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- PDB-6fci: Crystal Structure of Human APRT wild type in complex with Adenine... -

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Basic information

Entry
Database: PDB / ID: 6fci
TitleCrystal Structure of Human APRT wild type in complex with Adenine, 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 / grooming behavior / GMP salvage / Purine salvage / IMP salvage / AMP salvage ...Defective APRT disrupts adenine salvage / adenine binding / adenine salvage / adenine phosphoribosyltransferase / adenine phosphoribosyltransferase activity / grooming behavior / GMP salvage / Purine salvage / IMP salvage / AMP salvage / purine ribonucleoside salvage / AMP binding / secretory granule lumen / Neutrophil degranulation / extracellular exosome / extracellular region / nucleoplasm / cytoplasm / cytosol
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-PRP / Adenine phosphoribosyltransferase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.94 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

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)80,19216
Polymers77,9944
Non-polymers2,19812
Water5,603311
1
A: Adenine phosphoribosyltransferase
D: Adenine phosphoribosyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,0968
Polymers38,9972
Non-polymers1,0996
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5440 Å2
ΔGint-40 kcal/mol
Surface area13990 Å2
MethodPISA
2
B: Adenine phosphoribosyltransferase
C: Adenine phosphoribosyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,0968
Polymers38,9972
Non-polymers1,0996
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5440 Å2
ΔGint-40 kcal/mol
Surface area13950 Å2
MethodPISA
Unit cell
Length a, b, c (Å)49.710, 49.790, 71.490
Angle α, β, γ (deg.)90.050, 93.480, 101.910
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
Adenine phosphoribosyltransferase / APRT


Mass: 19498.531 Da / Num. of mol.: 4
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.: 4 / 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.: 4 / Source method: obtained synthetically / Formula: C5H13O14P3
IdentifierTypeProgram
a-D-Ribf1PO35PO3IUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
#4: Chemical
ChemComp-ADE / ADENINE


Mass: 135.127 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C5H5N5
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 311 / 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: 2.22 Å3/Da / Density % sol: 44.48 %
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: ID14-4 / Wavelength: 0.9762 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 19, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9762 Å / Relative weight: 1
ReflectionResolution: 1.94→71.351 Å / Num. all: 45067 / Num. obs: 45067 / % possible obs: 90.9 % / Redundancy: 2.8 % / Rpim(I) all: 0.075 / Rrim(I) all: 0.132 / Rsym value: 0.109 / Net I/av σ(I): 3.982 / Net I/σ(I): 6.7 / Num. measured all: 124409
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRpim(I) allRrim(I) allRsym valueNet I/σ(I) obs% possible all
1.94-2.042.70.1683.91659561520.1170.2060.1684.385.1
2.04-2.172.70.1334.81587359630.0940.1640.1335.286.6
2.17-2.322.60.1324.21522757850.0960.1640.1325.890.2
2.32-2.52.70.115.71490756040.0780.1350.116.293.2
2.5-2.742.80.10161454852030.0710.1240.1016.894.4
2.74-3.072.90.0975.61357147140.0660.1180.0977.794.9
3.07-3.542.90.0995.71208841470.0660.120.0998.794.3
3.54-4.342.80.1065.3958234050.0710.1280.1069.392.3
4.34-6.132.80.1084.6737626190.0760.1330.1089.290.6
6.13-41.3513.10.0984.4464214750.0610.1160.0989.594.6

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
REFMAC5.8.0131refinement
SCALA3.3.20data scaling
PHASERphasing
PDB_EXTRACT3.15data extraction
Cootmodel building
iMOSFLMdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5HND

5hnd
PDB Unreleased entry


Resolution: 1.94→71.35 Å / Cor.coef. Fo:Fc: 0.927 / Cor.coef. Fo:Fc free: 0.898 / SU B: 8.871 / SU ML: 0.124 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.23 / ESU R Free: 0.182 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2369 2271 5 %RANDOM
Rwork0.1964 ---
obs0.1984 42796 90.95 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 61.5 Å2 / Biso mean: 15.915 Å2 / Biso min: 3.7 Å2
Baniso -1Baniso -2Baniso -3
1-1.78 Å20.06 Å2-0.26 Å2
2---0.68 Å2-0.1 Å2
3----1.02 Å2
Refinement stepCycle: final / Resolution: 1.94→71.35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5466 0 132 311 5909
Biso mean--5.83 24.13 -
Num. residues----712
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0030.0195904
X-RAY DIFFRACTIONr_bond_other_d0.0050.025845
X-RAY DIFFRACTIONr_angle_refined_deg0.8732.0288036
X-RAY DIFFRACTIONr_angle_other_deg0.535313498
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3875742
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.00723.115244
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.726151042
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.1061554
X-RAY DIFFRACTIONr_chiral_restr0.0480.2926
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0216455
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021279
X-RAY DIFFRACTIONr_mcbond_it0.7320.9042878
X-RAY DIFFRACTIONr_mcbond_other0.7310.9032877
X-RAY DIFFRACTIONr_mcangle_it1.1571.3473599
LS refinement shellResolution: 1.94→1.99 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.261 178 -
Rwork0.219 2946 -
all-3124 -
obs--84.14 %
Refinement TLS params.

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

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
10.42520.0790.07151.0243-0.10431.0375-0.0377-0.00340.0548-0.01520.0288-0.0057-0.10.05310.00890.0172-0.0105-0.00770.0123-0.00050.0127-21.05911.6616-1.6492
20.8848-0.18710.05491.68780.37860.76470.0026-0.01040.08710.03370.0196-0.076-0.11430.0258-0.02210.0301-0.0045-0.00660.0011-0.00120.0206-10.210637.6055-29.7886
30.39240.1494-0.14381.00520.10441.1553-0.00490.012-0.0594-0.0550.02390.02010.0695-0.0298-0.01890.022-0.0127-0.00820.0162-0.00270.0171-16.294617.7984-37.1243
40.9443-0.16310.12781.6284-0.47250.72510.0018-0.0042-0.0810.04310.02210.06980.1097-0.0236-0.02390.0306-0.0024-0.00520.00310.00170.023-28.0005-8.39414.3315
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 180
2X-RAY DIFFRACTION2B4 - 180
3X-RAY DIFFRACTION3C2 - 180
4X-RAY DIFFRACTION4D4 - 180

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