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- PDB-3keu: Crystal Structure of Human PL Kinase with bound PLP and ATP -

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Basic information

Entry
Database: PDB / ID: 3keu
TitleCrystal Structure of Human PL Kinase with bound PLP and ATP
ComponentsPyridoxal kinase
KeywordsTRANSFERASE / Pyridoxal 5'-phosphate / Pyridoxal kinase / Vitamin B6 / PLP / ATP-binding / Kinase / Metal-binding / Nucleotide-binding / Phosphoprotein
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-5'-PHOSPHATE / Pyridoxal kinase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / isomorphous refinement / Resolution: 2.1 Å
AuthorsSafo, M.K. / Gandhi, A.K. / Musayev, F.N.
CitationJournal: To be Published
Title: Crystal structure of PL kinase in complex with MgATP and PLP: Structural basis of severe induced MgATP substrate inhibition of the enzyme
Authors: Gandhi, A.K. / Musayev, F.N. / Safo, M.K.
History
DepositionOct 26, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 3, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.2Nov 1, 2017Group: Refinement description / Category: software
Revision 1.3Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / 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_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)73,77029
Polymers70,2872
Non-polymers3,48427
Water5,819323
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12280 Å2
ΔGint-288 kcal/mol
Surface area23200 Å2
MethodPISA
Unit cell
Length a, b, c (Å)91.202, 114.585, 169.414
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-899-

HOH

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Components

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Protein , 1 types, 2 molecules AB

#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: C21orf124, C21orf97, PDXK, PKH, PNK / Plasmid: pET28 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta / References: UniProt: O00764, pyridoxal kinase

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Non-polymers , 7 types, 350 molecules

#2: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / 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-PLP / PYRIDOXAL-5'-PHOSPHATE / VITAMIN B6 Phosphate / Pyridoxal phosphate


Mass: 247.142 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H10NO6P
#6: Chemical
ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL / 2-Methyl-2,4-pentanediol


Mass: 118.174 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#7: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: SO4
#8: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 323 / 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: 60.93 %
Crystal growTemperature: 298 K / Method: hanging drop / pH: 8
Details: Saturated MgATP and PLP, 50-60% MPD precipitant, pH 8.0, hanging drop, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.54 Å
DetectorType: RIGAKU RAXIS / Detector: IMAGE PLATE / Date: Aug 28, 2009
RadiationProtocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2→26.98 Å / Num. obs: 59477 / % possible obs: 98.9 % / Redundancy: 3.1 % / Rmerge(I) obs: 0.049 / Χ2: 0.88 / Net I/σ(I): 13.3 / Scaling rejects: 19926
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allΧ2% possible all
2-2.072.810.33.41855858910.9899
2.07-2.152.830.2723.81885558700.9898.8
2.15-2.252.880.2524.11916758890.9899.1
2.25-2.372.950.2244.61964659290.9799.2
2.37-2.523.020.1815.52017459330.9599.4
2.52-2.713.110.13372075759400.9299.1
2.71-2.993.220.0959.42134959480.8799.3
2.99-3.423.370.05515.42173360000.7999.3
3.42-4.33.420.0327.12196260340.7499.4
4.3-26.983.370.019442216060430.7296.5

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Processing

Software
NameVersionClassificationNB
d*TREK9.2SSIdata scaling
CNS1refinement
PDB_EXTRACT3.005data extraction
CrystalCleardata collection
d*TREKdata reduction
RefinementMethod to determine structure: isomorphous refinement / Resolution: 2.1→26.98 Å / Rfactor Rfree error: 0.005 / Occupancy max: 1 / Occupancy min: 0.5 / Data cutoff high absF: 3564144 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.256 2606 5.1 %RANDOM
Rwork0.209 ---
obs-51485 98.9 %-
Displacement parametersBiso max: 100 Å2 / Biso mean: 44.453 Å2 / Biso min: 15.31 Å2
Baniso -1Baniso -2Baniso -3
1-12.56 Å20 Å20 Å2
2---8.76 Å20 Å2
3----3.79 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.35 Å0.27 Å
Luzzati d res low-5 Å
Luzzati sigma a0.6 Å0.49 Å
Refinement stepCycle: LAST / Resolution: 2.1→26.98 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4822 0 212 323 5357
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.01
X-RAY DIFFRACTIONc_angle_deg1.6
X-RAY DIFFRACTIONc_dihedral_angle_d23.5
X-RAY DIFFRACTIONc_improper_angle_d2.28
X-RAY DIFFRACTIONc_mcbond_it5.611.5
X-RAY DIFFRACTIONc_mcangle_it6.722
X-RAY DIFFRACTIONc_scbond_it8.512
X-RAY DIFFRACTIONc_scangle_it102.5
LS refinement shellResolution: 2.1→2.18 Å / Rfactor Rfree error: 0.026 / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.445 283 5.6 %
Rwork0.403 4801 -
all-5084 -
obs--98.7 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2atp.parion.top
X-RAY DIFFRACTION3ion.paramwater.top
X-RAY DIFFRACTION4mpd.paratp.top
X-RAY DIFFRACTION5water.paramplp.top

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