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- PDB-7cmj: Crystal structure of L.donovani Hypoxanthine-guanine phosphoribos... -

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Basic information

Entry
Database: PDB / ID: 7cmj
TitleCrystal structure of L.donovani Hypoxanthine-guanine phosphoribosyl transferase (HGPRT)
ComponentsHypoxanthine phosphoribosyltransferase
KeywordsTRANSFERASE / hypoxanthine / guanine / phosphoribosyl / complex / tetramer.
Function / homology
Function and homology information


hypoxanthine phosphoribosyltransferase / guanine phosphoribosyltransferase activity / hypoxanthine phosphoribosyltransferase activity / IMP salvage / purine ribonucleoside salvage / nucleotide binding / metal ion binding / cytoplasm
Similarity search - Function
Hypoxanthine phosphoribosyl transferase / : / Phosphoribosyl transferase domain / Phosphoribosyltransferase-like / Phosphoribosyltransferase domain
Similarity search - Domain/homology
: / DI(HYDROXYETHYL)ETHER / PHOSPHATE ION / Hypoxanthine phosphoribosyltransferase
Similarity search - Component
Biological speciesLeishmania donovani (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.76 Å
AuthorsParihar, P.S. / Pratap, J.V.
CitationJournal: Biochem.Biophys.Res.Commun. / Year: 2020
Title: The L.donovani Hypoxanthine-guanine phosphoribosyl transferase (HGPRT) oligomer is distinct from the human homolog.
Authors: Parihar, P.S. / Pratap, J.V.
History
DepositionJul 27, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 4, 2021Provider: repository / Type: Initial release
Revision 1.1Feb 15, 2023Group: Database references / Category: citation / database_2
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Hypoxanthine phosphoribosyltransferase
B: Hypoxanthine phosphoribosyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,27513
Polymers47,2852
Non-polymers99111
Water1,964109
1
A: Hypoxanthine phosphoribosyltransferase
B: Hypoxanthine phosphoribosyltransferase
hetero molecules

A: Hypoxanthine phosphoribosyltransferase
B: Hypoxanthine phosphoribosyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)96,55126
Polymers94,5694
Non-polymers1,98122
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation12_564x,x-y+1,-z-1/61
Buried area16650 Å2
ΔGint-111 kcal/mol
Surface area24850 Å2
MethodPISA
Unit cell
Length a, b, c (Å)80.800, 80.800, 344.321
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Hypoxanthine phosphoribosyltransferase


Mass: 23642.365 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: unlined residue have missing electron density, side chain of some residue also missing are with removed side chain.
Source: (gene. exp.) Leishmania donovani (strain BPK282A1) (eukaryote)
Strain: BPK282A1 / Gene: LDBPK_210980 / Production host: Escherichia coli BL21 (bacteria)
References: UniProt: E9BF84, hypoxanthine phosphoribosyltransferase

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Non-polymers , 7 types, 120 molecules

#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-BA / BARIUM ION


Mass: 137.327 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ba / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3 / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18O5 / Feature type: SUBJECT OF INVESTIGATION / Comment: precipitant*YM
#7: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl / Feature type: SUBJECT OF INVESTIGATION
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 109 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 3.64 Å3/Da / Density % sol: 70.39 %
Crystal growTemperature: 288 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.1M Sodium cacodylate, 0.2 M Ammonium sulfate, 20% PEG 4000
PH range: 6-7

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ELETTRA / Beamline: 11.2C / Wavelength: 0.9784 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 13, 2019 / Details: Monochromator
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9784 Å / Relative weight: 1
ReflectionResolution: 2.76→44.373 Å / Num. obs: 17049 / % possible obs: 93.7 % / Redundancy: 1.9 % / Biso Wilson estimate: 52.65 Å2 / Rmerge(I) obs: 0.04166 / Net I/σ(I): 10.15
Reflection shellResolution: 2.76→2.86 Å / Redundancy: 1.8 % / Rmerge(I) obs: 0.2919 / Num. unique obs: 1731 / % possible all: 98.1

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Processing

Software
NameVersionClassification
PHENIX(1.13_2998: ???)refinement
iMOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1PZM

1pzm


Resolution: 2.76→44.37 Å / SU ML: 0.34 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 22.91 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.225 864 5.07 %
Rwork0.181 --
obs0.183 17043 93.8 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.76→44.37 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2729 0 43 109 2881
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0082810
X-RAY DIFFRACTIONf_angle_d0.9333819
X-RAY DIFFRACTIONf_dihedral_angle_d10.591682
X-RAY DIFFRACTIONf_chiral_restr0.054465
X-RAY DIFFRACTIONf_plane_restr0.005472
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.76-2.93290.3151550.25392715X-RAY DIFFRACTION98
2.9329-3.15930.24081390.20892733X-RAY DIFFRACTION98
3.1593-3.47710.23581190.17582494X-RAY DIFFRACTION88
3.4771-3.980.23491320.16052388X-RAY DIFFRACTION84
3.98-5.01330.18371780.13782848X-RAY DIFFRACTION99
5.0133-40.240.23571410.20873001X-RAY DIFFRACTION96
Refinement TLS params.Method: refined / Origin x: -31.4031 Å / Origin y: 31.0988 Å / Origin z: -11.5201 Å
111213212223313233
T0.281 Å2-0.087 Å20.0064 Å2-0.4029 Å2-0.0481 Å2--0.2915 Å2
L2.0052 °20.3551 °2-0.3402 °2-1.6103 °20.3984 °2--2.7227 °2
S0.0597 Å °-0.1876 Å °0.0164 Å °0.1039 Å °0.0159 Å °-0.0135 Å °0.1301 Å °-0.0753 Å °-0.0774 Å °
Refinement TLS groupSelection details: ALL

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