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- PDB-5xtk: Crystal structure of Xanthine-guanine phosphoribosyltransferase f... -

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Basic information

Entry
Database: PDB / ID: 5xtk
TitleCrystal structure of Xanthine-guanine phosphoribosyltransferase from Yersinia pestis
ComponentsXanthine phosphoribosyltransferase
KeywordsTRANSFERASE
Function / homology
Function and homology information


xanthine phosphoribosyltransferase / XMP salvage / xanthine phosphoribosyltransferase activity / guanine phosphoribosyltransferase activity / hypoxanthine phosphoribosyltransferase activity / GMP salvage / IMP salvage / purine ribonucleoside salvage / Transferases; Glycosyltransferases; Pentosyltransferases / magnesium ion binding ...xanthine phosphoribosyltransferase / XMP salvage / xanthine phosphoribosyltransferase activity / guanine phosphoribosyltransferase activity / hypoxanthine phosphoribosyltransferase activity / GMP salvage / 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
GUANOSINE-5'-MONOPHOSPHATE / Xanthine-guanine phosphoribosyltransferase
Similarity search - Component
Biological speciesYersinia pestis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.74 Å
AuthorsPavithra, G.C. / Ramagopal, U.A.
CitationJournal: To be published
Title: Crystal structure of Xanthine-guanine phosphoribosyltransferase from Yersinia pestis
Authors: Pavithra, G.C. / Ramagopal, U.A.
History
DepositionJun 19, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 20, 2018Provider: repository / Type: Initial release
Revision 1.1Oct 16, 2019Group: Data collection / Category: reflns / Item: _reflns.pdbx_CC_half
Revision 1.2Oct 23, 2019Group: Data collection / Category: reflns / Item: _reflns.pdbx_CC_half
Revision 1.3Nov 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
Revision 2.0Jul 1, 2026Group: Atomic model / Data collection / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp_atom / chem_comp_bond / pdbx_entry_details
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_atom.atom_id / _chem_comp_bond.atom_id_1 / _chem_comp_bond.atom_id_2

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)34,4304
Polymers33,9712
Non-polymers4592
Water3,207178
1
A: Xanthine phosphoribosyltransferase
B: Xanthine phosphoribosyltransferase
hetero molecules

A: Xanthine phosphoribosyltransferase
B: Xanthine phosphoribosyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,8618
Polymers67,9424
Non-polymers9194
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555-x,y,-z1
Buried area12480 Å2
ΔGint-99 kcal/mol
Surface area24180 Å2
MethodPISA
Unit cell
Length a, b, c (Å)66.557, 66.557, 165.379
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number95
Space group name H-MP4322
Components on special symmetry positions
IDModelComponents
11A-461-

HOH

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Components

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


Mass: 16985.516 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: LIC-PET30A / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: Q8ZC05, xanthine phosphoribosyltransferase
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-5GP / GUANOSINE-5'-MONOPHOSPHATE


Mass: 363.221 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H14N5O8P
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 178 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationN

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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: 2.7 Å3/Da / Density % sol: 54.37 % / Mosaicity: 0.433 °
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.2M Lithium sulphate, 25% PEG 3350, 0.1M HEPES pH 7.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1.074 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 20, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.074 Å / Relative weight: 1
ReflectionResolution: 1.74→66.56 Å / Num. obs: 39181 / % possible obs: 99.9 % / Redundancy: 14.4 % / Biso Wilson estimate: 15.5 Å2 / CC1/2: 0.987 / Rmerge(I) obs: 0.067 / Rpim(I) all: 0.018 / Rrim(I) all: 0.069 / Rsym value: 0.054 / Χ2: 0.926 / Net I/av σ(I): 39.05 / Net I/σ(I): 10.6
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allRsym valueΧ2% possible all
1.74-1.7710.50.5843.7418930.9230.1860.6140.4910.72998.8
1.77-1.813.10.4960.9520.140.5160.795100
1.8-1.84150.4190.9770.1110.4340.811100
1.84-1.8714.80.350.9780.0930.3620.853100
1.87-1.9214.80.310.9860.0830.3210.896100
1.92-1.9614.70.2610.9860.070.2710.943100
1.96-2.0114.80.2070.9910.0550.2150.963100
2.01-2.0614.70.1790.9930.0480.1860.987100
2.06-2.1214.70.1520.9940.0410.1581.033100
2.12-2.1914.70.1310.9950.0350.1361.017100
2.19-2.2714.60.1180.9960.0320.1221.038100
2.27-2.3614.60.1040.9970.0280.1080.998100
2.36-2.4714.70.0920.9970.0250.0950.985100
2.47-2.614.70.0770.9980.0210.080.97100
2.6-2.7614.60.0680.9980.0180.0710.936100
2.76-2.9814.70.0630.9980.0170.0660.938100
2.98-3.2714.50.0610.9980.0170.0631.113100
3.27-3.7514.20.0570.9990.0160.0591.192100
3.75-4.7214.10.0420.9990.0120.0440.806100
4.72-66.5314.30.0320.9990.0090.0330.48399.6

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
SCALEPACKdata scaling
PDB_EXTRACT3.22data extraction
DENZOdata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1NUL

1nul


Resolution: 1.74→66.56 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.946 / SU B: 3.328 / SU ML: 0.055 / Cross valid method: THROUGHOUT / ESU R: 0.093 / ESU R Free: 0.093 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19654 1931 5 %RANDOM
Rwork0.16626 ---
obs0.16773 37024 99.43 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 20.616 Å2
Baniso -1Baniso -2Baniso -3
1--0.2 Å20 Å20 Å2
2---0.2 Å20 Å2
3---0.41 Å2
Refinement stepCycle: 1 / Resolution: 1.74→66.56 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2337 0 29 178 2544
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0192506
X-RAY DIFFRACTIONr_bond_other_d0.0010.022386
X-RAY DIFFRACTIONr_angle_refined_deg1.841.9693436
X-RAY DIFFRACTIONr_angle_other_deg0.79535505
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4955320
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.03923.241108
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.42115412
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.9561521
X-RAY DIFFRACTIONr_chiral_restr0.110.2393
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0212794
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02523
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.2941.621232
X-RAY DIFFRACTIONr_mcbond_other1.2671.6171231
X-RAY DIFFRACTIONr_mcangle_it2.1392.4161547
X-RAY DIFFRACTIONr_mcangle_other2.1412.4181548
X-RAY DIFFRACTIONr_scbond_it1.7491.8921274
X-RAY DIFFRACTIONr_scbond_other1.7491.8941275
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.8172.7371883
X-RAY DIFFRACTIONr_long_range_B_refined4.1619.022762
X-RAY DIFFRACTIONr_long_range_B_other4.0918.7482718
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.739→1.784 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.223 118 -
Rwork0.187 2514 -
obs--93.5 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.1169-0.04340.13540.2086-0.08670.22020.0341-0.0247-0.045-0.02380.02370.044-0.0045-0.0623-0.05770.04570.0178-0.01370.02810.0090.0234-13.7236-28.1016-15.1247
20.04680.01450.0580.3812-0.0330.2930.02740.0202-0.0134-0.05990.0094-0.07110.00010.0252-0.03680.03710.01330.00960.0196-0.00960.02086.9307-31.7346-19.5378
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA2 - 475
2X-RAY DIFFRACTION2allB2 - 283

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