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- PDB-8tez: Crystal Structure of Pyridoxal Reductase (PDXI)in complex with NADPH -

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Basic information

Entry
Database: PDB / ID: 8tez
TitleCrystal Structure of Pyridoxal Reductase (PDXI)in complex with NADPH
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 / : / cytosol / cytoplasm
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 / Pyridoxine 4-dehydrogenase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.3 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

Downloads & links

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Assembly

Deposited unit
A: Pyridoxine 4-dehydrogenase
B: Pyridoxine 4-dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,3506
Polymers65,8152
Non-polymers1,5354
Water3,639202
1
A: Pyridoxine 4-dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,6753
Polymers32,9071
Non-polymers7682
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Pyridoxine 4-dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,6753
Polymers32,9071
Non-polymers7682
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)48.713, 76.064, 85.759
Angle α, β, γ (deg.)90.00, 98.69, 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 / 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.: 2 / Source method: obtained synthetically / Formula: C21H28N7O17P3 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 202 / 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: 2.39 Å3/Da / Density % sol: 48.51 %
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: Jun 1, 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: 2.3→26.49 Å / Num. obs: 27634 / % possible obs: 99.9 % / Redundancy: 6.6 % / CC1/2: 0.997 / Rmerge(I) obs: 0.112 / Rpim(I) all: 0.047 / Rrim(I) all: 0.121 / Net I/σ(I): 11.8 / Num. measured all: 183688
Reflection shellResolution: 2.3→2.38 Å / % possible obs: 100 % / Redundancy: 6.7 % / Rmerge(I) obs: 0.437 / Num. measured all: 18133 / Num. unique obs: 2700 / CC1/2: 0.959 / Rpim(I) all: 0.181 / Rrim(I) all: 0.473 / Net I/σ(I) obs: 4

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
Aimlessdata scaling
PHASERphasing
CrysalisProdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.3→26.489 Å / SU ML: 0.28 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 29.73 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2834 1450 5.26 %
Rwork0.2104 --
obs0.2142 27587 99.87 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.3→26.489 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4267 0 98 202 4567
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.014456
X-RAY DIFFRACTIONf_angle_d1.1766086
X-RAY DIFFRACTIONf_dihedral_angle_d15.6911630
X-RAY DIFFRACTIONf_chiral_restr0.044713
X-RAY DIFFRACTIONf_plane_restr0.007784
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3-2.38220.33251560.22632579X-RAY DIFFRACTION100
2.3822-2.47750.29521550.22292568X-RAY DIFFRACTION100
2.4775-2.59010.30761540.23022609X-RAY DIFFRACTION100
2.5901-2.72660.33291450.22772619X-RAY DIFFRACTION100
2.7266-2.89720.27251190.23482612X-RAY DIFFRACTION100
2.8972-3.12060.33011620.23472587X-RAY DIFFRACTION100
3.1206-3.4340.31291530.22332629X-RAY DIFFRACTION100
3.434-3.92950.24041230.1982621X-RAY DIFFRACTION100
3.9295-4.94550.26771340.18142640X-RAY DIFFRACTION100
4.9455-26.480.22511490.19292673X-RAY DIFFRACTION100

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