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- PDB-7w93: Crystal structure of E.coli pseudouridine kinase PsuK complexed w... -

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Basic information

Entry
Database: PDB / ID: 7w93
TitleCrystal structure of E.coli pseudouridine kinase PsuK complexed with N1-methyl-pseudouridine
ComponentsPfkB domain protein
KeywordsSUGAR BINDING PROTEIN / Kinase / sugar / pseudouridine / m1-pseudouridine / mRNA vaccine
Function / homology
Function and homology information


kinase activity / cytosol
Similarity search - Function
pfkB 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 / Ribokinase-like / UDP-N-acetylmuramoyl-L-alanine:D-glutamate ligase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-8IZ / : / PfkB domain protein
Similarity search - Component
Biological speciesEscherichia coli BL21 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 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
DepositionDec 9, 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)34,0783
Polymers33,7811
Non-polymers2972
Water2,612145
1
A: PfkB domain protein
hetero molecules

A: PfkB domain protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,1576
Polymers67,5622
Non-polymers5954
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_554-y,-x,-z-1/21
Buried area3270 Å2
ΔGint-23 kcal/mol
Surface area25570 Å2
MethodPISA
Unit cell
Length a, b, c (Å)185.830, 185.830, 52.510
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-638-

HOH

21A-641-

HOH

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Components

#1: Protein PfkB domain protein


Mass: 33781.094 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli BL21(DE3) (bacteria) / Strain: B / BL21-DE3 / Gene: ECBD_1492 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A140N873
#2: Chemical ChemComp-8IZ / 5-[(2S,3R,4S,5R)-5-(hydroxymethyl)-3,4-bis(oxidanyl)oxolan-2-yl]-1-methyl-pyrimidine-2,4-dione


Mass: 258.228 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H14N2O6 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: K
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 145 / 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: 3.87 Å3/Da / Density % sol: 68.25 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.02 M Magnesium chloride hexahydrate, 0.1 M HEPES pH 7.5, 22% w/v Poly(acrylic acid sodium salt) 5100

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.97915 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Dec 2, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97915 Å / Relative weight: 1
ReflectionResolution: 1.9→30 Å / Num. obs: 41758 / % possible obs: 98.5 % / Redundancy: 28.2 % / Biso Wilson estimate: 32.58 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.146 / Rpim(I) all: 0.026 / Rrim(I) all: 0.148 / Net I/σ(I): 15.8
Reflection shellResolution: 1.9→2 Å / Redundancy: 21.6 % / Rmerge(I) obs: 1.462 / Num. unique obs: 5922 / CC1/2: 0.651 / Rpim(I) all: 0.301 / Rrim(I) all: 1.498 / % possible all: 97.1

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
iMOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7VKP

7vkp


Resolution: 1.9→29.19 Å / SU ML: 0.2182 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 20.169
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2153 2093 5.02 %
Rwork0.1962 39626 -
obs0.1972 41719 98.1 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 51.26 Å2
Refinement stepCycle: LAST / Resolution: 1.9→29.19 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2323 0 19 145 2487
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00922434
X-RAY DIFFRACTIONf_angle_d1.09823321
X-RAY DIFFRACTIONf_chiral_restr0.0654379
X-RAY DIFFRACTIONf_plane_restr0.0109435
X-RAY DIFFRACTIONf_dihedral_angle_d5.8678339
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9-1.940.34381380.322528X-RAY DIFFRACTION94.51
1.94-1.990.31361140.28192574X-RAY DIFFRACTION97.53
1.99-2.050.25431360.25062528X-RAY DIFFRACTION95.93
2.05-2.110.24341480.23522547X-RAY DIFFRACTION96.01
2.11-2.170.25611430.21962647X-RAY DIFFRACTION99.82
2.17-2.250.23431470.20832603X-RAY DIFFRACTION99.39
2.25-2.340.24621270.20022679X-RAY DIFFRACTION99.54
2.34-2.450.2041470.1922633X-RAY DIFFRACTION99.64
2.45-2.580.17761330.19632599X-RAY DIFFRACTION96.64
2.58-2.740.24091590.19892652X-RAY DIFFRACTION99.79
2.74-2.950.21581200.1992706X-RAY DIFFRACTION99.79
2.95-3.250.22071430.20252643X-RAY DIFFRACTION97.69
3.25-3.720.22351310.19022723X-RAY DIFFRACTION99.2
3.72-4.680.18331670.17082720X-RAY DIFFRACTION99.31
4.68-29.190.2021400.18132844X-RAY DIFFRACTION96.91
Refinement TLS params.Method: refined / Origin x: 74.5586871219 Å / Origin y: -19.8952284959 Å / Origin z: -3.95126651783 Å
111213212223313233
T0.411301892299 Å2-0.112811506381 Å20.147647016451 Å2-0.253120726151 Å2-0.12568821784 Å2--0.440124159361 Å2
L0.881142324719 °2-0.393030981943 °20.322536439725 °2-3.03242413476 °21.13167204634 °2--0.993346978904 °2
S-0.0380887868369 Å °0.0087420289052 Å °-0.295914365748 Å °0.370879734117 Å °-0.304554938984 Å °0.900816579035 Å °0.360002350729 Å °-0.261092523073 Å °0.0290547603631 Å °
Refinement TLS groupSelection details: all

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