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- PDB-1y0b: Crystal Structure of Xanthine Phosphoribosyltransferase from Baci... -

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Basic information

Entry
Database: PDB / ID: 1y0b
TitleCrystal Structure of Xanthine Phosphoribosyltransferase from Bacillus subtilis.
ComponentsXanthine phosphoribosyltransferase
KeywordsTRANSFERASE / xanthine / purine metabolism / phosphoribosyltransferase / structural genomics / PSI / Protein Structure Initative / Midwest Center for Structural Genomics / MCSG / Protein Structure Initiative
Function / homology
Function and homology information


xanthine metabolic process / xanthine phosphoribosyltransferase / xanthine phosphoribosyltransferase activity / XMP salvage / purine ribonucleoside salvage / cytoplasm
Similarity search - Function
Xanthine phosphoribosyltransferase / Rossmann fold - #2020 / Phosphoribosyl transferase domain / Phosphoribosyltransferase-like / Phosphoribosyltransferase domain / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
GUANOSINE-5',3'-TETRAPHOSPHATE / Xanthine phosphoribosyltransferase
Similarity search - Component
Biological speciesBacillus subtilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.8 Å
AuthorsCuff, M.E. / Wu, R. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published
Title: Crystal Structure of Xanthine Phosphoribosyltransferase from Bacillus subtilis
Authors: Cuff, M.E. / Wu, R. / Joachimiak, A. / MCSG
History
DepositionNov 15, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 22, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software / Item: _software.name
Remark 600HETEROGEN Ligand G4P co-purified and crystallized with the protein. To explain the electron ...HETEROGEN Ligand G4P co-purified and crystallized with the protein. To explain the electron density, the author modeled part of the naturally occurring mononucleotide guanosine 3',5'-bis(diphosphate). The 5' diphosphate was omitted because of poor density.

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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
C: Xanthine phosphoribosyltransferase
D: Xanthine phosphoribosyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)88,50516
Polymers85,9084
Non-polymers2,59712
Water15,133840
1
A: Xanthine phosphoribosyltransferase
B: Xanthine phosphoribosyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,2528
Polymers42,9542
Non-polymers1,2986
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5430 Å2
ΔGint-73 kcal/mol
Surface area15720 Å2
MethodPISA
2
C: Xanthine phosphoribosyltransferase
D: Xanthine phosphoribosyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,2528
Polymers42,9542
Non-polymers1,2986
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5320 Å2
ΔGint-74 kcal/mol
Surface area15780 Å2
MethodPISA
Unit cell
Length a, b, c (Å)42.503, 115.902, 73.985
Angle α, β, γ (deg.)90.00, 94.30, 90.00
Int Tables number4
Space group name H-MP1211
Detailsputative dimer, A and B, C and D

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Components

#1: Protein
Xanthine phosphoribosyltransferase


Mass: 21477.090 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (bacteria) / Gene: xpt / Plasmid: pMCSG7 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21
References: UniProt: P42085, Transferases; Glycosyltransferases; Pentosyltransferases
#2: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Na
#3: Chemical
ChemComp-G4P / GUANOSINE-5',3'-TETRAPHOSPHATE


Type: RNA linking / Mass: 603.160 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H17N5O17P4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 840 / 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: 2.2 Å3/Da / Density % sol: 42.6 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: Bis-tris, NaCl, PEG3350, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 150 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97981,0.97995, 0.990
DetectorType: CUSTOM-MADE / Detector: CCD / Date: Feb 18, 2003 / Details: SBC2
RadiationMonochromator: SAGITALLY FOCUSED Si(111) / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.979811
20.979951
30.991
ReflectionResolution: 1.8→34.23 Å / Num. all: 58399 / Num. obs: 58399 / % possible obs: 88.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0
Reflection shellResolution: 1.8→1.846 Å / % possible all: 49.66

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
d*TREKdata reduction
HKL-2000data scaling
SOLVEphasing
autoSHARPphasing
RefinementMethod to determine structure: MAD / Resolution: 1.8→20 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.924 / SU B: 5.194 / SU ML: 0.084 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.167 / ESU R Free: 0.152 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22818 2903 5 %RANDOM
Rwork0.17831 ---
all0.1807 55482 --
obs0.1807 55482 88.48 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 22.097 Å2
Baniso -1Baniso -2Baniso -3
1--0.82 Å20 Å20.48 Å2
2---1.44 Å20 Å2
3---2.34 Å2
Refinement stepCycle: LAST / Resolution: 1.8→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5837 0 120 840 6797
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0226027
X-RAY DIFFRACTIONr_angle_refined_deg1.8531.9968154
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.4665762
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.40625.167240
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.666151094
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.1761528
X-RAY DIFFRACTIONr_chiral_restr0.1670.2987
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.024316
X-RAY DIFFRACTIONr_nbd_refined0.1940.22794
X-RAY DIFFRACTIONr_nbtor_refined0.2970.24111
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1080.2784
X-RAY DIFFRACTIONr_metal_ion_refined0.1460.230
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1570.255
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0960.284
X-RAY DIFFRACTIONr_mcbond_it0.4421.53790
X-RAY DIFFRACTIONr_mcangle_it0.84526105
X-RAY DIFFRACTIONr_scbond_it1.53632277
X-RAY DIFFRACTIONr_scangle_it2.4884.52049
LS refinement shellResolution: 1.8→1.846 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.224 135 -
Rwork0.176 2289 -
obs--49.66 %
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)
11.4524-0.4233-0.39271.66680.38630.8266-0.030.1018-0.0685-0.01-0.00890.0811-0.0058-0.04730.039-0.062-0.01450.0061-0.0411-0.011-0.0451-4.927540.074536.2427
21.139-0.6604-0.27482.24020.42940.5441-0.01930.04390.10610.06750.0143-0.0196-0.0334-0.05730.005-0.0403-0.0033-0.003-0.05120.0111-0.0632-1.581164.556638.5259
31.85690.05910.66721.80250.40710.9591-0.0099-0.09940.0866-0.0055-0.03910.01760.0182-0.03710.049-0.06860.0076-0.0024-0.0326-0.0128-0.075313.167754.605674.6583
41.06740.01120.53112.2260.46440.58460.0306-0.0719-0.0622-0.1257-0.03720.14450.0144-0.06510.0066-0.0262-0.0004-0.0171-0.03010.0144-0.085516.902330.537572.1461
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA-1 - 1912 - 194
2X-RAY DIFFRACTION1AE - M886 - 8881
3X-RAY DIFFRACTION2BB-2 - 1921 - 195
4X-RAY DIFFRACTION2BG - N886 - 8881
5X-RAY DIFFRACTION3CC-2 - 1891 - 192
6X-RAY DIFFRACTION3CI - O886 - 8881
7X-RAY DIFFRACTION4DD-2 - 1911 - 194
8X-RAY DIFFRACTION4DK - P886 - 8881

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