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- PDB-4eoh: Crystal Structure of Human PL Kinase with bound Theophylline -

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Basic information

Entry
Database: PDB / ID: 4eoh
TitleCrystal Structure of Human PL Kinase with bound Theophylline
ComponentsPyridoxal Kinase
KeywordsTRANSFERASE/TRANSFERASE INHIBITOR / TRANSFERASE-TRANSFERASE INHIBITOR complex
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 / zinc ion binding / extracellular exosome / 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
THEOPHYLLINE / Pyridoxal kinase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsSafo, M.K. / Gandhi, A.K. / Musayev, F.N.
CitationJournal: Plos One / Year: 2012
Title: Crystal structures of human pyridoxal kinase in complex with the neurotoxins, ginkgotoxin and theophylline: insights into pyridoxal kinase inhibition.
Authors: Gandhi, A.K. / Desai, J.V. / Ghatge, M.S. / di Salvo, M.L. / Di Biase, S. / Danso-Danquah, R. / Musayev, F.N. / Contestabile, R. / Schirch, V. / Safo, M.K.
History
DepositionApr 14, 2012Deposition site: RCSB / Processing site: RCSB
SupersessionMay 2, 2012ID: 3KBI
Revision 1.0May 2, 2012Provider: repository / Type: Initial release
Revision 1.1Aug 22, 2012Group: Database references
Revision 1.2Sep 13, 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 / 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_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_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)73,02027
Polymers70,2872
Non-polymers2,73325
Water6,395355
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11440 Å2
ΔGint-270 kcal/mol
Surface area23350 Å2
MethodPISA
Unit cell
Length a, b, c (Å)92.302, 115.848, 171.904
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number23
Space group name H-MI222
Components on special symmetry positions
IDModelComponents
11B-501-

HOH

21B-502-

HOH

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Pyridoxal Kinase / PL 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, C21orf124, C21orf97, PKH, PNK, PRED79 / Plasmid: pET28 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta(DE3)pLysS / References: UniProt: O00764, pyridoxal kinase

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Non-polymers , 5 types, 380 molecules

#2: Chemical ChemComp-NA / SODIUM ION


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


Mass: 180.164 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C7H8N4O2
#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: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: SO4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 355 / 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: 3.27 Å3/Da / Density % sol: 62.37 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.2
Details: 48-50% MPD, pH 7.2, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE
RadiationMonochromator: Ni filter / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 2.1→37.68 Å / Num. obs: 52989 / % possible obs: 98.1 % / Redundancy: 2.97 % / Rmerge(I) obs: 0.032 / Χ2: 0.86 / Net I/σ(I): 18.5 / Scaling rejects: 17026
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allΧ2% possible all
2.1-2.182.840.2414.11606552110.9598
2.18-2.262.950.1924.81683352800.998.7
2.26-2.372.990.165.61722453380.9299.3
2.37-2.493.020.1256.91717052980.999.7
2.49-2.653.040.0889.21755553560.8499.6
2.65-2.853.110.066121767753320.8299.5
2.85-3.143.150.04716.41795553920.7799.7
3.14-3.593.110.02926.61793953740.7899.5
3.59-4.522.890.01942.21806353280.8197.2
4.52-37.682.620.01464.71814350800.9390.1

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Processing

Software
NameVersionClassificationNB
d*TREK9.2SSIdata reduction
CNS1refinement
PDB_EXTRACT3.11data extraction
CrystalCleardata collection
d*TREKdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3FHX

3fhx


Resolution: 2.1→29.19 Å / Rfactor Rfree error: 0.005 / Occupancy max: 1 / Occupancy min: 0.5 / Data cutoff high absF: 2572397 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.254 2688 5.1 %RANDOM
Rwork0.205 ---
obs-52986 98 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 74.3587 Å2 / ksol: 0.3571 e/Å3
Displacement parametersBiso max: 100 Å2 / Biso mean: 49.4575 Å2 / Biso min: 15.51 Å2
Baniso -1Baniso -2Baniso -3
1-11.05 Å20 Å20 Å2
2---2.66 Å20 Å2
3----8.39 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.32 Å0.26 Å
Luzzati d res low-5 Å
Luzzati sigma a0.41 Å0.35 Å
Refinement stepCycle: LAST / Resolution: 2.1→29.19 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4818 0 175 355 5348
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d22.3
X-RAY DIFFRACTIONc_improper_angle_d2.22
X-RAY DIFFRACTIONc_mcbond_it5.211.5
X-RAY DIFFRACTIONc_mcangle_it6.362
X-RAY DIFFRACTIONc_scbond_it7.552
X-RAY DIFFRACTIONc_scangle_it92.5
LS refinement shellResolution: 2.1→2.18 Å / Rfactor Rfree error: 0.023 / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.372 264 5.1 %
Rwork0.337 4941 -
all-5205 -
obs--98 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.param&_1_TOPOLOGY_INFILE_1
X-RAY DIFFRACTION2water_rep.param&_1_TOPOLOGY_INFILE_2
X-RAY DIFFRACTION3sulfate.par&_1_TOPOLOGY_INFILE_3
X-RAY DIFFRACTION4mpd.par&_1_TOPOLOGY_INFILE_4
X-RAY DIFFRACTION5ion.param&_1_TOPOLOGY_INFILE_5

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