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- PDB-2yxt: Human Pyridoxal Kinase -

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Basic information

Entry
Database: PDB / ID: 2yxt
TitleHuman Pyridoxal Kinase
ComponentsPyridoxal kinase
KeywordsTRANSFERASE / beta sheet with alpha helix / metal ion
Function / homology
Function and homology information


pyridoxal metabolic process / pyridoxamine metabolic process / Vitamin B6 activation to pyridoxal phosphate / lithium ion binding / pyridoxal kinase activity / pyridoxal 5'-phosphate salvage / pyridoxal kinase / sodium ion binding / potassium ion binding / specific granule lumen ...pyridoxal metabolic process / pyridoxamine metabolic process / Vitamin B6 activation to pyridoxal phosphate / lithium ion binding / pyridoxal kinase activity / pyridoxal 5'-phosphate salvage / pyridoxal kinase / sodium ion binding / potassium ion binding / specific granule lumen / pyridoxal phosphate binding / secretory granule lumen / Neutrophil degranulation / magnesium ion binding / protein homodimerization activity / extracellular exosome / extracellular region / zinc ion binding / nucleoplasm / ATP binding / nucleus / cytosol
Similarity search - Function
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
PHOSPHATE ION / Pyridoxal kinase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsSafo, M.K. / Musayev, F.N. / Ko, T.P. / Schirch, V.
CitationJournal: Protein Sci. / Year: 2007
Title: Crystal Structure of human pyridoxal kinase: structural basis of M(+) and M(2+) activation.
Authors: Musayev, F.N. / di Salvo, M.L. / Ko, T.P. / Gandhi, A.K. / Goswami, A. / Schirch, V. / Safo, M.K.
History
DepositionApr 27, 2007Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 11, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.2Oct 25, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / software / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _software.name / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)72,55724
Polymers70,2872
Non-polymers2,27022
Water9,332518
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10680 Å2
ΔGint-224 kcal/mol
Surface area23740 Å2
MethodPISA, PQS
2
A: Pyridoxal kinase
B: Pyridoxal kinase
hetero molecules

A: Pyridoxal kinase
B: Pyridoxal kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)145,11448
Polymers140,5734
Non-polymers4,54044
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_555-x,y,-z1
Buried area23110 Å2
ΔGint-455 kcal/mol
Surface area45730 Å2
MethodPISA
Unit cell
Length a, b, c (Å)90.630, 115.286, 172.403
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222
Components on special symmetry positions
IDModelComponents
11A-1443-

HOH

21A-1473-

HOH

31A-1474-

HOH

41B-1489-

HOH

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Components

#1: Protein Pyridoxal kinase / Pyridoxine kinase


Mass: 35143.266 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PDXK, PKH, PNK / Plasmid: pET 22b / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta(DE3) / References: UniProt: O00764, pyridoxal kinase
#2: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#3: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: PO4
#4: Chemical
ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 518 / 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: 3.2 Å3/Da / Density % sol: 61.59 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 20mM K-PO4 (pH 7.0), 100mM NaCl, 100mM Tris-HCl (pH 8.0), 50% MPD, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Nov 5, 2005 / Details: MSC Varimax confocal optics
RadiationMonochromator: Ni FILTER / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2→30 Å / Num. all: 61254 / Num. obs: 60825 / % possible obs: 99.3 % / Observed criterion σ(I): 3 / Redundancy: 4.7 % / Rmerge(I) obs: 0.073 / Net I/σ(I): 11.9
Reflection shellResolution: 2→2.07 Å / Redundancy: 4.5 % / Rmerge(I) obs: 0.34 / Mean I/σ(I) obs: 4.4 / Num. unique all: 6061 / % possible all: 99.9

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Processing

Software
NameVersionClassification
CrystalCleardata collection
CaspRmodel building
CNS1.1refinement
d*TREKdata reduction
d*TREKdata scaling
CaspRphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB code 1LHP

1lhp


Resolution: 2→30 Å / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.245 3044 -random
Rwork0.206 ---
all0.211 61214 --
obs0.211 60592 99 %-
Displacement parametersBiso mean: 40.9 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.33 Å0.28 Å
Luzzati d res low-5 Å
Luzzati sigma a0.63 Å0.56 Å
Refinement stepCycle: LAST / Resolution: 2→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4797 0 144 518 5459
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.02
X-RAY DIFFRACTIONc_angle_deg2
LS refinement shellResolution: 2→2.07 Å / Rfactor Rfree error: 0.025
RfactorNum. reflection% reflection
Rfree0.473 295 -
Rwork0.448 --
obs-6017 99.3 %

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