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- PDB-6fch: Crystal Structure of Human APRT wild type in complex with PRPP an... -

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Basic information

Entry
Database: PDB / ID: 6fch
TitleCrystal Structure of Human APRT wild type in complex with PRPP and Mg2+
ComponentsAdenine phosphoribosyltransferase
KeywordsTRANSFERASE / Rossman fold
Function / homology
Function and homology information


Defective APRT disrupts adenine salvage / adenine binding / adenine salvage / adenine phosphoribosyltransferase / adenine phosphoribosyltransferase activity / Purine salvage / GMP salvage / grooming behavior / IMP salvage / AMP salvage ...Defective APRT disrupts adenine salvage / adenine binding / adenine salvage / adenine phosphoribosyltransferase / adenine phosphoribosyltransferase activity / Purine salvage / GMP salvage / grooming behavior / IMP 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
Chem-PRP / Adenine phosphoribosyltransferase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.45 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 20, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 15, 2018Provider: repository / Type: Initial release
Revision 1.1Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / pdbx_struct_conn_angle / struct_conn / struct_site / struct_site_gen
Item: _chem_comp.mon_nstd_flag / _chem_comp.name ..._chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.2Jan 17, 2024Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _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)39,6846
Polymers38,8552
Non-polymers8294
Water5,332296
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4630 Å2
ΔGint-49 kcal/mol
Surface area14550 Å2
MethodPISA
Unit cell
Length a, b, c (Å)47.260, 47.350, 47.440
Angle α, β, γ (deg.)77.020, 69.530, 61.780
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 / Plasmid: pET29a / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: P07741, adenine phosphoribosyltransferase
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#3: Sugar ChemComp-PRP / 1-O-pyrophosphono-5-O-phosphono-alpha-D-ribofuranose / ALPHA-PHOSPHORIBOSYLPYROPHOSPHORIC ACID / 1-O-pyrophosphono-5-O-phosphono-alpha-D-ribose / 1-O-pyrophosphono-5-O-phosphono-D-ribose / 1-O-pyrophosphono-5-O-phosphono-ribose


Type: D-saccharide / Mass: 390.070 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C5H13O14P3
IdentifierTypeProgram
a-D-Ribf1PO35PO3IUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 296 / 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: 2.25 Å3/Da / Density % sol: 45.32 %
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: MASSIF-1 / Wavelength: 0.966 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Oct 2, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.966 Å / Relative weight: 1
ReflectionResolution: 1.45→44.33 Å / Num. obs: 54531 / % possible obs: 90.8 % / Redundancy: 1.6 % / CC1/2: 0.998 / Rmerge(I) obs: 0.039 / Rpim(I) all: 0.039 / Net I/σ(I): 9.7 / Num. measured all: 88620
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allCC1/2Rpim(I) all% possible all
1.45-1.471.70.2622.1442626470.7880.26286.9
7.94-44.331.80.03334.86303410.9950.03395

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
REFMAC5.8.0124refinement
Aimless0.5.12data scaling
PHASERphasing
PDB_EXTRACT3.15data extraction
Cootmodel building
MxCuBEdata collection
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5DCI

5dci
PDB Unreleased entry


Resolution: 1.45→44.33 Å / Cor.coef. Fo:Fc: 0.976 / Cor.coef. Fo:Fc free: 0.967 / SU B: 2.743 / SU ML: 0.046 / SU R Cruickshank DPI: 0.0797 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.08 / ESU R Free: 0.066
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1755 2743 5 %RANDOM
Rwork0.1405 ---
obs0.1423 51787 90.76 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 87.08 Å2 / Biso mean: 17.406 Å2 / Biso min: 8.28 Å2
Baniso -1Baniso -2Baniso -3
1-0.12 Å20.61 Å2-0.38 Å2
2--0.01 Å2-0.1 Å2
3---0.21 Å2
Refinement stepCycle: final / Resolution: 1.45→44.33 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2736 0 46 296 3078
Biso mean--13.34 28.58 -
Num. residues----356
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0192960
X-RAY DIFFRACTIONr_bond_other_d0.0030.022920
X-RAY DIFFRACTIONr_angle_refined_deg1.2322.0224033
X-RAY DIFFRACTIONr_angle_other_deg0.56536753
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0115380
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.92523.22118
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.56715520
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.5631525
X-RAY DIFFRACTIONr_chiral_restr0.0620.2464
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0213279
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02626
X-RAY DIFFRACTIONr_mcbond_it1.4761.4171478
X-RAY DIFFRACTIONr_mcbond_other1.4761.4161476
X-RAY DIFFRACTIONr_mcangle_it1.5842.121860
X-RAY DIFFRACTIONr_rigid_bond_restr6.00135880
X-RAY DIFFRACTIONr_sphericity_free14.407576
X-RAY DIFFRACTIONr_sphericity_bonded4.69656038
LS refinement shellResolution: 1.45→1.488 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.264 196 -
Rwork0.243 3711 -
all-3907 -
obs--87.37 %

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