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- PDB-6hgr: Crystal Structure of Human APRT wild type in complex with IMP -

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Basic information

Entry
Database: PDB / ID: 6hgr
TitleCrystal Structure of Human APRT wild type in complex with IMP
ComponentsAdenine phosphoribosyltransferase
KeywordsTRANSFERASE / Rossman fold
Function / homology
Function and homology information


Defective APRT disrupts adenine salvage / adenine binding / adenine salvage / adenine phosphoribosyltransferase activity / adenine phosphoribosyltransferase / GMP salvage / grooming behavior / IMP salvage / Purine salvage / AMP salvage ...Defective APRT disrupts adenine salvage / adenine binding / adenine salvage / adenine phosphoribosyltransferase activity / adenine phosphoribosyltransferase / GMP salvage / grooming behavior / IMP salvage / Purine salvage / AMP salvage / purine ribonucleoside salvage / AMP binding / secretory granule lumen / Neutrophil degranulation / extracellular exosome / extracellular region / nucleoplasm / cytosol / 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
INOSINIC ACID / Adenine phosphoribosyltransferase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.52 Å
Model detailsAPO
AuthorsNioche, P. / Huyet, J. / Ozeir, M.
CitationJournal: J.Biol.Chem. / Year: 2019
Title: Structural basis for substrate selectivity and nucleophilic substitution mechanisms in human adenine phosphoribosyltransferase catalyzed reaction.
Authors: Ozeir, M. / Huyet, J. / Burgevin, M.C. / Pinson, B. / Chesney, F. / Remy, J.M. / Siddiqi, A.R. / Lupoli, R. / Pinon, G. / Saint-Marc, C. / Gibert, J.F. / Morales, R. / Ceballos-Picot, I. / ...Authors: Ozeir, M. / Huyet, J. / Burgevin, M.C. / Pinson, B. / Chesney, F. / Remy, J.M. / Siddiqi, A.R. / Lupoli, R. / Pinon, G. / Saint-Marc, C. / Gibert, J.F. / Morales, R. / Ceballos-Picot, I. / Barouki, R. / Daignan-Fornier, B. / Olivier-Bandini, A. / Auge, F. / Nioche, P.
History
DepositionAug 23, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 31, 2019Provider: repository / Type: Initial release
Revision 1.1Aug 21, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.2Jan 17, 2024Group: 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)39,5514
Polymers38,8552
Non-polymers6962
Water2,954164
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4210 Å2
ΔGint-17 kcal/mol
Surface area14770 Å2
MethodPISA
Unit cell
Length a, b, c (Å)47.585, 47.625, 47.846
Angle α, β, γ (deg.)76.430, 69.240, 61.290
Int Tables number1
Space group name H-MP1

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Components

#1: Protein Adenine phosphoribosyltransferase / / APRT


Mass: 19427.453 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: protein bought from Euromedex, cat# ATGP0483 / Source: (gene. exp.) Homo sapiens (human) / Gene: APRT / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: P07741, adenine phosphoribosyltransferase
#2: Chemical ChemComp-IMP / INOSINIC ACID / Inosinic acid


Mass: 348.206 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H13N4O8P / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 164 / 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: 2.28 Å3/Da / Density % sol: 46.09 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5 / Details: NaOAc, PEG4000, Glycerol, Tris

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.966 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 4, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.966 Å / Relative weight: 1
ReflectionResolution: 1.52→44.6 Å / Num. obs: 46425 / % possible obs: 92.5 % / Redundancy: 3.6 % / Rmerge(I) obs: 0.051 / Net I/σ(I): 11.9
Reflection shellResolution: 1.52→1.57 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.67 / Mean I/σ(I) obs: 1.7 / % possible all: 89.9

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
REFMAC5.8.0131refinement
Aimlessdata scaling
PHASERphasing
PDB_EXTRACT3.15data extraction
Cootmodel building
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5DE6

5de6
PDB Unreleased entry


Resolution: 1.52→44.6 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.964 / SU B: 3.124 / SU ML: 0.053 / SU R Cruickshank DPI: 0.0789 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.079 / ESU R Free: 0.077 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.1931 2494 5.1 %RANDOM
Rwork0.1698 ---
obs0.1709 46425 92.53 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 96.1 Å2 / Biso mean: 26.428 Å2 / Biso min: 13.18 Å2
Baniso -1Baniso -2Baniso -3
1-0.17 Å20.45 Å2-0.27 Å2
2---0.33 Å20.11 Å2
3---0.51 Å2
Refinement stepCycle: final / Resolution: 1.52→44.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2697 0 46 164 2907
Biso mean--26.29 35 -
Num. residues----351
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0192860
X-RAY DIFFRACTIONr_bond_other_d00.022837
X-RAY DIFFRACTIONr_angle_refined_deg1.3012.0233890
X-RAY DIFFRACTIONr_angle_other_deg0.68336550
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9555364
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.80223.186113
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.89315498
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.1531524
X-RAY DIFFRACTIONr_chiral_restr0.2540.2452
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0213148
X-RAY DIFFRACTIONr_gen_planes_other00.02608
X-RAY DIFFRACTIONr_mcbond_it2.3911.841423
X-RAY DIFFRACTIONr_mcbond_other2.3781.8391422
X-RAY DIFFRACTIONr_mcangle_it3.0152.7481780
LS refinement shellResolution: 1.52→1.559 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.286 166 -
Rwork0.269 3350 -
all-3516 -
obs--90.02 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.0911-0.6893-0.1250.8480.11180.65170.05740.1063-0.0174-0.0836-0.0568-0.0208-0.04710.0047-0.00060.01840.0009-0.00410.0119-0.00020.008819.8161-14.865-1.9689
20.8626-0.2352-0.11250.65020.09120.4413-0.0247-0.06430.07860.00590.0292-0.0405-0.0298-0.0146-0.00450.01450.0032-0.00910.0064-0.00640.011427.4130.601111.8275
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A3 - 180
2X-RAY DIFFRACTION2B3 - 180

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