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- PDB-1zn7: Human Adenine Phosphoribosyltransferase Complexed with PRPP, ADE ... -

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Basic information

Entry
Database: PDB / ID: 1zn7
TitleHuman Adenine Phosphoribosyltransferase Complexed with PRPP, ADE and R5P
ComponentsAdenine phosphoribosyltransferase
KeywordsTRANSFERASE / Glycosyltransferase / Purine salvage
Function / homology
Function and homology information


Defective APRT disrupts adenine salvage / adenine binding / adenine salvage / adenine phosphoribosyltransferase activity / adenine phosphoribosyltransferase / GMP salvage / grooming behavior / IMP salvage / Purine salvage / AMP salvage ...Defective APRT disrupts adenine salvage / adenine binding / adenine salvage / adenine phosphoribosyltransferase activity / adenine phosphoribosyltransferase / GMP salvage / grooming behavior / IMP salvage / Purine 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
ADENINE / 5-O-phosphono-alpha-D-ribofuranose / PHOSPHATE ION / Chem-PRP / Adenine phosphoribosyltransferase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.83 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 / Derived calculations ...Advisory / Derived calculations / Refinement description / Version format compliance
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / pdbx_struct_conn_angle / struct_conn / struct_site / struct_site_gen
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_alt_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.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_alt_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.pdbx_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_label_alt_id / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr2_auth_asym_id / _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 2.1Feb 14, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Remark 600 HETEROGEN HOH 510 to HOH 515 are associated with adenine 508 and HOH 516 to HOH 521 are associated ... HETEROGEN HOH 510 to HOH 515 are associated with adenine 508 and HOH 516 to HOH 521 are associated with adenine 509.

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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)41,00912
Polymers39,2592
Non-polymers1,74910
Water6,612367
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5680 Å2
ΔGint-58 kcal/mol
Surface area14360 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)47.019, 47.267, 47.522
Angle α, β, γ (deg.)76.59, 69.26, 61.89
Int Tables number1
Space group name H-MP1

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Components

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Protein , 1 types, 2 molecules AB

#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

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Sugars , 2 types, 4 molecules

#4: 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 / Phosphoribosyl pyrophosphate


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
#5: Sugar ChemComp-HSX / 5-O-phosphono-alpha-D-ribofuranose / 5-O-phosphono-alpha-D-ribose / 5-O-phosphono-D-ribose / 5-O-phosphono-ribose


Type: D-saccharide, alpha linking / Mass: 230.110 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C5H11O8P
IdentifierTypeProgram
a-D-Ribf5PO3IUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0

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Non-polymers , 4 types, 373 molecules

#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#6: Chemical ChemComp-ADE / ADENINE / Adenine


Mass: 135.127 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C5H5N5
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 367 / 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: 2.11 Å3/Da / Density % sol: 41.23 %
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, temperature 291K, VAPOR DIFFUSION, HANGING DROP, pH 8.50

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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: 1.83→39.75 Å / Num. obs: 28504 / % possible obs: 96 % / Rmerge(I) obs: 0.069 / Net I/σ(I): 9
Reflection shellResolution: 1.83→1.93 Å / Rmerge(I) obs: 0.387 / Mean I/σ(I) obs: 1.9 / % possible all: 93.5

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Processing

SoftwareName: REFMAC / Version: 5.2.0003 / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.83→39.75 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.953 / SU B: 6.415 / SU ML: 0.088 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.134 / ESU R Free: 0.125 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19 1448 5.1 %RANDOM
Rwork0.146 ---
obs0.148 27055 97.2 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 18 Å2
Baniso -1Baniso -2Baniso -3
1--0.14 Å21.41 Å2-0.83 Å2
2---0.97 Å20.26 Å2
3---0.25 Å2
Refinement stepCycle: LAST / Resolution: 1.83→39.75 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2715 0 104 367 3186
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0223002
X-RAY DIFFRACTIONr_bond_other_d0.0020.022866
X-RAY DIFFRACTIONr_angle_refined_deg1.8152.0474091
X-RAY DIFFRACTIONr_angle_other_deg0.96536669
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4465360
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.83823.171123
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.15115527
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.4551527
X-RAY DIFFRACTIONr_chiral_restr0.1120.2479
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.023189
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02576
X-RAY DIFFRACTIONr_nbd_refined0.2170.2614
X-RAY DIFFRACTIONr_nbd_other0.2040.22904
X-RAY DIFFRACTIONr_nbtor_refined0.1680.21342
X-RAY DIFFRACTIONr_nbtor_other0.0850.21680
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2110.2298
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined0.0940.23
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1310.222
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2570.274
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2320.238
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.031.51862
X-RAY DIFFRACTIONr_mcbond_other0.2871.5734
X-RAY DIFFRACTIONr_mcangle_it1.47322927
X-RAY DIFFRACTIONr_scbond_it2.40731266
X-RAY DIFFRACTIONr_scangle_it3.5284.51164
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.83→1.88 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.311 118 -
Rwork0.239 1927 -
obs--97.29 %
Refinement TLS params.Method: refined / Origin x: 23.5728 Å / Origin y: 0.3303 Å / Origin z: -0.4341 Å
111213212223313233
T-0.0257 Å20.0013 Å20.0006 Å2--0.04 Å20.0183 Å2---0.0298 Å2
L0.4831 °2-0.2263 °20.0564 °2-0.441 °20.1951 °2--0.4796 °2
S0.0019 Å °0.0004 Å °0.0016 Å °-0.0233 Å °-0.0032 Å °0.0015 Å °-0.0107 Å °-0.0017 Å °0.0013 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A3 - 180
2X-RAY DIFFRACTION1A502
3X-RAY DIFFRACTION1A504
4X-RAY DIFFRACTION1A500
5X-RAY DIFFRACTION1A506
6X-RAY DIFFRACTION1A655
7X-RAY DIFFRACTION1A656 - 661
8X-RAY DIFFRACTION1B3 - 180
9X-RAY DIFFRACTION1B503
10X-RAY DIFFRACTION1A505
11X-RAY DIFFRACTION1B501
12X-RAY DIFFRACTION1B507
13X-RAY DIFFRACTION1B656
14X-RAY DIFFRACTION1B657 - 662
15X-RAY DIFFRACTION1A662 - 832
16X-RAY DIFFRACTION1B663 - 846

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