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- PDB-1zn9: Human Adenine Phosphoribosyltransferase in Apo and AMP Complexed Forms -

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Basic information

Entry
Database: PDB / ID: 1zn9
TitleHuman Adenine Phosphoribosyltransferase in Apo and AMP Complexed Forms
ComponentsAdenine phosphoribosyltransferase
KeywordsTRANSFERASE / Glycosyltransferase / Purine salvage
Function / homology
Function and homology information


Defective APRT disrupts adenine salvage / adenine binding / adenine salvage / adenine phosphoribosyltransferase / adenine phosphoribosyltransferase activity / grooming behavior / Purine salvage / GMP salvage / IMP salvage / AMP salvage ...Defective APRT disrupts adenine salvage / adenine binding / adenine salvage / adenine phosphoribosyltransferase / adenine phosphoribosyltransferase activity / grooming behavior / Purine salvage / GMP 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
ADENOSINE MONOPHOSPHATE / Adenine phosphoribosyltransferase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.05 Å
AuthorsIulek, J. / Silva, M. / Tomich, C.H.T.P. / Thiemann, O.H.
CitationJournal: J.Biomol.Struct.Dyn. / Year: 2008
Title: Structural Complexes of Human Adenine Phosphoribosyltransferase Reveal Novel Features of the APRT Catalytic Mechanism
Authors: Silva, C.H. / Silva, M. / Iulek, J. / Thiemann, O.H.
History
DepositionMay 11, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 25, 2006Provider: repository / Type: Initial release
Revision 1.1Apr 21, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,6073
Polymers39,2592
Non-polymers3471
Water4,918273
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)47.511, 49.252, 140.105
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Adenine phosphoribosyltransferase / APRT


Mass: 19629.727 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: APRT / Plasmid: pET29a / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: P07741, adenine phosphoribosyltransferase
#2: Chemical ChemComp-AMP / ADENOSINE MONOPHOSPHATE


Mass: 347.221 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H14N5O7P / Comment: AMP*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 273 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.06 Å3/Da / Density % sol: 39.93 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 15.0 % (V/V) glycerol, 25.5 % (w/V) polyethylene glycol 4000, 0.17 mol/L sodium acetate and 0.085 mol/L Tris-HCl pH 8.5 , VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.05→28.52 Å / Num. all: 20179 / Num. obs: 20179

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Processing

SoftwareName: REFMAC / Version: 5.2.0005 / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.05→28.52 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.916 / SU B: 8.512 / SU ML: 0.122 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.218 / ESU R Free: 0.193 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22514 1032 5.1 %RANDOM
Rwork0.15064 ---
all0.15436 ---
obs0.15436 19146 94.1 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 27.082 Å2
Baniso -1Baniso -2Baniso -3
1--0.15 Å20 Å20 Å2
2--0.24 Å20 Å2
3----0.09 Å2
Refinement stepCycle: LAST / Resolution: 2.05→28.52 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2733 0 23 273 3029
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0222890
X-RAY DIFFRACTIONr_bond_other_d0.0020.022794
X-RAY DIFFRACTIONr_angle_refined_deg1.7932.0173925
X-RAY DIFFRACTIONr_angle_other_deg0.96536495
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5265356
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.10423.689122
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.61715514
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.2051524
X-RAY DIFFRACTIONr_chiral_restr0.1070.2462
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.023143
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02562
X-RAY DIFFRACTIONr_nbd_refined0.20.2555
X-RAY DIFFRACTIONr_nbd_other0.1810.22734
X-RAY DIFFRACTIONr_nbtor_refined0.1690.21309
X-RAY DIFFRACTIONr_nbtor_other0.0870.21793
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1960.2217
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.0030.21
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.220.215
X-RAY DIFFRACTIONr_symmetry_vdw_other0.30.2100
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2770.219
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.0071.51977
X-RAY DIFFRACTIONr_mcbond_other0.2331.5732
X-RAY DIFFRACTIONr_mcangle_it1.45522903
X-RAY DIFFRACTIONr_scbond_it2.33831178
X-RAY DIFFRACTIONr_scangle_it3.4044.51022
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.05→2.101 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.283 61 -
Rwork0.175 1217 -
obs--83.2 %
Refinement TLS params.Method: refined / Origin x: 11.915 Å / Origin y: 7.06 Å / Origin z: 51.172 Å
111213212223313233
T-0.1849 Å2-0.0119 Å2-0.0068 Å2--0.1351 Å2-0.0015 Å2---0.2042 Å2
L0.8255 °2-0.1874 °2-0.1885 °2-0.8456 °2-0.0208 °2--0.7721 °2
S-0.0322 Å °-0.0412 Å °0.0201 Å °0.082 Å °-0.0008 Å °-0.0241 Å °-0.01 Å °0.0689 Å °0.033 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA2 - 1802 - 180
2X-RAY DIFFRACTION1BB2 - 1802 - 180
3X-RAY DIFFRACTION1BC10311

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