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- PDB-6kp5: crystal structure of Xanthine-guanine phosphoribosyltransferase (... -

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Basic information

Entry
Database: PDB / ID: 6kp5
Titlecrystal structure of Xanthine-guanine phosphoribosyltransferase (XGPRT) from Yersinia pestis in P21212 space group with sulphate ions in the active site
ComponentsXanthine phosphoribosyltransferase
KeywordsTRANSFERASE / xanthine-guanine phosphoribosyltransferase / Yersinia pestis
Function / homology
Function and homology information


xanthine phosphoribosyltransferase / XMP salvage / xanthine phosphoribosyltransferase activity / GMP salvage / guanine phosphoribosyltransferase activity / hypoxanthine phosphoribosyltransferase activity / IMP salvage / purine ribonucleoside salvage / Transferases; Glycosyltransferases; Pentosyltransferases / magnesium ion binding ...xanthine phosphoribosyltransferase / XMP salvage / xanthine phosphoribosyltransferase activity / GMP salvage / guanine phosphoribosyltransferase activity / hypoxanthine phosphoribosyltransferase activity / IMP salvage / purine ribonucleoside salvage / Transferases; Glycosyltransferases; Pentosyltransferases / magnesium ion binding / plasma membrane / cytosol
Similarity search - Function
Xanthine-guanine phosphoribosyltransferase / 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
Xanthine-guanine phosphoribosyltransferase
Similarity search - Component
Biological speciesYersinia pestis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.1 Å
AuthorsLankipalli, S. / Ramagopal, U.A.
CitationJournal: To be published
Title: crystal structure of Xanthine-guanine phosphoribosyltransferase (XGPRT) from Yersinia pestis in P21212 space group
Authors: Lankipalli, S. / Ramagopal, U.A.
History
DepositionAug 14, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 25, 2019Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _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: Xanthine phosphoribosyltransferase
B: Xanthine phosphoribosyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,5296
Polymers34,1452
Non-polymers3844
Water4,107228
1
A: Xanthine phosphoribosyltransferase
B: Xanthine phosphoribosyltransferase
hetero molecules

A: Xanthine phosphoribosyltransferase
B: Xanthine phosphoribosyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,05912
Polymers68,2904
Non-polymers7698
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
Buried area12180 Å2
ΔGint-146 kcal/mol
Surface area21020 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.320, 94.630, 51.670
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11A-344-

HOH

21A-396-

HOH

31B-397-

HOH

41B-404-

HOH

51B-412-

HOH

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Components

#1: Protein Xanthine phosphoribosyltransferase / / Xanthine-guanine phosphoribosyltransferase / XGPRT


Mass: 17072.594 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Yersinia pestis (bacteria) / Gene: gpt, YPO3225, y0963, YP_0708 / Plasmid: pNIC28-Bsa4 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: Q8ZC05, xanthine phosphoribosyltransferase
#2: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 228 / Source method: isolated from a natural source / Formula: H2O
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: 2.09 Å3/Da / Density % sol: 41.09 % / Mosaicity: 0.23 °
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.2M Lithium sulphate, 0.1M Tris:HCl pH 8.5, 1.26M Ammonium Sulfate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ELETTRA / Beamline: 11.2C / Wavelength: 0.9762 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 6, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9762 Å / Relative weight: 1
ReflectionResolution: 1.1→47.32 Å / Num. obs: 116357 / % possible obs: 99.9 % / Redundancy: 11.3 % / CC1/2: 0.998 / Rmerge(I) obs: 0.112 / Rpim(I) all: 0.035 / Rrim(I) all: 0.117 / Net I/σ(I): 10.4
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
1.1-1.1210.81.07756720.8290.3381.1399.7
6.02-47.329.90.0558290.9940.0180.05899.8

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Processing

Software
NameVersionClassification
REFMAC5.8.0238refinement
Aimless0.7.3data scaling
PDB_EXTRACT3.25data extraction
iMOSFLMdata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5XTK

5xtk


Resolution: 1.1→47.315 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.963 / SU B: 1.346 / SU ML: 0.029 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.031 / ESU R Free: 0.031
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1864 5934 5.1 %RANDOM
Rwork0.1618 ---
obs0.163 110114 99.6 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 66.01 Å2 / Biso mean: 12.589 Å2 / Biso min: 5.62 Å2
Baniso -1Baniso -2Baniso -3
1--2.36 Å20 Å2-0 Å2
2--1.32 Å2-0 Å2
3---1.04 Å2
Refinement stepCycle: final / Resolution: 1.1→47.315 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2139 0 20 229 2388
Biso mean--24.6 20.73 -
Num. residues----277
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0132322
X-RAY DIFFRACTIONr_bond_other_d0.0050.0172246
X-RAY DIFFRACTIONr_angle_refined_deg2.1531.6373181
X-RAY DIFFRACTIONr_angle_other_deg1.6021.5775170
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6645296
X-RAY DIFFRACTIONr_dihedral_angle_2_deg28.16520.561107
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.18715383
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.8411518
X-RAY DIFFRACTIONr_chiral_restr0.1130.2308
X-RAY DIFFRACTIONr_gen_planes_refined0.0150.022600
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02502
X-RAY DIFFRACTIONr_rigid_bond_restr6.53534568
LS refinement shellResolution: 1.1→1.129 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.218 433 -
Rwork0.234 7995 -
all-8428 -
obs--99.29 %

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