP001425-PA
KeywordsTRANSFERASE / Anopheles gambiae / Cytosolic Sulfotransferase / Sulfation / Vanillin / 3'-phosphoadenosine 5-phosphate.
Function / homologysulfation / sulfotransferase activity / Sulfotransferase domain / Sulfotransferase domain / P-loop containing nucleoside triphosphate hydrolase / cytoplasm / ADENOSINE-3'-5'-DIPHOSPHATE / 4-hydroxy-3-methoxybenzaldehyde / AGAP001425-PA
Function and homology information
Biological speciesAnopheles gambiae (African malaria mosquito)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsEsposito Verza, A. / Miggiano, R. / Rizzi, R. / Rossi, F.
Funding support Italy, 1items
OrganizationGrant numberCountry
Fondazione CARIPLO Italy
CitationJournal: Curr Res Struct Biol / Year: 2022
Title: Biochemical and structural analysis of a cytosolic sulfotransferase of the malaria vector Anopheles gambiae overexpressed in the reproductive tissues.
Authors: Esposito Verza, A. / Miggiano, R. / Lombardo, F. / Fiorillo, C. / Arca, B. / Purghe, B. / Del Grosso, E. / Galli, U. / Rizzi, M. / Rossi, F.
History
DepositionFeb 2, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 10, 2022Provider: repository / Type: Initial release
Revision 1.1Aug 24, 2022Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id ..._struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: AGAP001425-PA
B: AGAP001425-PA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)87,0759
Polymers85,6402
Non-polymers1,4357
Water1,51384
1
A: AGAP001425-PA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,3993
Polymers42,8201
Non-polymers5792
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: AGAP001425-PA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,6766
Polymers42,8201
Non-polymers8565
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)78.240, 91.820, 103.450
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: PRO / Beg label comp-ID: PRO / End auth comp-ID: PRO / End label comp-ID: PRO / Refine code: _ / Auth seq-ID: 2 - 337 / Label seq-ID: 23 - 358

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

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Components

#1: Protein AGAP001425-PA / Sulfotransferase (Sult)


Mass: 42820.055 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: Some residues belonging to N-terminal and C-terminal on both polypeptide chains are defined in the electron density.
Source: (gene. exp.) Anopheles gambiae (African malaria mosquito)
Gene: 1281751, AgaP_AGAP001425 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q7PXJ0
#2: Chemical ChemComp-V55 / 4-hydroxy-3-methoxybenzaldehyde / p-vanillin


Mass: 152.147 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H8O3 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-A3P / ADENOSINE-3'-5'-DIPHOSPHATE


Type: RNA linking / Mass: 427.201 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H15N5O10P2
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 84 / 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: 2.17 Å3/Da / Density % sol: 43.3 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: KSCN 0.1 M and PEG 2000 MME 30%

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Data collection

DiffractionMean temperature: 193 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9159 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Oct 20, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9159 Å / Relative weight: 1
ReflectionResolution: 2.5→62.4 Å / Num. obs: 26122 / % possible obs: 98.79 % / Redundancy: 7.3 % / Rmerge(I) obs: 0.07742 / Net I/σ(I): 14.21
Reflection shellResolution: 2.5→2.59 Å / Rmerge(I) obs: 0.3712 / Num. unique obs: 2462

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Processing

Software
NameVersionClassification
SCALAdata scaling
REFMAC5.8.0238refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7R0O

7r0o


Resolution: 2.5→62.4 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.937 / SU B: 11.362 / SU ML: 0.251 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 1.028 / ESU R Free: 0.312 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2523 1315 5 %RANDOM
Rwork0.2064 ---
obs0.2089 24809 98.86 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 128.46 Å2 / Biso mean: 44.859 Å2 / Biso min: 11.58 Å2
Baniso -1Baniso -2Baniso -3
1--0.76 Å20 Å20 Å2
2---4.86 Å20 Å2
3---5.62 Å2
Refinement stepCycle: final / Resolution: 2.5→62.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5642 0 94 84 5820
Biso mean--54.06 39.53 -
Num. residues----672
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0135901
X-RAY DIFFRACTIONr_bond_other_d0.0010.0175210
X-RAY DIFFRACTIONr_angle_refined_deg1.6841.6677987
X-RAY DIFFRACTIONr_angle_other_deg1.2541.58112094
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8485670
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.6122.022366
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.83715992
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.2881544
X-RAY DIFFRACTIONr_chiral_restr0.0740.2720
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.026554
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021392
Refine LS restraints NCS

Ens-ID: 1 / Number: 11712 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.07 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 2.5→2.565 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.234 70 -
Rwork0.267 1734 -
all-1804 -
obs--93.76 %

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