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- PDB-6fd6: Crystal Structure of Human APRT-Tyr105Phe variant in complex with... -

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Basic information

Entry
Database: PDB / ID: 6fd6
TitleCrystal Structure of Human APRT-Tyr105Phe variant in complex with Adenine, PRPP and Mg2+, 30 days post crystallization (with AMP and PPi products fully generated)
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
ADENOSINE MONOPHOSPHATE / PYROPHOSPHATE / Adenine phosphoribosyltransferase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
Model detailsAPO
AuthorsNioche, P. / Huyet, J. / Ozeir, M.
CitationJournal: Cell Chem Biol / Year: 2018
Title: Structural Insights into the Forward and Reverse Enzymatic Reactions in Human Adenine Phosphoribosyltransferase.
Authors: Huyet, J. / Ozeir, M. / 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: Huyet, J. / Ozeir, M. / 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
DepositionDec 21, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 15, 2018Provider: repository / Type: Initial release
Revision 1.1Jan 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)39,8987
Polymers38,8232
Non-polymers1,0755
Water3,225179
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5220 Å2
ΔGint-38 kcal/mol
Surface area14680 Å2
MethodPISA
Unit cell
Length a, b, c (Å)47.170, 47.790, 47.920
Angle α, β, γ (deg.)76.930, 61.500, 69.410
Int Tables number1
Space group name H-MP1

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Components

#1: Protein Adenine phosphoribosyltransferase / / APRT


Mass: 19411.453 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 / Plasmid: pET29a / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: P07741, adenine phosphoribosyltransferase
#2: Chemical ChemComp-AMP / ADENOSINE MONOPHOSPHATE / Adenosine monophosphate


Mass: 347.221 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H14N5O7P / Comment: AMP*YM
#3: Chemical ChemComp-PPV / PYROPHOSPHATE / Pyrophosphate


Mass: 177.975 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: H4O7P2
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 179 / 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: 46.13 %
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: SOLEIL / Beamline: PROXIMA 2 / Wavelength: 0.98 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Sep 20, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.8→44.62 Å / Num. obs: 29551 / % possible obs: 92.8 % / Redundancy: 3.8 % / CC1/2: 0.982 / Rmerge(I) obs: 0.126 / Net I/σ(I): 9.7
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsCC1/2Diffraction-ID% possible all
1.8-1.843.90.5860.823193.2
1.8-1.843.10.0710.984198.4

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Processing

Software
NameVersionClassification
Aimless0.5.15data scaling
REFMAC5.8.0158refinement
PDB_EXTRACT3.22data extraction
iMOSFLMdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5LN6

5ln6
PDB Unreleased entry


Resolution: 1.8→44.62 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.944 / SU B: 4.574 / SU ML: 0.07 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.126 / ESU R Free: 0.114 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.1828 1510 5.1 %RANDOM
Rwork0.1512 ---
obs0.1528 28037 92.81 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 84.22 Å2 / Biso mean: 18.294 Å2 / Biso min: 7.2 Å2
Baniso -1Baniso -2Baniso -3
1--0.11 Å2-0.21 Å20.42 Å2
2--0.3 Å2-0.1 Å2
3---0.02 Å2
Refinement stepCycle: final / Resolution: 1.8→44.62 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2734 0 65 179 2978
Biso mean--17.53 25.72 -
Num. residues----356
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0192980
X-RAY DIFFRACTIONr_bond_other_d0.0010.022875
X-RAY DIFFRACTIONr_angle_refined_deg1.3822.0284065
X-RAY DIFFRACTIONr_angle_other_deg0.63236675
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6735381
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.41923.279122
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.14415518
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.7841526
X-RAY DIFFRACTIONr_chiral_restr0.0750.2463
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0213281
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02603
LS refinement shellResolution: 1.8→1.847 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.229 104 -
Rwork0.195 2116 -
all-2220 -
obs--93.59 %
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)
11.1069-0.0431-0.49150.76440.03070.80680.048-0.04320.1122-0.0314-0.0046-0.0212-0.07990.043-0.04340.009-0.00410.00490.003-0.0040.0118-19.66093.333513.1309
20.9838-0.0801-0.17630.55730.05910.5995-0.0220.0875-0.0826-0.0251-0.01240.02880.0186-0.06660.03440.0039-0.0030.00290.0124-0.0090.0099-27.4356-11.8379-1.0423
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A3 - 180
2X-RAY DIFFRACTION2B3 - 180

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