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- PDB-5vjp: Crystal Structure of Adenine Phosphoribosyltransferase from Sacch... -

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Basic information

Entry
Database: PDB / ID: 5vjp
TitleCrystal Structure of Adenine Phosphoribosyltransferase from Saccharomyces cerevisiae Complexed with L-2,5-Dideoxy-2,5-Imino-Altritol 1,6-Bisphosphate (L-DIAB) and Adenine
ComponentsAdenine phosphoribosyltransferase 1
KeywordsTRANSFERASE/TRANSFERASE INHIBITOR / Adenine phosphoribosyltransferase / Transition state analogue / L-2 / 5-Dideoxy-2 / 5-imino-altritol-1 / 6-bisphosphate / L-DIAB / TRANSFERASE-TRANSFERASE INHIBITOR complex
Function / homology
Function and homology information


Purine salvage / adenine binding / adenine salvage / adenine phosphoribosyltransferase / adenine phosphoribosyltransferase activity / AMP salvage / purine ribonucleoside salvage / AMP binding / Neutrophil degranulation / metal ion binding ...Purine salvage / adenine binding / adenine salvage / adenine phosphoribosyltransferase / adenine phosphoribosyltransferase activity / AMP salvage / purine ribonucleoside salvage / AMP binding / Neutrophil degranulation / metal ion binding / nucleus / cytoplasm
Similarity search - Function
Adenine phosphoribosyl transferase / : / Purine/pyrimidine phosphoribosyl transferases signature. / Rossmann fold - #2020 / Phosphoribosyl transferase domain / Phosphoribosyltransferase-like / Phosphoribosyltransferase domain / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ADENINE / Chem-IR9 / Adenine phosphoribosyltransferase 1
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.98 Å
AuthorsHarijan, R.K. / Ducati, R.G. / Bonanno, J.B. / Almo, S.C. / Schramm, V.L.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM41916 United States
CitationJournal: ACS Chem. Biol. / Year: 2018
Title: Synthesis of bis-Phosphate Iminoaltritol Enantiomers and Structural Characterization with Adenine Phosphoribosyltransferase.
Authors: Harris, L.D. / Harijan, R.K. / Ducati, R.G. / Evans, G.B. / Hirsch, B.M. / Schramm, V.L.
History
DepositionApr 19, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 27, 2017Provider: repository / Type: Initial release
Revision 1.1Jan 31, 2018Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year
Revision 1.2Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Oct 4, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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: Adenine phosphoribosyltransferase 1
B: Adenine phosphoribosyltransferase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,44912
Polymers41,2342
Non-polymers1,21610
Water3,243180
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5110 Å2
ΔGint7 kcal/mol
Surface area14470 Å2
MethodPISA
Unit cell
Length a, b, c (Å)138.087, 49.219, 95.354
Angle α, β, γ (deg.)90.00, 130.55, 90.00
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: MET / Beg label comp-ID: MET / End auth comp-ID: ASN / End label comp-ID: ASN / Refine code: _ / Auth seq-ID: 1 - 179 / Label seq-ID: 1 - 179

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

NCS ensembles :
ID
1
2

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Components

#1: Protein Adenine phosphoribosyltransferase 1 / APRT 1


Mass: 20616.814 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: APT1, YML022W / Production host: Escherichia coli (E. coli)
References: UniProt: P49435, adenine phosphoribosyltransferase
#2: Chemical ChemComp-IR9 / [(2S,3R,4S,5S)-3,4-dihydroxypyrrolidine-2,5-diyl]bis(methylene) bis[dihydrogen (phosphate)]


Mass: 323.132 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H15NO10P2
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-ADE / ADENINE


Mass: 135.127 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H5N5
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 180 / Source method: isolated from a natural source / Formula: H2O

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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: 2.99 Å3/Da / Density % sol: 58.8 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop
Details: 100 mM sodium acetate, 0.2 M ammonium sulfate, 22% PEG4000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 31-ID / Wavelength: 0.97931 Å
DetectorType: RAYONIX MX-225HE / Detector: CCD / Date: Feb 9, 2017
RadiationMonochromator: diamond(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97931 Å / Relative weight: 1
ReflectionResolution: 1.98→72.45 Å / Num. obs: 33741 / % possible obs: 98.7 % / Redundancy: 3.7 % / Biso Wilson estimate: 26 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.12 / Net I/σ(I): 7.9
Reflection shellResolution: 1.98→2.03 Å / Redundancy: 3.7 % / Mean I/σ(I) obs: 2 / Num. unique obs: 2392 / CC1/2: 0.77 / % possible all: 99.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1G2Q

1g2q


Resolution: 1.98→72.45 Å / Cor.coef. Fo:Fc: 0.925 / Cor.coef. Fo:Fc free: 0.916 / SU B: 8.081 / SU ML: 0.204 / Cross valid method: THROUGHOUT / ESU R: 0.204 / ESU R Free: 0.174 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.28079 1727 5.1 %RANDOM
Rwork0.26194 ---
obs0.26295 31993 98.55 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 40.204 Å2
Baniso -1Baniso -2Baniso -3
1-3.78 Å20 Å22.41 Å2
2---4.07 Å20 Å2
3----1.55 Å2
Refinement stepCycle: 1 / Resolution: 1.98→72.45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2718 0 76 181 2975
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0192856
X-RAY DIFFRACTIONr_bond_other_d0.0020.022724
X-RAY DIFFRACTIONr_angle_refined_deg1.2472.013860
X-RAY DIFFRACTIONr_angle_other_deg0.87336319
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1685350
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.58625.041121
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.09215462
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.38158
X-RAY DIFFRACTIONr_chiral_restr0.0670.2434
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0213104
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02567
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_it1.313.9851406
X-RAY DIFFRACTIONr_mcbond_other1.3073.9831405
X-RAY DIFFRACTIONr_mcangle_it2.2075.9641754
X-RAY DIFFRACTIONr_mcangle_other2.2075.9651755
X-RAY DIFFRACTIONr_scbond_it1.2144.1841450
X-RAY DIFFRACTIONr_scbond_other1.2134.1851451
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.0666.1922107
X-RAY DIFFRACTIONr_long_range_B_refined4.17347.5523104
X-RAY DIFFRACTIONr_long_range_B_other4.17247.5513105
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Number: 10622 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.06 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 1.98→2.031 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.414 113 -
Rwork0.352 2398 -
obs--99.88 %

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