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- PDB-7y94: Crystal structure of Escherichia coli Adenine Phosphoribosyltrans... -

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Basic information

Entry
Database: PDB / ID: 7y94
TitleCrystal structure of Escherichia coli Adenine Phosphoribosyltransferase (APRT) in complex with Adenine
ComponentsAdenine phosphoribosyltransferase
KeywordsTRANSFERASE / Adenine Phosphoribosyltransferase / Substrate Complex / Escherichia coli / Purine Salvage Pathway / Nucleotide Metabolism
Function / homology
Function and homology information


adenine salvage / adenine phosphoribosyltransferase / adenine phosphoribosyltransferase activity / AMP salvage / purine ribonucleoside salvage / magnesium ion binding / protein homodimerization activity / cytosol
Similarity search - Function
Adenine phosphoribosyl transferase / : / Purine/pyrimidine phosphoribosyl transferases signature. / Phosphoribosyl transferase domain / Phosphoribosyltransferase-like / Phosphoribosyltransferase domain
Similarity search - Domain/homology
ACETATE ION / ADENINE / Adenine phosphoribosyltransferase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsYadav, P. / Kushwaha, G.S. / Bhavesh, N.S.
Funding support India, 1items
OrganizationGrant numberCountry
Indian Council of Medical ResearchBMI/11(45)/2020 India
CitationJournal: To Be Published
Title: Crystal structure of Escherichia coli Adenine Phosphoribosyltransferase (APRT) in complex with Adenine
Authors: Yadav, P. / Kushwaha, G.S. / Bhavesh, N.S.
History
DepositionJun 24, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 2, 2023Provider: repository / Type: Initial release
Revision 1.1May 29, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Adenine phosphoribosyltransferase
B: Adenine phosphoribosyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,00014
Polymers40,3262
Non-polymers67412
Water6,918384
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, Dimer
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4720 Å2
ΔGint-60 kcal/mol
Surface area15430 Å2
MethodPISA
Unit cell
Length a, b, c (Å)44.656, 87.073, 47.830
Angle α, β, γ (deg.)90.00, 111.20, 90.00
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 Adenine phosphoribosyltransferase / APRT


Mass: 20163.100 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (strain K12) (bacteria)
Strain: K12 / Gene: apt, b0469, JW0458 / Production host: Escherichia coli (E. coli)
References: UniProt: P69503, adenine phosphoribosyltransferase

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Non-polymers , 6 types, 396 molecules

#2: Chemical ChemComp-ADE / ADENINE


Mass: 135.127 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C5H5N5 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#4: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Cl
#5: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#6: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 384 / 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: 2.18 Å3/Da / Density % sol: 43.68 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8 / Details: 100 mM Tris-HCl pH 8.0, 20 % PEG 4000, 0.2 M MgCl2

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.8856 Å
DetectorType: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Jan 21, 2022 / Details: Toroidal mirror
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8856 Å / Relative weight: 1
ReflectionResolution: 1.498→41.63 Å / Num. obs: 54573 / % possible obs: 99.8 % / Redundancy: 5.2 % / CC1/2: 0.99 / Rmerge(I) obs: 0.07 / Rpim(I) all: 0.034 / Rrim(I) all: 0.078 / Net I/σ(I): 12.1
Reflection shellResolution: 1.498→1.524 Å / Redundancy: 5.4 % / Rmerge(I) obs: 0.727 / Mean I/σ(I) obs: 2.2 / Num. unique obs: 2710 / CC1/2: 0.812 / Rpim(I) all: 0.342 / Rrim(I) all: 0.805 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
autoPROCdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2DY0

2dy0


Resolution: 1.5→41.63 Å / Cor.coef. Fo:Fc: 0.974 / Cor.coef. Fo:Fc free: 0.968 / SU B: 1.617 / SU ML: 0.059 / Cross valid method: THROUGHOUT / ESU R: 0.075 / ESU R Free: 0.074 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19326 2723 5 %RANDOM
Rwork0.17093 ---
obs0.17205 51805 99.67 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 20.831 Å2
Baniso -1Baniso -2Baniso -3
1--0.72 Å20 Å2-0.88 Å2
2--0.9 Å20 Å2
3---0.38 Å2
Refinement stepCycle: 1 / Resolution: 1.5→41.63 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2788 0 39 384 3211
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0132911
X-RAY DIFFRACTIONr_bond_other_d0.0010.0152873
X-RAY DIFFRACTIONr_angle_refined_deg1.7561.6473959
X-RAY DIFFRACTIONr_angle_other_deg1.4961.5786627
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7775377
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.84722.672131
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.57915499
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.151516
X-RAY DIFFRACTIONr_chiral_restr0.0910.2386
X-RAY DIFFRACTIONr_gen_planes_refined0.010.023292
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02614
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.8531.9221474
X-RAY DIFFRACTIONr_mcbond_other1.8521.9211472
X-RAY DIFFRACTIONr_mcangle_it2.6412.881840
X-RAY DIFFRACTIONr_mcangle_other2.642.881841
X-RAY DIFFRACTIONr_scbond_it3.0182.2691437
X-RAY DIFFRACTIONr_scbond_other3.0172.271438
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.5233.2632113
X-RAY DIFFRACTIONr_long_range_B_refined5.71924.7473280
X-RAY DIFFRACTIONr_long_range_B_other5.7124.6993274
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.5→1.537 Å
RfactorNum. reflection% reflection
Rfree0.279 204 -
Rwork0.257 3844 -
obs--99.88 %

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