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- PDB-1rfu: Crystal structure of pyridoxal kinase complexed with ADP and PLP -

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Basic information

Entry
Database: PDB / ID: 1rfu
TitleCrystal structure of pyridoxal kinase complexed with ADP and PLP
Componentspyridoxal kinase
KeywordsTRANSFERASE
Function / homology
Function and homology information


pyridoxal kinase activity / pyridoxal 5'-phosphate salvage / pyridoxal kinase / phosphorylation / ATP binding / metal ion binding / 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'-DIPHOSPHATE / PYRIDOXAL-5'-PHOSPHATE / Pyridoxal kinase
Similarity search - Component
Biological speciesOvis aries (sheep)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsLiang, D.-C. / Jiang, T. / Li, M.-H.
Citation
Journal: J.BIOL.CHEM. / Year: 2004
Title: Conformational changes in the reaction of pyridoxal kinase
Authors: Li, M.-H. / Kwok, F. / Chang, W.-R. / Liu, S.-Q. / Lo, S.C.L. / Zhang, J.-P. / Jiang, T. / Liang, D.-C.
#1: Journal: J.Biol.Chem. / Year: 2002
Title: Crystal Structure of Brain Pyridoxal Kinase, a Novel Member of the Ribokinase Superfamily
Authors: Li, M.-H. / Kwok, F. / Chang, W.-R. / Lau, C.-K. / Zhang, J.-P. / Lo, S.C.L. / Jiang, T. / Liang, D.-C.
#2: Journal: Acta Crystallogr.,Sect.D / Year: 2002
Title: Crystallization and preliminary crystallographic studies of pyridoxal kinase from sheep brain
Authors: Li, M.-H. / Kwok, F. / An, X.-M. / Chang, W.-R. / Lau, C.-K. / Zhang, J.-P. / Liu, S.-Q. / Leung, Y.-C. / Jiang, T. / Liang, D.-C.
History
DepositionNov 10, 2003Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Apr 27, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.3Oct 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 / 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 / _struct_conn.pdbx_dist_value / _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.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
C: pyridoxal kinase
D: pyridoxal kinase
E: pyridoxal kinase
F: pyridoxal kinase
G: pyridoxal kinase
H: pyridoxal kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)284,80532
Polymers278,8878
Non-polymers5,91824
Water4,810267
1
A: pyridoxal kinase
E: pyridoxal kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,2018
Polymers69,7222
Non-polymers1,4806
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6990 Å2
ΔGint-103 kcal/mol
Surface area23490 Å2
MethodPISA
2
B: pyridoxal kinase
F: pyridoxal kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,2018
Polymers69,7222
Non-polymers1,4806
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: pyridoxal kinase
H: pyridoxal kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,2018
Polymers69,7222
Non-polymers1,4806
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7070 Å2
ΔGint-105 kcal/mol
Surface area23350 Å2
MethodPISA
4
D: pyridoxal kinase
G: pyridoxal kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,2018
Polymers69,7222
Non-polymers1,4806
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)109.088, 109.088, 284.272
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number78
Space group name H-MP43
DetailsThe biological assembly is a homodimer. The eight monomers in the asymmetric unit form four such homodimers.

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Components

#1: Protein
pyridoxal kinase / Pyridoxine kinase


Mass: 34860.879 Da / Num. of mol.: 8 / Source method: isolated from a natural source / Source: (natural) Ovis aries (sheep) / References: UniProt: P82197, pyridoxal kinase
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Zn
#3: Chemical
ChemComp-PLP / PYRIDOXAL-5'-PHOSPHATE / VITAMIN B6 Phosphate


Mass: 247.142 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C8H10NO6P
#4: Chemical
ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 267 / 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: 3.04 Å3/Da / Density % sol: 59.25 %
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop / pH: 8.2
Details: ammonium sulphate, potassium phosphate, ADP, PLP, zinc acetate, pH 8.2, VAPOR DIFFUSION, HANGING DROP, temperature 290K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SEALED TUBE / Wavelength: 1.5418 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Aug 12, 2002
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.8→20 Å / Num. all: 86300 / Num. obs: 75513 / % possible obs: 87.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 4.8 % / Rmerge(I) obs: 0.087 / Net I/σ(I): 11.4
Reflection shellResolution: 2.8→2.86 Å / Rmerge(I) obs: 0.465 / Mean I/σ(I) obs: 2.3 / Num. unique all: 5131 / % possible all: 95.2

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
CNSrefinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1LHP

1lhp


Resolution: 2.8→20 Å / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): -3 / Stereochemistry target values: Engh & Huber
Details: used least squares procedure for hemihedral twinning, with a twinning operation of "h,-k,-l", and a twinning fraction of 0.5
RfactorNum. reflection% reflectionSelection details
Rfree0.281 1971 -RANDOM
Rwork0.229 ---
all0.23 86300 --
obs0.23 75513 87.5 %-
Refinement stepCycle: LAST / Resolution: 2.8→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms19512 0 344 267 20123
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.01
X-RAY DIFFRACTIONc_angle_deg1.5

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