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- PDB-7vkp: Crystal structure of E.coli pseudouridine kinase PsuK -

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Basic information

Entry
Database: PDB / ID: 7vkp
TitleCrystal structure of E.coli pseudouridine kinase PsuK
ComponentsPfkB domain protein
KeywordsRNA BINDING PROTEIN / pseudouridine / kinase / yeiC
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
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 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
DepositionSep 30, 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

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Assembly

Deposited unit
A: PfkB domain protein


Theoretical massNumber of molelcules
Total (without water)33,7811
Polymers33,7811
Non-polymers00
Water66737
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area14360 Å2
Unit cell
Length a, b, c (Å)186.183, 186.183, 52.213
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

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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 (strain B / BL21-DE3) (bacteria)
Strain: B / BL21-DE3 / Gene: ECBD_1492 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A140N873
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 37 / 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: 3.87 Å3/Da / Density % sol: 68.22 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting 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 PILATUS 6M / Detector: PIXEL / Date: Sep 21, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97915 Å / Relative weight: 1
ReflectionResolution: 2.3→30 Å / Num. obs: 24045 / % possible obs: 99.9 % / Redundancy: 21 % / Biso Wilson estimate: 23.14 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.148 / Rpim(I) all: 0.029 / Rrim(I) all: 0.151 / Net I/σ(I): 22.25
Reflection shellResolution: 2.3→2.38 Å / Redundancy: 9.6 % / Rmerge(I) obs: 0.52 / Mean I/σ(I) obs: 3.5 / Num. unique obs: 2362 / CC1/2: 0.294 / CC star: 0.674 / Rpim(I) all: 0.169 / Rrim(I) all: 0.549 / % possible all: 99.9

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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: 7C1Y

7c1y


Resolution: 2.3→29.18 Å / SU ML: 0.2796 / Cross valid method: FREE R-VALUE / σ(F): 1.53 / Phase error: 23.7643
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2619 1137 4.95 %
Rwork0.2232 21841 -
obs0.2252 22978 95.48 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 42.24 Å2
Refinement stepCycle: LAST / Resolution: 2.3→29.18 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2323 0 0 37 2360
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00832365
X-RAY DIFFRACTIONf_angle_d0.99693217
X-RAY DIFFRACTIONf_chiral_restr0.0521368
X-RAY DIFFRACTIONf_plane_restr0.0119420
X-RAY DIFFRACTIONf_dihedral_angle_d6.3608327
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3-2.410.3524910.29761874X-RAY DIFFRACTION66.88
2.41-2.540.30951370.28732731X-RAY DIFFRACTION97.55
2.54-2.70.29551370.2762815X-RAY DIFFRACTION99.83
2.7-2.90.28381460.23712830X-RAY DIFFRACTION100
2.9-3.20.26271420.23362831X-RAY DIFFRACTION100
3.2-3.660.25481620.21362844X-RAY DIFFRACTION99.97
3.66-4.60.25371690.19232884X-RAY DIFFRACTION100
4.61-29.180.21841530.18583032X-RAY DIFFRACTION98.85
Refinement TLS params.Method: refined / Origin x: 74.4502827355 Å / Origin y: -20.2127539345 Å / Origin z: -3.90177952866 Å
111213212223313233
T0.507328826407 Å2-0.201288395989 Å20.101031104826 Å2--0.138004975628 Å2-0.320342638925 Å2--0.414433683671 Å2
L0.820799595064 °2-0.163665965054 °20.248383229137 °2-0.820750124713 °2-0.0592220021542 °2--0.645698038156 °2
S0.0393836013437 Å °0.0407426572102 Å °-0.507764198711 Å °0.0915051239382 Å °-0.150754743463 Å °0.707990534969 Å °0.444197878174 Å °-0.397518226449 Å °0.038580769121 Å °
Refinement TLS groupSelection details: all

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