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- PDB-7m7k: Crystal structure of uridine bound to Geobacillus thermoglucosida... -

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Basic information

Entry
Database: PDB / ID: 7m7k
TitleCrystal structure of uridine bound to Geobacillus thermoglucosidasius pyrimidine nucleoside phosphorylase PyNP
ComponentsPyrimidine-nucleoside phosphorylase
KeywordsTRANSFERASE / Pyrimidine / Nucleoside / Phosphorylase / Enzyme
Function / homology
Function and homology information


deoxyuridine phosphorylase activity / pyrimidine-nucleoside phosphorylase / pyrimidine nucleoside metabolic process / pyrimidine-nucleoside phosphorylase activity / thymidine phosphorylase activity / pyrimidine nucleobase metabolic process / 1,4-alpha-oligoglucan phosphorylase activity / uridine phosphorylase activity / metal ion binding
Similarity search - Function
Pyrimidine-nucleoside phosphorylase, bacterial/eukaryotic / Thymidine/pyrimidine-nucleoside phosphorylase / Pyrimidine nucleoside phosphorylase, C-terminal / Pyrimidine-nucleoside phosphorylase, conserved site / Pyrimidine nucleoside phosphorylase-like, C-terminal domain superfamily / Pyrimidine nucleoside phosphorylase C-terminal domain / Thymidine and pyrimidine-nucleoside phosphorylases signature. / Pyrimidine nucleoside phosphorylase C-terminal domain / Glycosyl transferase family 3, N-terminal domain / Glycosyl transferase family 3, N-terminal domain superfamily ...Pyrimidine-nucleoside phosphorylase, bacterial/eukaryotic / Thymidine/pyrimidine-nucleoside phosphorylase / Pyrimidine nucleoside phosphorylase, C-terminal / Pyrimidine-nucleoside phosphorylase, conserved site / Pyrimidine nucleoside phosphorylase-like, C-terminal domain superfamily / Pyrimidine nucleoside phosphorylase C-terminal domain / Thymidine and pyrimidine-nucleoside phosphorylases signature. / Pyrimidine nucleoside phosphorylase C-terminal domain / Glycosyl transferase family 3, N-terminal domain / Glycosyl transferase family 3, N-terminal domain superfamily / Glycosyl transferase family, helical bundle domain / Glycosyl transferase, family 3 / Glycosyl transferase family, a/b domain / Nucleoside phosphorylase/phosphoribosyltransferase catalytic domain superfamily
Similarity search - Domain/homology
URIDINE / Pyrimidine-nucleoside phosphorylase
Similarity search - Component
Biological speciesParageobacillus thermoglucosidasius (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.89 Å
AuthorsPausch, P. / Bange, G.
CitationJournal: Acs Catalysis / Year: 2021
Title: Diversification of 4'-Methylated Nucleosides by Nucleoside Phosphorylases
Authors: Kaspar, F. / Seeger, M. / Westarp, S. / Kollmann, C. / Lehmann, A.P. / Pausch, P. / Kemper, S. / Neubauer, P. / Bange, G. / Schallmey, A. / Werz, D.B. / Kurreck, A.
History
DepositionMar 28, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 25, 2021Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
B: Pyrimidine-nucleoside phosphorylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,3975
Polymers46,8651
Non-polymers5324
Water6,485360
1
B: Pyrimidine-nucleoside phosphorylase
hetero molecules

B: Pyrimidine-nucleoside phosphorylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)94,79410
Polymers93,7302
Non-polymers1,0658
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_554-y,-x,-z-1/21
Buried area3770 Å2
ΔGint-96 kcal/mol
Surface area34720 Å2
MethodPISA
Unit cell
Length a, b, c (Å)84.262, 84.262, 121.694
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212
Space group name HallP4abw2nw
Symmetry operation#1: x,y,z
#2: -y+1/2,x+1/2,z+1/4
#3: y+1/2,-x+1/2,z+3/4
#4: x+1/2,-y+1/2,-z+3/4
#5: -x+1/2,y+1/2,-z+1/4
#6: -x,-y,z+1/2
#7: y,x,-z
#8: -y,-x,-z+1/2

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Components

#1: Protein Pyrimidine-nucleoside phosphorylase


Mass: 46864.805 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Parageobacillus thermoglucosidasius (bacteria)
Gene: DV714_16680 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: A0A369WPE5, pyrimidine-nucleoside phosphorylase
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-URI / URIDINE


Mass: 244.201 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C9H12N2O6 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 360 / 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: 2.3 Å3/Da / Density % sol: 46.63 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.2 M Ammonium sulfate and 20% PEG3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.979 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 16, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.89→49.33 Å / Num. obs: 35436 / % possible obs: 99.51 % / Redundancy: 13.9 % / Biso Wilson estimate: 26.33 Å2 / CC1/2: 0.999 / Net I/σ(I): 13.26
Reflection shellResolution: 1.893→1.961 Å / Num. unique obs: 3340 / CC1/2: 0.489

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Processing

Software
NameVersionClassification
PHENIX1.18_3845refinement
PHENIX1.18_3845refinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1BRW

1brw


Resolution: 1.89→49.33 Å / SU ML: 0.2094 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 21.9736
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2078 3296 4.97 %
Rwork0.1737 63019 -
obs0.1755 35431 99.48 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 31.54 Å2
Refinement stepCycle: LAST / Resolution: 1.89→49.33 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3229 0 32 360 3621
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00593300
X-RAY DIFFRACTIONf_angle_d0.79274457
X-RAY DIFFRACTIONf_chiral_restr0.0502531
X-RAY DIFFRACTIONf_plane_restr0.0047563
X-RAY DIFFRACTIONf_dihedral_angle_d16.57381227
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.89-1.920.34591350.30272302X-RAY DIFFRACTION87.82
1.92-1.950.30471340.27892672X-RAY DIFFRACTION100
1.95-1.980.31731180.26322650X-RAY DIFFRACTION100
1.98-2.010.29141310.24772631X-RAY DIFFRACTION100
2.01-2.050.26121440.23242617X-RAY DIFFRACTION100
2.05-2.080.30221460.2182637X-RAY DIFFRACTION100
2.08-2.120.25511250.2112655X-RAY DIFFRACTION100
2.12-2.170.21131160.20452700X-RAY DIFFRACTION100
2.17-2.210.2621400.19492619X-RAY DIFFRACTION99.93
2.21-2.270.25721350.18522628X-RAY DIFFRACTION99.96
2.27-2.320.21271290.17542630X-RAY DIFFRACTION100
2.32-2.390.23871370.16582699X-RAY DIFFRACTION100
2.39-2.460.18241260.16282572X-RAY DIFFRACTION100
2.46-2.530.19321450.1682679X-RAY DIFFRACTION100
2.53-2.630.2181380.17122630X-RAY DIFFRACTION99.96
2.63-2.730.19421470.16332633X-RAY DIFFRACTION100
2.73-2.850.22021760.17952577X-RAY DIFFRACTION100
2.85-3.010.26071480.16632638X-RAY DIFFRACTION99.96
3.01-3.190.25141240.17282662X-RAY DIFFRACTION100
3.19-3.440.18781440.16072635X-RAY DIFFRACTION100
3.44-3.790.171440.15332630X-RAY DIFFRACTION100
3.79-4.330.1661320.13212640X-RAY DIFFRACTION100
4.33-5.460.17281440.1412641X-RAY DIFFRACTION100
5.46-49.330.16251380.18262642X-RAY DIFFRACTION99.89

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