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- PDB-3fhy: Crystal structure of D235N mutant of human pyridoxal kinase -

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Basic information

Entry
Database: PDB / ID: 3fhy
TitleCrystal structure of D235N mutant of human pyridoxal kinase
ComponentsPyridoxal kinase
KeywordsTRANSFERASE / beta sheet with alpha helix / ATP complex / metal ion / Acetylation / Alternative splicing / ATP-binding / Cytoplasm / Kinase / Metal-binding / Nucleotide-binding / Zinc
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 / phosphorylation / Neutrophil degranulation / magnesium ion binding / protein homodimerization activity / extracellular exosome / zinc ion binding / extracellular region / 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
ADENOSINE-5'-TRIPHOSPHATE / Pyridoxal kinase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsSafo, M.K. / Gandhi, A.K. / Musayev, F.N. / Ghatge, M. / Di Salvo, M.L. / Schirch, V.
CitationJournal: Biochem.Biophys.Res.Commun. / Year: 2009
Title: Kinetic and structural studies of the role of the active site residue Asp235 of human pyridoxal kinase.
Authors: Gandhi, A.K. / Ghatge, M.S. / Musayev, F.N. / Sease, A. / Aboagye, S.O. / di Salvo, M.L. / Schirch, V. / Safo, M.K.
History
DepositionDec 10, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 23, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 20, 2021Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...database_2 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Sep 6, 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: Pyridoxal kinase
B: Pyridoxal kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,49228
Polymers70,2852
Non-polymers3,20726
Water3,603200
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4200 Å2
ΔGint-7 kcal/mol
Surface area24600 Å2
MethodPISA
Unit cell
Length a, b, c (Å)91.110, 114.643, 169.681
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
11B-397-

HOH

21B-398-

HOH

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Pyridoxal kinase / / Pyridoxine kinase


Mass: 35142.277 Da / Num. of mol.: 2 / Mutation: D235N
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: C21orf124, C21orf97, PDXK, PKH, PNK / Plasmid: pET28 / Production host: Escherichia coli (E. coli)
Strain (production host): Rosetta (DE3)pLysS competent cells
References: UniProt: O00764, pyridoxal kinase

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Non-polymers , 6 types, 226 molecules

#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#4: Chemical ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE / Adenosine triphosphate


Mass: 507.181 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Comment: ATP, energy-carrying molecule*YM
#5: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: SO4
#6: Chemical
ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL / 2-Methyl-2,4-pentanediol


Mass: 118.174 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 200 / 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: 3.15 Å3/Da / Density % sol: 60.98 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8
Details: Protein solution: 20 mM Sodium BES buffer pH 7.2, 100 mM NaCl, 5 mM BME, 2.5 mM MgATP. Precipitant: 100 mM Tris-HCl pH 8.0, 57%, MPD, 5 mM MgSO4, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.54178 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Mar 3, 2008 / Details: MSC Varimax confocal optics
RadiationMonochromator: Ni Filter / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54178 Å / Relative weight: 1
ReflectionResolution: 2.3→32.54 Å / Num. obs: 39415 / % possible obs: 99 % / Redundancy: 3.39 % / Rmerge(I) obs: 0.049 / Χ2: 0.86 / Scaling rejects: 14423
Reflection shellResolution: 2.3→2.38 Å / Redundancy: 3.18 % / Rmerge(I) obs: 0.25 / Mean I/σ(I) obs: 4.6 / Num. measured all: 14255 / Num. unique all: 3924 / Χ2: 0.97 / % possible all: 99.3

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Processing

Software
NameVersionClassificationNB
d*TREK9.2SSIdata processing
CNS1.2refinement
PDB_EXTRACT3.006data extraction
CrystalCleardata collection
d*TREKdata reduction
d*TREKdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 2YXU

2yxu


Resolution: 2.3→29.36 Å / Rfactor Rfree error: 0.006 / Occupancy max: 1 / Occupancy min: 0.7 / Data cutoff high absF: 3017435 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.261 1954 5 %RANDOM
Rwork0.214 ---
all0.219 39410 --
obs0.219 39410 98.8 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 57.616 Å2 / ksol: 0.35 e/Å3
Displacement parametersBiso max: 100 Å2 / Biso mean: 45.209 Å2 / Biso min: 5.86 Å2
Baniso -1Baniso -2Baniso -3
1-16.26 Å20 Å20 Å2
2---8.17 Å20 Å2
3----8.09 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.4 Å0.31 Å
Luzzati d res low-5 Å
Luzzati sigma a0.65 Å0.51 Å
Refinement stepCycle: LAST / Resolution: 2.3→29.36 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4828 0 126 264 5218
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_dihedral_angle_d22.9
X-RAY DIFFRACTIONc_improper_angle_d0.95
X-RAY DIFFRACTIONc_mcbond_it6.191.5
X-RAY DIFFRACTIONc_mcangle_it7.772
X-RAY DIFFRACTIONc_scbond_it9.42
X-RAY DIFFRACTIONc_scangle_it10.712.5
LS refinement shellResolution: 2.3→2.38 Å / Rfactor Rfree error: 0.033 / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.438 179 4.6 %
Rwork0.382 3745 -
all-3924 -
obs-3745 99.3 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2atp.paratp.top
X-RAY DIFFRACTION3ion.parammpd.top
X-RAY DIFFRACTION4mpd.parion.top
X-RAY DIFFRACTION5water.paramwater.top

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