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- PDB-8tf1: Crystal Structure of Pyridoxal Reductase (PDXI)in complex with NA... -

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Basic information

Entry
Database: PDB / ID: 8tf1
TitleCrystal Structure of Pyridoxal Reductase (PDXI)in complex with NADPH and Pyridoxal
ComponentsPyridoxine 4-dehydrogenase
KeywordsOXIDOREDUCTASE / PDXI / Aldo-keto reductases superfamily / Vitamin B6 / NADPH / Pyridoxal
Function / homology
Function and homology information


pyridoxine 4-dehydrogenase / pyridoxine 4-dehydrogenase (NADP+) activity / pyridoxal 5'-phosphate salvage / : / cytoplasm / cytosol
Similarity search - Function
: / NADP-dependent oxidoreductase domain / Aldo/keto reductase family / NADP-dependent oxidoreductase domain superfamily
Similarity search - Domain/homology
NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / 4,5-bis(hydroxymethyl)-2-methyl-pyridin-3-ol / Pyridoxine 4-dehydrogenase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsDonkor, A.K. / Safo, M.K. / Musayev, F.N.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI)1R61HL156158 United States
CitationJournal: Febs J. / Year: 2023
Title: Functional and structural properties of pyridoxal reductase (PdxI) from Escherichia coli: a pivotal enzyme in the vitamin B6 salvage pathway.
Authors: Tramonti, A. / Donkor, A.K. / Parroni, A. / Musayev, F.N. / Barile, A. / Ghatge, M.S. / Graziani, C. / Alkhairi, M. / AlAwadh, M. / di Salvo, M.L. / Safo, M.K. / Contestabile, R.
History
DepositionJul 7, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 18, 2024Provider: repository / Type: Initial release
Revision 1.1Jul 2, 2025Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Pyridoxine 4-dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,8444
Polymers32,9071
Non-polymers9373
Water5,567309
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)91.952, 75.745, 43.094
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11A-682-

HOH

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Components

#1: Protein Pyridoxine 4-dehydrogenase


Mass: 32907.258 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: pdxI / Plasmid: pET28b(+) / Production host: Escherichia coli (E. coli) / Strain (production host): HMS174(DE3) / References: UniProt: P25906, pyridoxine 4-dehydrogenase
#2: Chemical ChemComp-NAP / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / 2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE


Mass: 743.405 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H28N7O17P3
#3: Chemical ChemComp-UEG / 4,5-bis(hydroxymethyl)-2-methyl-pyridin-3-ol


Mass: 169.178 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H11NO3 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 309 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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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: 2.28 Å3/Da / Density % sol: 46.12 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: 0.1M MES/NaOH, pH 6.5, 30% PEG400, 0.1M MgCl2

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5406 Å
DetectorType: DECTRIS EIGER R 4M / Detector: PIXEL / Date: May 19, 2022 / Details: Rigaku VariMax-VHF Arc) Sec Confocal
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5406 Å / Relative weight: 1
ReflectionResolution: 2→27.18 Å / Num. obs: 21054 / % possible obs: 100 % / Redundancy: 7 % / CC1/2: 0.999 / Rmerge(I) obs: 0.068 / Rpim(I) all: 0.027 / Rrim(I) all: 0.073 / Net I/σ(I): 23.8 / Num. measured all: 147270
Reflection shellResolution: 2→2.05 Å / % possible obs: 100 % / Redundancy: 6.9 % / Rmerge(I) obs: 0.443 / Num. measured all: 10752 / Num. unique obs: 1562 / CC1/2: 0.913 / Rpim(I) all: 0.18 / Rrim(I) all: 0.479 / Net I/σ(I) obs: 4.2

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
Aimlessdata scaling
PHASERphasing
CrysalisProdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→27.177 Å / SU ML: 0.2 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 22.29 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2367 1017 4.84 %
Rwork0.1786 --
obs0.1813 21010 99.97 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2→27.177 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2159 0 61 309 2529
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0082265
X-RAY DIFFRACTIONf_angle_d1.2273094
X-RAY DIFFRACTIONf_dihedral_angle_d15.043828
X-RAY DIFFRACTIONf_chiral_restr0.051360
X-RAY DIFFRACTIONf_plane_restr0.009397
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.0001-2.10550.24451470.18472790X-RAY DIFFRACTION100
2.1055-2.23730.25741630.18162804X-RAY DIFFRACTION100
2.2373-2.410.22571390.18432819X-RAY DIFFRACTION100
2.41-2.65230.25941410.19032819X-RAY DIFFRACTION100
2.6523-3.03570.25431490.19112842X-RAY DIFFRACTION100
3.0357-3.8230.22011310.16982894X-RAY DIFFRACTION100
3.823-27.170.22541470.17013025X-RAY DIFFRACTION100

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