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- PDB-9f17: Crystal structure of N term His-tag Adenylosuccinate synthetase f... -

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Basic information

Entry
Database: PDB / ID: 9f17
TitleCrystal structure of N term His-tag Adenylosuccinate synthetase from Helicobacter pylori
ComponentsAdenylosuccinate synthetase
KeywordsLIGASE / Adenylosuccinate synthetase / H. pylori
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
GUANOSINE-5'-DIPHOSPHATE / INOSINIC ACID / Adenylosuccinate synthetase
Similarity search - Component
Biological speciesHelicobacter pylori 26695 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsStefanic, Z.
Funding support Croatia, 1items
OrganizationGrant numberCountry
Croatian Science FoundationIP-2019-04-6764 Croatia
CitationJournal: Int J Mol Sci / Year: 2024
Title: Location Is Everything: Influence of His-Tag Fusion Site on Properties of Adenylosuccinate Synthetase from Helicobacter pylori.
Authors: Miskovic, M.Z. / Wojtys, M. / Winiewska-Szajewska, M. / Wielgus-Kutrowska, B. / Matkovic, M. / Domazet Jurasin, D. / Stefanic, Z. / Bzowska, A. / Lescic Asler, I.
History
DepositionApr 18, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 4, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Adenylosuccinate synthetase
B: Adenylosuccinate synthetase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)95,04222
Polymers92,0702
Non-polymers2,97220
Water15,043835
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: homology
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)69.150, 122.700, 70.150
Angle α, β, γ (deg.)90.000, 113.360, 90.000
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 2 molecules AB

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


Mass: 46034.918 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Helicobacter pylori 26695 (bacteria) / Gene: purA, HP_0255 / Plasmid: pET21b / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: P56137, adenylosuccinate synthase

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Non-polymers , 6 types, 855 molecules

#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-GDP / GUANOSINE-5'-DIPHOSPHATE


Type: RNA linking / Mass: 443.201 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H15N5O11P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: GDP, energy-carrying molecule*YM
#4: Chemical ChemComp-IMP / INOSINIC ACID


Mass: 348.206 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H13N4O8P / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4 / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C3H8O3
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 835 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.97 Å3/Da / Density % sol: 58.55 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8.5 / Details: 20% PEG3350, 0.2 M ammonium sulphate, 0.1 M Tris

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ELETTRA / Beamline: 11.2C / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 8, 2023
RadiationMonochromator: Double Crystal Si111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.6→44.42 Å / Num. obs: 143274 / % possible obs: 69.4 % / Redundancy: 5.346 % / Biso Wilson estimate: 24.45 Å2 / CC1/2: 0.868 / Rmerge(I) obs: 0.518 / Rrim(I) all: 0.563 / Χ2: 0.553 / Net I/σ(I): 1.92 / Num. measured all: 765952
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsCC1/2Rrim(I) all% possible all
1.6-1.693.5521.7160.42110353320831070.3372.0289.4
1.69-1.813.4291.160.57340223123499230.5091.37831.8
1.81-1.963.6520.8590.77303429125200000.5511.00868.7
1.96-2.144.3180.6221.0110625226795246080.8920.70591.8
2.14-2.395.4580.6451.4913113024280240240.8080.70698.9
2.39-2.766.6130.6322.2114142221429213840.7450.68399.8
2.76-3.386.740.543.0712248318182181730.7890.583100
3.38-4.786.7360.4853.949514614124141240.7970.524100
4.78-44.426.4840.4444.3151428794279310.840.48299.9

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Processing

Software
NameVersionClassification
PHENIX1.19refinement
XSCALEdata scaling
PDB_EXTRACT3.28data extraction
XDSdata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.7→44.42 Å / SU ML: 0.21 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 24.21 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2095 5721 4.88 %
Rwork0.1777 111592 -
obs0.1792 117313 99.71 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 85 Å2 / Biso mean: 32.7106 Å2 / Biso min: 15.94 Å2
Refinement stepCycle: final / Resolution: 1.7→44.42 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6436 0 183 835 7454
Biso mean--32.54 40.74 -
Num. residues----826
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.7-1.720.39331610.337436903851100
1.72-1.740.33251860.33023645383197
1.74-1.760.35952030.30193668387199
1.76-1.780.3212170.289136793896100
1.78-1.810.29252110.278336663877100
1.81-1.830.2631920.265337273919100
1.83-1.860.28582090.263137183927100
1.86-1.890.32431870.256437023889100
1.89-1.910.25931590.252337403899100
1.91-1.950.27712080.247137053913100
1.95-1.980.27211870.223937293916100
1.98-2.020.26451910.212537143905100
2.02-2.050.23391780.213437193897100
2.05-2.10.25891850.198637373922100
2.1-2.140.23872000.19943681388199
2.14-2.190.24071850.19173696388199
2.19-2.250.22971830.192637283911100
2.25-2.310.22862010.196237263927100
2.31-2.380.24411580.193137363894100
2.38-2.450.23321740.19437633937100
2.45-2.540.22731790.178337163895100
2.54-2.640.21982230.181337203943100
2.64-2.760.21292030.18437263929100
2.76-2.910.19661940.177637063900100
2.91-3.090.21371840.177737503934100
3.09-3.330.19471760.161937733949100
3.33-3.660.18542110.154137113922100
3.66-4.190.15461940.132837363930100
4.19-5.280.15111990.124237683967100
5.28-44.420.17171830.146138174000100

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