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- PDB-5vn4: Crystal structure of adenine phosphoribosyl transferase from Tryp... -

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Basic information

Entry
Database: PDB / ID: 5vn4
TitleCrystal structure of adenine phosphoribosyl transferase from Trypanosoma brucei in complex with AMP, pyrophosphate, and ribose-5-phosphate
ComponentsAdenine phosphoribosyltransferase, putative
KeywordsTRANSFERASE / SSGCID / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease
Function / homology
Function and homology information


adenine phosphoribosyltransferase activity / adenine phosphoribosyltransferase / nucleoside metabolic process / nuclear lumen / glycosome / ciliary plasm / cytoplasm
Similarity search - Function
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 / PYROPHOSPHATE / Adenine phosphoribosyltransferase, putative
Similarity search - Component
Biological speciesTrypanosoma brucei brucei (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.35 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: to be published
Title: Crystal structure of adenine phosphoribosyl transferase from Trypanosoma brucei in complex with AMP, pyrophosphate, and ribose-5-phosphate
Authors: Mayclin, S.J. / Dranow, D.M. / Lorimer, D.D. / Edwards, T.E.
History
DepositionApr 28, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 24, 2017Provider: repository / Type: Initial release
Revision 1.1Jun 28, 2017Group: Database references / Category: citation_author / Item: _citation_author.name
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection / Derived calculations
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp / pdbx_chem_comp_identifier / 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 / _atom_site_anisotrop.pdbx_auth_atom_id / _atom_site_anisotrop.pdbx_label_atom_id / _chem_comp.mon_nstd_flag / _chem_comp.type
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Oct 4, 2023Group: 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

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Assembly

Deposited unit
A: Adenine phosphoribosyltransferase, putative
B: Adenine phosphoribosyltransferase, putative
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,1819
Polymers54,0702
Non-polymers1,1117
Water11,584643
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6930 Å2
ΔGint-34 kcal/mol
Surface area17990 Å2
MethodPISA
Unit cell
Length a, b, c (Å)72.840, 72.850, 85.610
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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Protein / Sugars , 2 types, 4 molecules AB

#1: Protein Adenine phosphoribosyltransferase, putative /


Mass: 27035.182 Da / Num. of mol.: 2 / Fragment: TrbrA.01405.a.B1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Trypanosoma brucei brucei (strain 927/4 GUTat10.1) (eukaryote)
Strain: 927/4 GUTat10.1 / Gene: Tb927.7.1780 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: Q57V32, adenine phosphoribosyltransferase
#3: 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: obtained synthetically / Formula: C5H11O8P
IdentifierTypeProgram
a-D-Ribf5PO3IUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0

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Non-polymers , 4 types, 648 molecules

#2: Chemical ChemComp-ADE / ADENINE / Adenine


Mass: 135.127 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C5H5N5
#4: Chemical ChemComp-PPV / PYROPHOSPHATE / Pyrophosphate


Mass: 177.975 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: H4O7P2
#5: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 643 / 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: 2.1 Å3/Da / Density % sol: 41.6 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: MCSG1 H10 (289135h10): 25% PEG3350, 100mM HEPES:NaOH, pH 7.5, 5mM AMP, 5mM pyrophosphate, protein conc. 23.85mg/mL, cryo 25% ethylene glycol: unique puck ID: xhs1-4

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: Mar 15, 2017
RadiationMonochromator: Diamond [111] / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 1.35→50 Å / Num. obs: 100141 / % possible obs: 99.7 % / Observed criterion σ(I): -3 / Redundancy: 4.877 % / Biso Wilson estimate: 13.47 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.04 / Rrim(I) all: 0.045 / Χ2: 1.052 / Net I/σ(I): 20.54
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
1.35-1.394.8210.5512.5273380.8480.62100
1.39-1.424.8290.4363.2171690.9120.489100
1.42-1.464.8510.3334.2169580.9440.374100
1.46-1.514.8490.2615.4267950.9630.29399.9
1.51-1.564.8710.2096.7965480.9760.23599.9
1.56-1.614.8790.1728.5463760.980.19399.9
1.61-1.674.8930.13910.4161180.9870.15699.9
1.67-1.744.8870.11113.0459330.9910.12599.9
1.74-1.824.8970.08416.8256920.9940.09499.9
1.82-1.914.8990.06521.5854130.9960.07399.8
1.91-2.014.9120.05126.5851680.9980.05799.7
2.01-2.134.9230.04232.2448820.9980.04799.6
2.13-2.284.9020.03636.2846310.9990.04199.7
2.28-2.464.9410.03340.142950.9990.03799.7
2.46-2.74.9210.02943.9239770.9990.03399.4
2.7-3.024.940.02648.536140.9990.02999.4
3.02-3.494.9110.02353.0931660.9990.02699.2
3.49-4.274.8970.02256.9727460.9990.02499
4.27-6.044.8220.02157.2821310.9990.02398.3
6.04-504.4630.02355.0111910.9990.02695

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
XSCALEdata scaling
Cootmodel building
PHENIX(dev_2744)refinement
PDB_EXTRACT3.22data extraction
XDSdata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1qb7

1qb7


Resolution: 1.35→50 Å / SU ML: 0.11 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 16.79
RfactorNum. reflection% reflection
Rfree0.175 2090 2.09 %
Rwork0.1434 --
obs0.144 100130 99.67 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 69.48 Å2 / Biso mean: 21.1722 Å2 / Biso min: 7.42 Å2
Refinement stepCycle: final / Resolution: 1.35→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3629 0 57 656 4342
Biso mean--21.58 33.45 -
Num. residues----469
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0053984
X-RAY DIFFRACTIONf_angle_d1.0185451
X-RAY DIFFRACTIONf_chiral_restr0.09624
X-RAY DIFFRACTIONf_plane_restr0.006694
X-RAY DIFFRACTIONf_dihedral_angle_d19.1031514
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 15

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.35-1.38140.2481150.208465006615100
1.3814-1.41590.2491250.182964586583100
1.4159-1.45420.19711550.161164916646100
1.4542-1.4970.18721270.148864876614100
1.497-1.54530.19591480.13764746622100
1.5453-1.60060.16151240.129664906614100
1.6006-1.66460.16511350.130565296664100
1.6646-1.74040.17241470.130165286675100
1.7404-1.83210.17721390.131865126651100
1.8321-1.94690.16461540.138465056659100
1.9469-2.09720.18161660.138865036669100
2.0972-2.30830.16581210.136365716692100
2.3083-2.64220.1571540.148965746728100
2.6422-3.32860.16821130.15326675678899
3.3286-36.91820.17751670.13846743691098

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