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- PDB-1ore: Human Adenine Phosphoribosyltransferase -

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Basic information

Entry
Database: PDB / ID: 1ore
TitleHuman Adenine Phosphoribosyltransferase
ComponentsAdenine phosphoribosyltransferase
KeywordsTRANSFERASE / Human Adenine Phosphoribosyltransferase / Leishmaniasis / Urolithiasis / glycosyl transferase / 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: 2.1 Å
AuthorsThiemann, O.H. / Silva, M. / Oliva, G. / Silva, C.H.T.P. / Iulek, J.
CitationJournal: Biochemistry / Year: 2004
Title: Three-dimensional structure of human adenine phosphoribosyltransferase and its relation to DHA-urolithiasis.
Authors: Silva, M. / Silva, C.H.T.P. / Iulek, J. / Thiemann, O.H.
History
DepositionMar 12, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 30, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Derived calculations / Version format compliance
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.4Feb 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

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Assembly

Deposited unit
A: Adenine phosphoribosyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,0123
Polymers19,6301
Non-polymers3832
Water3,567198
1
A: Adenine phosphoribosyltransferase
hetero molecules

A: Adenine phosphoribosyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,0256
Polymers39,2592
Non-polymers7654
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_665-y+1,-x+1,-z+1/21
Buried area4610 Å2
ΔGint-42 kcal/mol
Surface area14630 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)58.309, 58.309, 109.535
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
DetailsThe biological assembly is a dimer generated from the monomer in the asymmetric unit by the operation: 1-y, 1-x, -z+1/2.

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Components

#1: Protein Adenine phosphoribosyltransferase / APRT


Mass: 19629.727 Da / Num. of mol.: 1
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-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-AMP / ADENOSINE MONOPHOSPHATE


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


Mass: 18.015 Da / Num. of mol.: 198 / 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: 2.04 Å3/Da / Density % sol: 39.38 %
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
Crystal grow
*PLUS
Temperature: 291 K / pH: 7.4 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
115.0 %(v/v)glycerol1reservoir
225.5 %(w/v)PEG40001reservoir
30.17 Msodium acetate1reservoir
40.085 MTris-HCl1reservoirpH8.5
56 mg/mlprotein1drop
62 mMAMP1drop
720 mMTris-HCl1droppH7.4
85 mM1dropMgCl2

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: LNLS / Beamline: D03B-MX1 / Wavelength: 1.4538 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Aug 4, 2002
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.4538 Å / Relative weight: 1
ReflectionResolution: 2.1→30 Å / Num. all: 11527 / Num. obs: 11527 / % possible obs: 99.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0
Reflection
*PLUS
Lowest resolution: 40 Å / Num. measured all: 95875 / Rmerge(I) obs: 0.04
Reflection shell
*PLUS
Highest resolution: 2.1 Å / Lowest resolution: 2.22 Å / % possible obs: 97 % / Rmerge(I) obs: 0.112

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Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
MAR345data collection
CCP4(SCALA)data scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.1→30 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.947 / SU B: 3.206 / SU ML: 0.087 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.173 / ESU R Free: 0.146 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.1763 554 4.8 %RANDOM
Rwork0.13318 ---
all0.13514 ---
obs0.13514 10948 99.2 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 12.479 Å2
Baniso -1Baniso -2Baniso -3
1-0.06 Å20 Å20 Å2
2--0.06 Å20 Å2
3----0.12 Å2
Refinement stepCycle: LAST / Resolution: 2.1→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1350 0 24 198 1572
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0211456
X-RAY DIFFRACTIONr_bond_other_d0.0030.021392
X-RAY DIFFRACTIONr_angle_refined_deg1.6182.0181980
X-RAY DIFFRACTIONr_angle_other_deg0.9133235
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2495178
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_chiral_restr0.10.2232
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.021575
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02277
X-RAY DIFFRACTIONr_nbd_refined0.2180.2373
X-RAY DIFFRACTIONr_nbd_other0.250.21609
X-RAY DIFFRACTIONr_nbtor_other0.1210.21085
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2070.2138
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1850.217
X-RAY DIFFRACTIONr_symmetry_vdw_other0.3060.288
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1730.214
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_mcbond_it0.8591.5898
X-RAY DIFFRACTIONr_mcangle_it1.52121451
X-RAY DIFFRACTIONr_scbond_it2.263558
X-RAY DIFFRACTIONr_scangle_it3.654.5529
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.1→2.156 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.257 40
Rwork0.134 741
Refinement TLS params.Method: refined / Origin x: 18.038 Å / Origin y: 26.693 Å / Origin z: 21.495 Å
111213212223313233
T0.0564 Å20.0133 Å20.0226 Å2-0.0563 Å20.0064 Å2--0.0106 Å2
L0.891 °20.1649 °2-0.1269 °2-1.0837 °2-0.865 °2--1.6506 °2
S-0.0837 Å °0.1184 Å °-0.0589 Å °-0.0928 Å °0.0479 Å °0.0488 Å °0.1749 Å °-0.0916 Å °0.0358 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA2 - 1802 - 180
2X-RAY DIFFRACTION1AB20012 - 1
3X-RAY DIFFRACTION1AC10011
4X-RAY DIFFRACTION1AD2002 - 21991 - 198
Refinement
*PLUS
Lowest resolution: 40 Å / Rfactor Rfree: 0.176 / Rfactor Rwork: 0.133
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONr_bond_d0.016
X-RAY DIFFRACTIONr_angle_d
X-RAY DIFFRACTIONr_angle_deg1.618
LS refinement shell
*PLUS
Highest resolution: 2.102 Å

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