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- PDB-7r0o: Structure of a cytosolic sulfotransferase of Anopheles gambiae (A... -

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Basic information

Entry
Database: PDB / ID: 7r0o
TitleStructure of a cytosolic sulfotransferase of Anopheles gambiae (AGAP001425).
ComponentsAGAP001425-PA
KeywordsTRANSFERASE / Anopheles gambiae / Cytosolic Sulfotransferase / Sulfation.
Function / homologysulfation / Sulfotransferase domain / Sulfotransferase domain / sulfotransferase activity / P-loop containing nucleoside triphosphate hydrolase / cytoplasm / AGAP001425-PA
Function and homology information
Biological speciesAnopheles gambiae (African malaria mosquito)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 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

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)86,26410
Polymers85,6402
Non-polymers6238
Water5,513306
1
A: AGAP001425-PA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,1325
Polymers42,8201
Non-polymers3124
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: AGAP001425-PA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,1325
Polymers42,8201
Non-polymers3124
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)78.773, 92.147, 101.761
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
11B
21A

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
1BB
2AA

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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: In both polypeptide chains the residues belonging to N-terminal his-tag are not defined. Moreover aa 284-285 and C-terminal 2 residues in chain A are not defined in the electron density. ...Details: In both polypeptide chains the residues belonging to N-terminal his-tag are not defined. Moreover aa 284-285 and C-terminal 2 residues in chain A are not defined in the electron density. Threonine 283 and last C-terminal residue is not defined in the electron density. Numeration refers to wild type, untagged protein.
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-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 306 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.16 Å3/Da / Density % sol: 42.96 % / Description: Thin plates
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 25% PEG 3350, 0.3 M NaCl, Bis-tris 0.1 M pH 5.5

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Data collection

DiffractionMean temperature: 193 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID30B / Wavelength: 0.9677 Å
DetectorType: DECTRIS EIGER X 4M / Detector: PIXEL / Date: Sep 29, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9677 Å / Relative weight: 1
ReflectionResolution: 2→42.78 Å / Num. obs: 50299 / % possible obs: 98.96 % / Redundancy: 2 % / Biso Wilson estimate: 25.25 Å2 / Rmerge(I) obs: 0.05168 / Net I/σ(I): 8.4
Reflection shellResolution: 2→2.072 Å / Rmerge(I) obs: 0.3938 / Mean I/σ(I) obs: 1.95 / Num. unique obs: 9858 / % possible all: 99.28

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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: 1FMJ

1fmj


Resolution: 2→42.78 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.955 / SU B: 4.994 / SU ML: 0.132 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.196 / ESU R Free: 0.163 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.226 2538 5 %RANDOM
Rwork0.1922 ---
obs0.1939 47756 99.11 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 83.03 Å2 / Biso mean: 26.133 Å2 / Biso min: 8.68 Å2
Baniso -1Baniso -2Baniso -3
1--1.07 Å20 Å20 Å2
2---1.48 Å20 Å2
3---2.55 Å2
Refinement stepCycle: final / Resolution: 2→42.78 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5628 0 38 306 5972
Biso mean--53.35 29.65 -
Num. residues----670
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0135820
X-RAY DIFFRACTIONr_bond_other_d0.0010.0175186
X-RAY DIFFRACTIONr_angle_refined_deg1.4951.6527859
X-RAY DIFFRACTIONr_angle_other_deg1.3251.57612039
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2335666
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.67622.022366
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.89215989
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.7041544
X-RAY DIFFRACTIONr_chiral_restr0.0720.2709
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.026476
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021368
Refine LS restraints NCS

Ens-ID: 1 / Number: 11875 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.05 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1B
2A
LS refinement shellResolution: 2→2.052 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.388 188 -
Rwork0.312 3503 -
all-3691 -
obs--99.43 %

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