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- PDB-6w1i: Re-interpretation of ppGpp (G4P) electron density in the deposite... -

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Basic information

Entry
Database: PDB / ID: 6w1i
TitleRe-interpretation of ppGpp (G4P) electron density in the deposited crystal structure of Xanthine phosphoribosyltransferase (XPRT) (1Y0B).
ComponentsXanthine phosphoribosyltransferase
KeywordsTRANSFERASE / (p)ppGpp / salvage / GTP / homeostasis / XPRT / PRPP / purine / Structural Genomics / PSI-2 / Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG
Function / homology
Function and homology information


xanthine metabolic process / xanthine phosphoribosyltransferase / XMP salvage / xanthine phosphoribosyltransferase activity / purine ribonucleoside salvage / cytoplasm
Similarity search - Function
Xanthine phosphoribosyltransferase / : / Phosphoribosyl transferase domain / Phosphoribosyltransferase-like / Phosphoribosyltransferase domain
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
AuthorsSatyshur, K.A. / Anderson, B.W. / Keck, J.L. / Midwest Center for Structural Genomics (MCSG)
Funding support United States, 3items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM62414 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35 GM127088 United States
National Science Foundation (NSF, United States)GRFP DGE-1256259 United States
CitationJournal: To Be Published
Title: Crystal Structure of Xanthine Phosphoribosyltransferase from Bacillus subtilis
Authors: Cuff, M.E. / Wu, R. / Joachimiak, A. / MCSG
History
DepositionMar 4, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 29, 2020Provider: repository / Type: Initial release
Revision 1.1Apr 7, 2021Group: Data collection / Category: reflns / Item: _reflns.pdbx_redundancy
Revision 1.2Oct 23, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_entry_details.has_protein_modification
Remark 0THIS ENTRY 6W1I REFLECTS AN ALTERNATIVE MODELING OF THE ORIGINAL DATA IN 1Y0B, DETERMINED BY Cuff, ...THIS ENTRY 6W1I REFLECTS AN ALTERNATIVE MODELING OF THE ORIGINAL DATA IN 1Y0B, DETERMINED BY Cuff, M.E., Wu, R., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

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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
Water13,493749
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: native gel electrophoresis
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)42.503, 115.902, 73.985
Angle α, β, γ (deg.)90.000, 94.300, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

#1: Protein
Xanthine phosphoribosyltransferase / XPRTase


Mass: 21477.090 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (strain 168) (bacteria)
Strain: 168 / Gene: xpt, BSU22070 / Production host: Escherichia coli (E. coli)
References: UniProt: P42085, xanthine phosphoribosyltransferase
#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 / guanosine tetraphosphate;ppGpp


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


Mass: 18.015 Da / Num. of mol.: 749 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

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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: 2.12 Å3/Da / Density % sol: 41.85 % / Description: Author used the SF data from the entry 1Y0B
Crystal growTemperature: 100 K / Method: vapor diffusion, hanging drop / Details: BIS-TRIS, NaCl, PEG3350, PH 5.5

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Data collection

DiffractionMean temperature: 198 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9798 Å
DetectorType: CUSTOM-MADE / Detector: CCD / Date: Feb 18, 2003
RadiationMonochromator: SAGITALLY FOCUSED SI(111) / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9798 Å / Relative weight: 1
ReflectionResolution: 1.8→34.23 Å / Num. obs: 58401 / % possible obs: 88.5 % / Observed criterion σ(I): 0 / Biso Wilson estimate: 19.3 Å2 / CC1/2: 1 / Net I/σ(I): 0
Reflection shellResolution: 1.8→1.85 Å / Rmerge(I) obs: 0.1 / Mean I/σ(I) obs: 0.1 / Num. unique obs: 600000 / CC1/2: 1 / Rsym value: 0.1 / % possible all: 49.7

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Processing

Software
NameVersionClassification
d*TREKdata reduction
HKL-2000data scaling
SOLVEphasing
SHARPphasing
PHENIX1.17.1_3660refinement
RefinementMethod to determine structure: MAD / Resolution: 1.8→34.23 Å / SU ML: 0.1659 / Cross valid method: FREE R-VALUE / σ(F): 1.2 / Phase error: 20.4997
RfactorNum. reflection% reflection
Rfree0.2083 2904 4.97 %
Rwork0.1598 --
obs0.1621 58401 88.45 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 24.69 Å2
Refinement stepCycle: LAST / Resolution: 1.8→34.23 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5811 0 152 749 6712
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00546031
X-RAY DIFFRACTIONf_angle_d0.89598183
X-RAY DIFFRACTIONf_chiral_restr0.0567984
X-RAY DIFFRACTIONf_plane_restr0.00351022
X-RAY DIFFRACTIONf_dihedral_angle_d20.0458863
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8-1.830.2341840.19431455X-RAY DIFFRACTION49.08
1.83-1.860.2255860.17451574X-RAY DIFFRACTION52.68
1.86-1.890.20111070.18541747X-RAY DIFFRACTION59.79
1.89-1.930.26941110.18441940X-RAY DIFFRACTION64.82
1.93-1.970.23761000.18092127X-RAY DIFFRACTION71.86
1.97-2.010.24181380.1882395X-RAY DIFFRACTION79.96
2.01-2.060.23181410.17462794X-RAY DIFFRACTION93.95
2.06-2.110.19411700.17772973X-RAY DIFFRACTION99.78
2.11-2.170.23471520.16942958X-RAY DIFFRACTION99.65
2.17-2.230.26141430.17023002X-RAY DIFFRACTION99.87
2.23-2.30.20371570.16142949X-RAY DIFFRACTION99.97
2.3-2.390.21571770.16472979X-RAY DIFFRACTION99.78
2.39-2.480.23091620.16382965X-RAY DIFFRACTION99.87
2.48-2.60.21531540.16592968X-RAY DIFFRACTION99.78
2.6-2.730.19841560.16862996X-RAY DIFFRACTION99.94
2.73-2.90.22711570.16352962X-RAY DIFFRACTION99.81
2.9-3.130.23041470.16753000X-RAY DIFFRACTION99.9
3.13-3.440.18281490.14983005X-RAY DIFFRACTION99.72
3.44-3.940.18711280.13623015X-RAY DIFFRACTION99.46
3.94-4.960.16431370.12732965X-RAY DIFFRACTION98.04
4.96-34.230.20671480.17892728X-RAY DIFFRACTION89.62

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