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- PDB-7pvo: Adenylosuccinate Synthetase from H. pylori in complex with IMP -

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Basic information

Entry
Database: PDB / ID: 7pvo
TitleAdenylosuccinate Synthetase from H. pylori in complex with IMP
ComponentsAdenylosuccinate synthetaseAdenylosuccinate synthase
KeywordsLIGASE / purine salvage pathway / complex with one of substrates / AMP precursos synthesis
Function / homology
Function and homology information


adenylosuccinate synthase / adenylosuccinate synthase activity / IMP metabolic process / 'de novo' AMP biosynthetic process / GTP binding / magnesium ion binding / cytoplasm
Similarity search - Function
Adenylosuccinate synthase, active site / Adenylosuccinate synthetase active site. / Adenylosuccinate synthase, GTP-binding site / Adenylosuccinate synthetase, domain 2 / Adenylosuccinate synthetase, domain 3 / Adenylosuccinate synthetase GTP-binding site. / Adenylosuccinate synthetase / Adenylosuccinate synthetase, domain 1 / Adenylosuccinate synthetase / Adenylosuccinate synthetase / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
INOSINIC ACID / Adenylosuccinate synthetase
Similarity search - Component
Biological speciesHelicobacter pylori (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsNarczyk, M. / Bzowska, A. / Maksymiuk, W.
Funding support Poland, 2items
OrganizationGrant numberCountry
Polish National Science Centre2015/18/M/NZ1/00776 Poland
Ministry of Science and Higher Education (Poland)BST-173300/BF Poland
CitationJournal: Int.J.Biol.Macromol. / Year: 2023
Title: The pursuit of new alternative ways to eradicate Helicobacter pylori continues: Detailed characterization of interactions in the adenylosuccinate synthetase active site.
Authors: Bubic, A. / Narczyk, M. / Petek, A. / Wojtys, M.I. / Maksymiuk, W. / Wielgus-Kutrowska, B. / Winiewska-Szajewska, M. / Pavkov-Keller, T. / Bertosa, B. / Stefanic, Z. / Luic, M. / Bzowska, A. / Lescic Asler, I.
History
DepositionOct 5, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 16, 2022Provider: repository / Type: Initial release
Revision 1.1Jun 7, 2023Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Feb 7, 2024Group: 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: Adenylosuccinate synthetase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,3504
Polymers45,8101
Non-polymers5403
Water4,270237
1
A: Adenylosuccinate synthetase
hetero molecules

A: Adenylosuccinate synthetase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)92,7008
Polymers91,6192
Non-polymers1,0816
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_455-x-1,y,-z1
Buried area7370 Å2
ΔGint-104 kcal/mol
Surface area29430 Å2
MethodPISA
Unit cell
Length a, b, c (Å)69.105, 61.326, 119.636
Angle α, β, γ (deg.)90.000, 98.417, 90.000
Int Tables number5
Space group name H-MI121
Space group name HallC2y(x,y,-x+z)
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z+1/2
#4: -x+1/2,y+1/2,-z+1/2

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Components

#1: Protein Adenylosuccinate synthetase / Adenylosuccinate synthase / AMPSase / AdSS / IMP--aspartate ligase


Mass: 45809.695 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Helicobacter pylori (strain ATCC 700392 / 26695) (bacteria)
Strain: ATCC 700392 / 26695 / Gene: purA, HP_0255 / Production host: Escherichia coli K-12 (bacteria) / References: UniProt: P56137, adenylosuccinate synthase
#2: Chemical ChemComp-IMP / INOSINIC ACID / Inosinic acid


Mass: 348.206 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H13N4O8P / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 237 / 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: 2.74 Å3/Da / Density % sol: 55.19 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 8.35 / Details: PEG 3350, ammonium sulphate, Bis-Tris Propane

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SEALED TUBE / Type: OXFORD DIFFRACTION SUPERNOVA / Wavelength: 1.54 Å
DetectorType: AGILENT ATLAS CCD / Detector: CCD / Date: Jun 16, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2→23.51 Å / Num. obs: 33613 / % possible obs: 99.9 % / Redundancy: 13.6 % / Biso Wilson estimate: 16.55 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.053 / Rpim(I) all: 0.015 / Rrim(I) all: 0.055 / Net I/σ(I): 38.7
Reflection shellResolution: 2→2.05 Å / Redundancy: 9.3 % / Num. unique obs: 2477 / CC1/2: 0.987 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
PHENIX1.19.2_4158refinement
CrysalisProdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4m9d

4m9d


Resolution: 2→23.45 Å / SU ML: 0.1791 / Cross valid method: FREE R-VALUE / σ(F): 1.91 / Phase error: 21.0791
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.21 1679 5 %
Rwork0.1773 31913 -
obs0.1789 33592 99.93 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 17.88 Å2
Refinement stepCycle: LAST / Resolution: 2→23.45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3196 0 33 237 3466
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0073303
X-RAY DIFFRACTIONf_angle_d0.88554465
X-RAY DIFFRACTIONf_chiral_restr0.0573500
X-RAY DIFFRACTIONf_plane_restr0.006566
X-RAY DIFFRACTIONf_dihedral_angle_d7.3126456
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.060.24521380.2052632X-RAY DIFFRACTION100
2.06-2.130.23211250.19292649X-RAY DIFFRACTION100
2.13-2.20.21861240.18392692X-RAY DIFFRACTION100
2.2-2.290.1981510.18482611X-RAY DIFFRACTION99.96
2.29-2.390.24121340.19352654X-RAY DIFFRACTION99.96
2.39-2.520.23851400.1952646X-RAY DIFFRACTION100
2.52-2.680.25611360.19742660X-RAY DIFFRACTION100
2.68-2.880.2451450.20522667X-RAY DIFFRACTION100
2.88-3.170.24091480.19322638X-RAY DIFFRACTION99.93
3.17-3.630.19291550.17732662X-RAY DIFFRACTION99.93
3.63-4.570.17351470.13772655X-RAY DIFFRACTION99.79
4.57-23.450.16171360.1532747X-RAY DIFFRACTION99.62

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