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- PDB-5tqi: Crystal structure of a pyridoxal kinase from Burkholderia multivorans -

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Basic information

Entry
Database: PDB / ID: 5tqi
TitleCrystal structure of a pyridoxal kinase from Burkholderia multivorans
ComponentsPyridoxal kinase PdxY
KeywordsTRANSFERASE / SSGCID / Burkholderia multivorans / pyridoxal kinase / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease
Function / homology
Function and homology information


pyridoxal kinase activity / pyridoxal 5'-phosphate salvage / pyridoxal kinase / magnesium ion binding / ATP binding / cytosol
Similarity search - Function
Pyridoxal kinase PdxY / Pyridoxine kinase / Pyridoxamine kinase/Phosphomethylpyrimidine kinase / Phosphomethylpyrimidine kinase / Ribokinase / Ribokinase-like / UDP-N-acetylmuramoyl-L-alanine:D-glutamate ligase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Pyridoxal kinase PdxY
Similarity search - Component
Biological speciesBurkholderia multivorans (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: TO BE PUBLISHED
Title: Crystal structure of a pyridoxal kinase from Burkholderia multivorans
Authors: Levin, E.J. / Abendroth, J. / Lorimer, D.D. / Edwards, T.E.
History
DepositionOct 24, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 16, 2016Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2017Group: Derived calculations / Refinement description / Category: pdbx_struct_oper_list / software / Item: _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Mar 6, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Pyridoxal kinase PdxY
B: Pyridoxal kinase PdxY
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,5474
Polymers64,4762
Non-polymers712
Water12,124673
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3610 Å2
ΔGint-46 kcal/mol
Surface area21260 Å2
MethodPISA
Unit cell
Length a, b, c (Å)82.970, 42.490, 90.510
Angle α, β, γ (deg.)90.000, 115.560, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Pyridoxal kinase PdxY / PL kinase


Mass: 32237.840 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Burkholderia multivorans (strain ATCC 17616 / 249) (bacteria)
Strain: ATCC 17616 / 249 / Gene: pdxK, pdxY, BMULJ_01107 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: A0A0H3KDL9, pyridoxal kinase
#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 673 / 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: 2.18 Å3/Da / Density % sol: 43.5 % / Mosaicity: 0.22 °
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop / pH: 9
Details: RigakuReagents JCSG+ screen, B3: 20% PEG 6000, 100 mM BICINE; BumuA.00129.a.B1.PS37843 at 18.12 mg/ml; cryo: 20% EG, 2 steps; tray 270818b3, puck fsu3-5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: Apr 13, 2016
RadiationMonochromator: Diamond [111] / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 1.5→44.9 Å / Num. obs: 91157 / % possible obs: 99.3 % / Observed criterion σ(I): -3 / Redundancy: 3.73 % / Biso Wilson estimate: 12.04 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.076 / Net I/σ(I): 11.27
Reflection shell
Resolution (Å)Highest resolution (Å)Rmerge(I) obsMean I/σ(I) obsCC1/2Diffraction-ID% possible all
1.5-1.540.4922.820.807198.8
1.54-1.580.4243.310.844198.8
1.58-1.630.3444.010.892199.6
1.63-1.680.2944.60.915199.4
1.68-1.730.2435.530.939199.2
1.73-1.790.26.440.957199.5
1.79-1.860.1637.680.97199.5
1.86-1.940.1378.80.981199.5
1.94-2.020.10610.910.987199.7
2.02-2.120.08513.070.991199.4
2.12-2.240.07714.230.992199.6
2.24-2.370.06815.710.993199.6
2.37-2.540.05917.740.995199.4
2.54-2.740.05419.440.995199.4
2.74-30.04821.460.996199.4
3-3.350.04523.040.995199.3
3.35-3.870.04523.930.996199.5
3.87-4.740.04826.160.994198.9
4.74-6.710.05125.880.994198.9
6.710.04924.720.995194.5

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Processing

Software
NameVersionClassification
XDSdata reduction
XSCALEdata scaling
MOLREPphasing
Cootmodel building
PHENIXrefinement
PDB_EXTRACT3.2data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.5→40.826 Å / SU ML: 0.13 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 16.8
RfactorNum. reflection% reflection
Rfree0.1778 2073 2.27 %
Rwork0.1377 --
obs0.1386 91127 99.41 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 55.09 Å2 / Biso mean: 16.9738 Å2 / Biso min: 5.1 Å2
Refinement stepCycle: final / Resolution: 1.5→40.826 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4369 0 2 677 5048
Biso mean--24.35 30.28 -
Num. residues----575
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0054619
X-RAY DIFFRACTIONf_angle_d0.7966329
X-RAY DIFFRACTIONf_chiral_restr0.077711
X-RAY DIFFRACTIONf_plane_restr0.005833
X-RAY DIFFRACTIONf_dihedral_angle_d16.3851686
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 15

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.5-1.53490.24231440.16975838598299
1.5349-1.57330.23341290.16295900602999
1.5733-1.61580.21291540.149158666020100
1.6158-1.66340.21711550.14495864601999
1.6634-1.7170.20261270.14035910603799
1.717-1.77840.19711410.137859166057100
1.7784-1.84960.19451160.132659716087100
1.8496-1.93380.17081220.132859336055100
1.9338-2.03580.17321330.131159436076100
2.0358-2.16330.18721360.130359356071100
2.1633-2.33030.17421450.128159536098100
2.3303-2.56480.20961470.138259226069100
2.5648-2.93580.16211710.13559576128100
2.9358-3.69840.13931370.136160176154100
3.6984-40.84120.15721160.14026129624598

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