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- PDB-7xi2: Crystal structure of Escherichia coli Adenine Phosphoribosyltrans... -

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Basic information

Entry
Database: PDB / ID: 7xi2
TitleCrystal structure of Escherichia coli Adenine Phosphoribosyltransferase (APRT) in complex with phosphate
ComponentsAdenine phosphoribosyltransferase
KeywordsTRANSFERASE / APRT / Adenine Phosphoribosyltransferase / Nucleotide metabolism / Purine Salvage pathway
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 / PHOSPHATE ION / Adenine phosphoribosyltransferase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.65 Å
AuthorsYadav, P. / Kushwaha, G.S. / Bhavesh, N.S.
Funding support India, 1items
OrganizationGrant numberCountry
Indian Council of Mefical ResearchBMI/11(45)/2020 India
CitationJournal: To Be Published
Title: Crystal structure of Escherichia coli Adenine Phosphoribosyltransferase (APRT) in complex with phosphate
Authors: Yadav, P. / Kushwaha, G.S. / Bhavesh, N.S.
History
DepositionApr 11, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 12, 2023Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: 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

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)40,0827
Polymers39,7622
Non-polymers3205
Water7,692427
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, Dimer
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4030 Å2
ΔGint-56 kcal/mol
Surface area14520 Å2
MethodPISA
Unit cell
Length a, b, c (Å)40.014, 47.752, 54.074
Angle α, β, γ (deg.)106.72, 103.09, 111.02
Int Tables number1
Space group name H-MP1

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Components

#1: Protein Adenine phosphoribosyltransferase / APRT


Mass: 19880.820 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
#2: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#3: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-CL / CHLORIDE ION


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


Mass: 18.015 Da / Num. of mol.: 427 / 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: 2.16 Å3/Da / Density % sol: 43.13 %
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: ROTATING ANODE / Type: RIGAKU FR-E+ SUPERBRIGHT / Wavelength: 1.54178 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Dec 8, 2021
RadiationMonochromator: M / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54178 Å / Relative weight: 1
ReflectionResolution: 1.65→48.14 Å / Num. obs: 36928 / % possible obs: 92.3 % / Redundancy: 3.9 % / CC1/2: 1 / Rmerge(I) obs: 0.02 / Rpim(I) all: 0.013 / Net I/σ(I): 24.5
Reflection shellResolution: 1.65→1.68 Å / Redundancy: 4 % / Rmerge(I) obs: 0.114 / Mean I/σ(I) obs: 7.6 / Num. unique obs: 1709 / CC1/2: 0.99 / Rpim(I) all: 0.066 / % possible all: 87.2

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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: 1.65→35.61 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.959 / SU B: 1.666 / SU ML: 0.058 / Cross valid method: THROUGHOUT / ESU R: 0.104 / ESU R Free: 0.097 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.18387 1832 5 %RANDOM
Rwork0.157 ---
obs0.15834 35083 92.23 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 20.871 Å2
Baniso -1Baniso -2Baniso -3
1-0.41 Å20.97 Å20.08 Å2
2--0.44 Å20.21 Å2
3----1.24 Å2
Refinement stepCycle: 1 / Resolution: 1.65→35.61 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2770 0 16 427 3213
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0132874
X-RAY DIFFRACTIONr_bond_other_d0.0010.0152840
X-RAY DIFFRACTIONr_angle_refined_deg1.7481.6453908
X-RAY DIFFRACTIONr_angle_other_deg1.4771.5816558
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.0795373
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.30822.672131
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.47415499
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.821516
X-RAY DIFFRACTIONr_chiral_restr0.0870.2379
X-RAY DIFFRACTIONr_gen_planes_refined0.010.023233
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02599
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_it2.0121.9341466
X-RAY DIFFRACTIONr_mcbond_other2.0091.9311465
X-RAY DIFFRACTIONr_mcangle_it2.8162.891832
X-RAY DIFFRACTIONr_mcangle_other2.8172.8921833
X-RAY DIFFRACTIONr_scbond_it2.8932.2831408
X-RAY DIFFRACTIONr_scbond_other2.8952.2791400
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.3433.2982059
X-RAY DIFFRACTIONr_long_range_B_refined6.07425.0363237
X-RAY DIFFRACTIONr_long_range_B_other5.86424.3233143
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.65→1.693 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.258 110 -
Rwork0.181 2489 -
obs--87.86 %

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