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- PDB-7vsk: Crystal structure of E.coli pseudouridine kinase PsuK complexed w... -

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Basic information

Entry
Database: PDB / ID: 7vsk
TitleCrystal structure of E.coli pseudouridine kinase PsuK complexed with pseudouridine.
ComponentsPfkB domain protein
KeywordsRNA BINDING PROTEIN / pseudouridine / kinase / yeiC
Function / homologypfkB family of carbohydrate kinases signature 1. / pfkB family of carbohydrate kinases signature 2. / Carbohydrate/purine kinase, PfkB, conserved site / Carbohydrate kinase PfkB / pfkB family carbohydrate kinase / Ribokinase-like / kinase activity / Chem-FJF / PfkB domain protein
Function and homology information
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.31 Å
AuthorsLi, K.J. / Li, X.J. / Wu, B.X.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Front Microbiol / Year: 2022
Title: Structure Characterization of Escherichia coli Pseudouridine Kinase PsuK.
Authors: Li, X. / Li, K. / Guo, W. / Wen, Y. / Meng, C. / Wu, B.
History
DepositionOct 26, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 22, 2022Provider: repository / Type: Initial release
Revision 1.1Jul 20, 2022Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.2Nov 29, 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

Downloads & links

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Assembly

Deposited unit
A: PfkB domain protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,0252
Polymers33,7811
Non-polymers2441
Water1,15364
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)182.634, 182.634, 51.228
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number182
Space group name H-MP6322
Space group name HallP6c2c
Symmetry operation#1: x,y,z
#2: x-y,x,z+1/2
#3: y,-x+y,z+1/2
#4: -y,x-y,z
#5: -x+y,-x,z
#6: x-y,-y,-z
#7: -x,-x+y,-z
#8: -x,-y,z+1/2
#9: y,x,-z
#10: -y,-x,-z+1/2
#11: -x+y,y,-z+1/2
#12: x,x-y,-z+1/2
Components on special symmetry positions
IDModelComponents
11A-513-

HOH

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Components

#1: Protein PfkB domain protein / PsuK


Mass: 33781.094 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (strain B / BL21-DE3) (bacteria)
Strain: B / BL21-DE3 / Gene: ECBD_1492 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A140N873
#2: Chemical ChemComp-FJF / 5-[(2~{S},3~{R},4~{S},5~{R})-5-(hydroxymethyl)-3,4-bis(oxidanyl)oxolan-2-yl]-1~{H}-pyrimidine-2,4-dione


Mass: 244.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H12N2O6 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 64 / 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: 3.65 Å3/Da / Density % sol: 66.31 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 20% (w/v) Polyacrylic acid 5100, 0.1M HEPES/Sodium hydroxide pH 7.0, 0.02M Magnesium chloride

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17B1 / Wavelength: 0.97853 Å
DetectorType: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Oct 23, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97853 Å / Relative weight: 1
ReflectionResolution: 2.3→30 Å / Num. obs: 22581 / % possible obs: 99.5 % / Redundancy: 17.7 % / Biso Wilson estimate: 26.09 Å2 / CC1/2: 0.995 / CC star: 0.999 / Rmerge(I) obs: 0.137 / Rpim(I) all: 0.029 / Rrim(I) all: 0.141 / Net I/σ(I): 13.67
Reflection shellResolution: 2.3→2.38 Å / Redundancy: 8.3 % / Rmerge(I) obs: 0.454 / Mean I/σ(I) obs: 3 / Num. unique obs: 2166 / CC1/2: 0.13 / CC star: 0.48 / Rpim(I) all: 0.158 / Rrim(I) all: 0.483 / % possible all: 98.2

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7VKP

7vkp


Resolution: 2.31→28.41 Å / SU ML: 0.355 / Cross valid method: FREE R-VALUE / σ(F): 1.51 / Phase error: 25.8437
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2755 1111 5.13 %
Rwork0.2279 20562 -
obs0.2303 21673 95.32 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 40.03 Å2
Refinement stepCycle: LAST / Resolution: 2.31→28.41 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2059 0 17 64 2140
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00822116
X-RAY DIFFRACTIONf_angle_d0.98842876
X-RAY DIFFRACTIONf_chiral_restr0.055324
X-RAY DIFFRACTIONf_plane_restr0.0075373
X-RAY DIFFRACTIONf_dihedral_angle_d8.2725295
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.31-2.410.35671060.29271919X-RAY DIFFRACTION72.61
2.41-2.540.34411290.30742502X-RAY DIFFRACTION95.08
2.54-2.70.411310.31882592X-RAY DIFFRACTION97.11
2.7-2.90.25021230.25232662X-RAY DIFFRACTION99.93
2.9-3.20.26781420.23332690X-RAY DIFFRACTION99.93
3.2-3.660.27071530.23212674X-RAY DIFFRACTION99.54
3.66-4.60.25041600.18932696X-RAY DIFFRACTION99.69
4.61-28.410.22881670.17472827X-RAY DIFFRACTION98.2
Refinement TLS params.Method: refined / Origin x: 73.51216288 Å / Origin y: -19.1078119552 Å / Origin z: -5.5795924673 Å
111213212223313233
T0.39270388341 Å2-0.117409598181 Å20.0864121394232 Å2-0.147040252902 Å2-0.0946004670473 Å2--0.280684680521 Å2
L0.629002710695 °20.0614943508933 °20.180487489173 °2-0.886191852983 °20.351037541924 °2--0.481448686741 °2
S-0.0863999309136 Å °0.0604152081319 Å °-0.226892326029 Å °0.113068500032 Å °-0.101721354704 Å °0.349776319668 Å °0.222183422341 Å °-0.212113206299 Å °0.0334233881126 Å °
Refinement TLS groupSelection details: all

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