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- PDB-6kqc: Crystal structure of E136F mutant of Xanthine-guanine phosphoribo... -

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Basic information

Entry
Database: PDB / ID: 6kqc
TitleCrystal structure of E136F mutant of Xanthine-guanine phosphoribosyltransferase from Yersinia pestis
ComponentsXanthine phosphoribosyltransferase
KeywordsTRANSFERASE / E136F mutant / xanthine-guanine phosphoribosyltransferase / Yersinia pestis
Function / homology
Function and homology information


xanthine phosphoribosyltransferase / XMP salvage / xanthine phosphoribosyltransferase activity / guanine phosphoribosyltransferase activity / GMP salvage / hypoxanthine phosphoribosyltransferase activity / IMP salvage / purine ribonucleoside salvage / Transferases; Glycosyltransferases; Pentosyltransferases / magnesium ion binding ...xanthine phosphoribosyltransferase / XMP salvage / xanthine phosphoribosyltransferase activity / guanine phosphoribosyltransferase activity / GMP salvage / 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: 1.7 Å
AuthorsLankipalli, S. / Ramagopal, U.A.
CitationJournal: To be published
Title: Crystal structure of E136F mutant of Xanthine-guanine phosphoribosyltransferase from Yersinia pestis
Authors: Lankipalli, S. / Ramagopal, U.A.
History
DepositionAug 16, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 11, 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)34,3806
Polymers34,1812
Non-polymers1984
Water2,324129
1
A: Xanthine phosphoribosyltransferase
B: Xanthine phosphoribosyltransferase
hetero molecules

A: Xanthine phosphoribosyltransferase
B: Xanthine phosphoribosyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,76012
Polymers68,3634
Non-polymers3978
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,-y,z1
Buried area11860 Å2
ΔGint-123 kcal/mol
Surface area22360 Å2
MethodPISA
Unit cell
Length a, b, c (Å)56.380, 96.650, 51.029
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212

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Components

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


Mass: 17090.654 Da / Num. of mol.: 2 / Mutation: E136F
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-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 129 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.03 Å3/Da / Density % sol: 39.52 % / Mosaicity: 1.2 °
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 0.2M Lithium chloride, 20% (w/v) PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 1.072 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Dec 3, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.072 Å / Relative weight: 1
ReflectionResolution: 1.7→37.86 Å / Num. obs: 30317 / % possible obs: 97 % / Redundancy: 3.8 % / CC1/2: 0.993 / Rmerge(I) obs: 0.113 / Rpim(I) all: 0.063 / Rrim(I) all: 0.131 / Net I/σ(I): 7.1
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
1.7-1.733.90.603618015930.4620.3340.6952.299
9-37.8340.0349972470.9960.0190.03917.594.4

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Processing

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

5xtk


Resolution: 1.7→37.86 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.942 / SU B: 5.361 / SU ML: 0.082 / Cross valid method: THROUGHOUT / ESU R: 0.11 / ESU R Free: 0.106
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.212 1484 4.9 %RANDOM
Rwork0.1804 ---
obs0.182 28789 96.36 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 54.22 Å2 / Biso mean: 15.591 Å2 / Biso min: 9.16 Å2
Baniso -1Baniso -2Baniso -3
1-0.19 Å20 Å2-0 Å2
2---0.52 Å2-0 Å2
3---0.32 Å2
Refinement stepCycle: final / Resolution: 1.7→37.86 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2187 0 15 129 2331
Biso mean--22.39 22.79 -
Num. residues----283
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0132264
X-RAY DIFFRACTIONr_bond_other_d0.0010.0172199
X-RAY DIFFRACTIONr_angle_refined_deg1.8541.6373086
X-RAY DIFFRACTIONr_angle_other_deg1.4791.5785060
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.1115285
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.06421.226106
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.80215365
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.1461516
X-RAY DIFFRACTIONr_chiral_restr0.0970.2304
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.022509
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02479
LS refinement shellResolution: 1.7→1.744 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.327 91 -
Rwork0.293 2125 -
all-2216 -
obs--98.49 %
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)
10.2680.228-0.0810.6172-0.31160.19180.0138-0.0084-0.01170.05040.00730.0354-0.0257-0.0168-0.02110.00420.00060.00420.0058-0.00340.033518.0691-11.8679-3.7104
20.42690.39570.02540.74470.20390.1610.01460.04150.0131-0.0180.00180.0415-0.0011-0.009-0.01640.00550.0055-0.0080.00870.00070.048715.6717-14.7942-23.499
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A3 - 201
2X-RAY DIFFRACTION2B2 - 301

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