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- PDB-1zn8: Human Adenine Phosphoribosyltransferase Complexed with AMP, in Sp... -

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Basic information

Entry
Database: PDB / ID: 1zn8
TitleHuman Adenine Phosphoribosyltransferase Complexed with AMP, in Space Group P1 at 1.76 A Resolution
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 / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.76 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_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _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)39,9895
Polymers39,2592
Non-polymers7303
Water6,395355
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)47.060, 47.470, 47.840
Angle α, β, γ (deg.)75.41, 68.42, 61.49
Int Tables number1
Space group name H-MP1

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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.: 2 / Source method: obtained synthetically / Formula: C10H14N5O7P / Comment: AMP*YM
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 355 / 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: 2.17 Å3/Da / Density % sol: 42.91 %
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 291 K, pH 8.50

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Data collection

Diffraction
IDCrystal-ID
11
21
Diffraction source
SourceSiteBeamlineTypeIDWavelength (Å)
ROTATING ANODERIGAKU11.5418
SYNCHROTRONLNLS D03B-MX121.4538
DetectorType: MARRESEARCH / Detector: IMAGE PLATE
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
11.54181
21.45381
ReflectionResolution: 1.76→44 Å / Num. obs: 31837

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Processing

SoftwareName: REFMAC / Version: 5.2.0005 / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.76→44 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.939 / SU B: 5.533 / SU ML: 0.088 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.123 / ESU R Free: 0.125 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.211 1629 5.1 %RANDOM
Rwork0.157 ---
obs0.16 30208 95.5 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 17.51 Å2
Baniso -1Baniso -2Baniso -3
1--0.48 Å20.96 Å2-0.34 Å2
2---0.37 Å2-0.24 Å2
3---0.31 Å2
Refinement stepCycle: LAST / Resolution: 1.76→44 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2717 0 47 355 3119
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.0222919
X-RAY DIFFRACTIONr_bond_other_d0.0070.022801
X-RAY DIFFRACTIONr_angle_refined_deg1.9322.0253966
X-RAY DIFFRACTIONr_angle_other_deg0.96236499
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3175355
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.74723.252123
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.39715512
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.2711526
X-RAY DIFFRACTIONr_chiral_restr0.1330.2459
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.023165
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02584
X-RAY DIFFRACTIONr_nbd_refined0.2140.2561
X-RAY DIFFRACTIONr_nbd_other0.2030.22792
X-RAY DIFFRACTIONr_nbtor_refined0.180.21362
X-RAY DIFFRACTIONr_nbtor_other0.0880.21732
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.230.2282
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2840.230
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2950.292
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2190.229
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.4671.51930
X-RAY DIFFRACTIONr_mcbond_other0.31.5730
X-RAY DIFFRACTIONr_mcangle_it1.60722893
X-RAY DIFFRACTIONr_scbond_it2.75831229
X-RAY DIFFRACTIONr_scangle_it4.0064.51073
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.76→1.81 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.288 93 -
Rwork0.22 1683 -
obs--72.22 %
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)
11.1542-0.58250.10450.64320.13050.5324-0.0486-0.04510.11860.04220.0546-0.061-0.02090.0185-0.006-0.0294-0.0155-0.0025-0.02710.0017-0.02227.51887.91956.7282
21.2066-0.63560.03890.56050.06930.7070.0890.1627-0.0643-0.0589-0.0870.062-0.00530.0149-0.0021-0.0266-0.0058-0.007-0.01230.0031-0.030619.5023-7.4347-7.4523
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA3 - 1803 - 180
2X-RAY DIFFRACTION1AD10311
3X-RAY DIFFRACTION2BB2 - 1802 - 180
4X-RAY DIFFRACTION2BE10321

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