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- PDB-1qcd: CRYSTAL STRUCTURES OF ADENINE PHOSPHORIBOSYLTRANSFERASE FROM LEIS... -

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Basic information

Entry
Database: PDB / ID: 1qcd
TitleCRYSTAL STRUCTURES OF ADENINE PHOSPHORIBOSYLTRANSFERASE FROM LEISHMANIA DONOVANI
ComponentsADENINE PHOSPHORIBOSYLTRANSFERASE
KeywordsTRANSFERASE / DINUCLEOTIDE BINDING FOLD
Function / homology
Function and homology information


adenine phosphoribosyltransferase / adenine phosphoribosyltransferase activity / purine ribonucleoside salvage / nucleotide binding / metal ion binding / 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 phosphoribosyltransferase
Similarity search - Component
Biological speciesLeishmania donovani (eukaryote)
MethodX-RAY DIFFRACTION / Resolution: 2.48 Å
AuthorsPhillips, C.L. / Ullman, B. / Brennan, R.G. / Hill, C.P.
CitationJournal: EMBO J. / Year: 1999
Title: Crystal structures of adenine phosphoribosyltransferase from Leishmania donovani.
Authors: Phillips, C.L. / Ullman, B. / Brennan, R.G. / Hill, C.P.
History
DepositionMay 1, 1999Deposition site: RCSB / Processing site: NDB
Revision 1.0Jul 21, 1999Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / 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

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Assembly

Deposited unit
A: ADENINE PHOSPHORIBOSYLTRANSFERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,2893
Polymers26,0971
Non-polymers1922
Water2,594144
1
A: ADENINE PHOSPHORIBOSYLTRANSFERASE
hetero molecules

A: ADENINE PHOSPHORIBOSYLTRANSFERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,5786
Polymers52,1942
Non-polymers3844
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation12_555x,x-y,-z+1/61
Buried area6170 Å2
ΔGint-105 kcal/mol
Surface area21810 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)64.040, 64.040, 240.530
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122

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Components

#1: Protein ADENINE PHOSPHORIBOSYLTRANSFERASE / APRT


Mass: 26096.920 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Leishmania donovani (eukaryote) / Production host: Escherichia coli (E. coli) / References: UniProt: Q27679
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 144 / 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: 3

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Sample preparation

CrystalDensity Matthews: 2.73 Å3/Da / Density % sol: 54.88 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 4.9
Details: AMMONIUM SULFATE, SODIUM CITRATE, MAGNESIUM CHLORIDE, pH 4.9, VAPOR DIFFUSION, HANGING DROP, temperature 277.0K
Crystal grow
*PLUS
pH: 6
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
110 mg/mlprotein1drop
210 mMMES1drop
31 mMdithiothreitol1drop
45 mM1dropMgCl2
51.2-1.6 Mammonium sulfate1reservoir
60.1 Msodium citrate1reservoir
710 mM1reservoirMgCl2

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418
DetectorType: OTHER / Detector: AREA DETECTOR / Date: Sep 1, 1995
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionBiso Wilson estimate: 40.7 Å2
Reflection
*PLUS
Highest resolution: 2.48 Å / Lowest resolution: 18.6 Å / Num. obs: 9680 / % possible obs: 87.2 % / Num. measured all: 33527 / Rmerge(I) obs: 0.06
Reflection shell
*PLUS
% possible obs: 50.1 % / Rmerge(I) obs: 0.149 / Mean I/σ(I) obs: 4.5

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Processing

Software
NameVersionClassification
PHASESphasing
X-PLOR3.843refinement
SDMSdata reduction
SDMSdata scaling
RefinementResolution: 2.48→18.57 Å / Rfactor Rfree error: 0.008 / Data cutoff high absF: 10000000 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.25 1005 10.4 %RANDOM
Rwork0.174 ---
obs-9680 87.2 %-
Displacement parametersBiso mean: 32.4 Å2
Baniso -1Baniso -2Baniso -3
1--0.06 Å2-0.33 Å20 Å2
2---0.06 Å20 Å2
3---0.12 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.33 Å0.23 Å
Luzzati d res low-8 Å
Luzzati sigma a0.38 Å0.3 Å
Refinement stepCycle: LAST / Resolution: 2.48→18.57 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1836 0 10 144 1990
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.007
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.3
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d24.9
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.13
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
LS refinement shellResolution: 2.48→2.64 Å / Rfactor Rfree error: 0.03 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.339 127 11.3 %
Rwork0.277 996 -
obs--63.2 %
Software
*PLUS
Name: X-PLOR / Version: 3.843 / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg24.9
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.13

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