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

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Basic information

Entry
Database: PDB / ID: 1qcc
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
CITRIC ACID / adenine phosphoribosyltransferase
Similarity search - Component
Biological speciesLeishmania donovani (eukaryote)
MethodX-RAY DIFFRACTION / Resolution: 1.98 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)26,2892
Polymers26,0971
Non-polymers1921
Water3,873215
1
A: ADENINE PHOSPHORIBOSYLTRANSFERASE
hetero molecules

A: ADENINE PHOSPHORIBOSYLTRANSFERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,5784
Polymers52,1942
Non-polymers3842
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation12_555x,x-y,-z+1/61
Buried area6220 Å2
ΔGint-35 kcal/mol
Surface area21200 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)63.757, 63.757, 236.617
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-CIT / CITRIC ACID


Mass: 192.124 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H8O7
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 215 / 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: 2.66 Å3/Da / Density % sol: 53.73 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 5
Details: REG 5000 MME, AMMONIUM ACETATE, SODIUM CITRATE, MAGNESIUM CHLORIDE, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 277.0K
Crystal grow
*PLUS
Temperature: 4 ℃ / pH: 6
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
110 mg/mlprotein1drop
210 mMMES1drop
31 mMdithiothreitol1drop
45 mM1dropMgCl2
57-11 %mPEG50001reservoir
60.2 Mammonium acetate1reservoir
70.1 Msodium citrate1reservoir
810 mM1reservoirMgCl2

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Feb 1, 1997
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionBiso Wilson estimate: 22.3 Å2
Reflection
*PLUS
Highest resolution: 1.98 Å / Lowest resolution: 19.7 Å / Num. obs: 19055 / % possible obs: 91.5 % / Num. measured all: 349744 / Rmerge(I) obs: 0.051
Reflection shell
*PLUS
% possible obs: 61.3 % / Rmerge(I) obs: 0.124 / Mean I/σ(I) obs: 10.2

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Processing

Software
NameVersionClassification
PHASESphasing
X-PLOR3.843refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementResolution: 1.98→19.7 Å / Rfactor Rfree error: 0.006 / 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
Rfree0.241 1892 9.9 %RANDOM
Rwork0.187 ---
obs-19055 91.5 %-
Displacement parametersBiso mean: 23.8 Å2
Baniso -1Baniso -2Baniso -3
1-0.08 Å2-0.57 Å20 Å2
2--0.08 Å20 Å2
3----0.16 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.26 Å0.21 Å
Luzzati d res low-8 Å
Luzzati sigma a0.16 Å0.19 Å
Refinement stepCycle: LAST / Resolution: 1.98→19.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1836 0 13 215 2064
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.006
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_deg1.4
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
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: 1.98→2.1 Å / Rfactor Rfree error: 0.02 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.298 217 10.6 %
Rwork0.284 1837 -
obs--61.3 %
Software
*PLUS
Name: X-PLOR / Version: 3.843 / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_deg24.7
X-RAY DIFFRACTIONx_improper_angle_deg1.21

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