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- PDB-8te8: Crystal Structure of Pyridoxal Reductase (PDXI) -

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Basic information

Entry
Database: PDB / ID: 8te8
TitleCrystal Structure of Pyridoxal Reductase (PDXI)
ComponentsPyridoxine 4-dehydrogenase
KeywordsOXIDOREDUCTASE / PDXI / Aldo-keto reductases superfamily / Vitamin B6 / 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
Pyridoxine 4-dehydrogenase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.2 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 5, 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
B: Pyridoxine 4-dehydrogenase


Theoretical massNumber of molelcules
Total (without water)65,8152
Polymers65,8152
Non-polymers00
Water6,251347
1
A: Pyridoxine 4-dehydrogenase


Theoretical massNumber of molelcules
Total (without water)32,9071
Polymers32,9071
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Pyridoxine 4-dehydrogenase


Theoretical massNumber of molelcules
Total (without water)32,9071
Polymers32,9071
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)46.523, 74.924, 85.134
Angle α, β, γ (deg.)90.00, 98.33, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Pyridoxine 4-dehydrogenase


Mass: 32907.258 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: pdxI, ydbC, b1406, JW1403 / Plasmid: pET28b(+) / Production host: Escherichia coli (E. coli) / Strain (production host): HMS174(DE3) / References: UniProt: P25906, pyridoxine 4-dehydrogenase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 347 / Source method: isolated from a natural source / Formula: H2O
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: 2.23 Å3/Da / Density % sol: 44.9 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: 0.1M MES/NaOH, pH6.5, 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: Nov 24, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5406 Å / Relative weight: 1
ReflectionResolution: 2.2→27.992 Å / Num. obs: 29498 / % possible obs: 99.9 % / Redundancy: 5.8 % / CC1/2: 0.997 / Rmerge(I) obs: 0.107 / Rpim(I) all: 0.048 / Rrim(I) all: 0.118 / Net I/σ(I): 10.6
Reflection shellResolution: 2.2→2.27 Å / % possible obs: 100 % / Redundancy: 5.5 % / Rmerge(I) obs: 0.401 / Num. measured all: 14089 / Num. unique obs: 2563 / CC1/2: 0.944 / Rpim(I) all: 0.188 / Rrim(I) all: 0.444 / Net I/σ(I) obs: 3.8

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
Aimlessdata scaling
PHASERphasing
CrysalisPro41_64.122adata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.2→27.992 Å / SU ML: 0.27 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 26.96 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2476 1446 4.92 %
Rwork0.1798 --
obs0.1831 29420 99.76 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.2→27.992 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4267 0 0 347 4614
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0084349
X-RAY DIFFRACTIONf_angle_d1.1145926
X-RAY DIFFRACTIONf_dihedral_angle_d14.4911576
X-RAY DIFFRACTIONf_chiral_restr0.042697
X-RAY DIFFRACTIONf_plane_restr0.006778
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2-2.27860.33541400.21562760X-RAY DIFFRACTION100
2.2786-2.36980.31731310.21292805X-RAY DIFFRACTION100
2.3698-2.47760.28271680.2022758X-RAY DIFFRACTION100
2.4776-2.60810.26981310.20422809X-RAY DIFFRACTION100
2.6081-2.77140.27511580.2012787X-RAY DIFFRACTION100
2.7714-2.98520.3211230.20312793X-RAY DIFFRACTION100
2.9852-3.28510.26541360.19292816X-RAY DIFFRACTION100
3.2851-3.75950.2291580.1682787X-RAY DIFFRACTION100
3.7595-4.73290.20261400.14712812X-RAY DIFFRACTION99
4.7329-27.9920.19141610.15232847X-RAY DIFFRACTION100

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