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- PDB-3rwb: Crystal structure of complex of 4PAL (4-Pyridoxolactone) and PLDH... -

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Basic information

Entry
Database: PDB / ID: 3rwb
TitleCrystal structure of complex of 4PAL (4-Pyridoxolactone) and PLDH (tetrameric pyridoxal 4-dehydrogenase) from Mesorhizobium loti
ComponentsPyridoxal 4-dehydrogenase
KeywordsOXIDOREDUCTASE / SHORT CHAIN DEHYDROGENASE/REDUCTASE / PYRIDOXAL / 4-PYRIDOXOLACTONE / NAD+
Function / homology
Function and homology information


pyridoxal 4-dehydrogenase / pyridoxal 4-dehydrogenase activity / vitamin B6 catabolic process
Similarity search - Function
Short-chain dehydrogenase/reductase, conserved site / Short-chain dehydrogenases/reductases family signature. / Enoyl-(Acyl carrier protein) reductase / Short-chain dehydrogenase/reductase SDR / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
7-hydroxy-6-methylfuro[3,4-c]pyridin-1(3H)-one / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / Pyridoxal 4-dehydrogenase
Similarity search - Component
Biological speciesMesorhizobium loti (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.699 Å
AuthorsChu, H.N.
CitationJournal: TO BE PUBLISHED
Title: Crystal structure of complex of 4PAL (4-Pyridoxolactone) and PLDH (tetrameric pyridoxal 4-dehydrogenase) from Mesorhizobium loti
Authors: Yagi, T. / Chu, H.N.
History
DepositionMay 8, 2011Deposition site: RCSB / Processing site: PDBJ
Revision 1.0May 9, 2012Provider: repository / Type: Initial release
Revision 1.1Nov 1, 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 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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 4-dehydrogenase
B: Pyridoxal 4-dehydrogenase
C: Pyridoxal 4-dehydrogenase
D: Pyridoxal 4-dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)105,48217
Polymers101,7084
Non-polymers3,77513
Water16,466914
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14020 Å2
ΔGint-58 kcal/mol
Surface area30390 Å2
MethodPISA
Unit cell
Length a, b, c (Å)85.537, 50.211, 94.266
Angle α, β, γ (deg.)90.00, 90.47, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Pyridoxal 4-dehydrogenase / tPLDH


Mass: 25426.914 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mesorhizobium loti (bacteria) / Gene: mlr6807, pldh-t / Plasmid: pET21a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q988B7, pyridoxal 4-dehydrogenase
#2: Chemical
ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE


Mass: 663.425 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Comment: NAD*YM
#3: Chemical
ChemComp-4PL / 7-hydroxy-6-methylfuro[3,4-c]pyridin-1(3H)-one / 4-Pyridoxolactone


Mass: 165.146 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C8H7NO3
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 914 / 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: 1.99 Å3/Da / Density % sol: 38.2 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 0.1M Sodium acetate, 0.1M Tris-HCl, PEG 4000 30%, 0.65mM Pyridoxal, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL38B1 / Wavelength: 1 Å
DetectorType: RIGAKU JUPITER 210 / Detector: CCD / Date: Nov 9, 2010
RadiationMonochromator: DOUBLE-CRYSTAL MONOCHROMATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.699→39.066 Å / Num. obs: 88415 / Redundancy: 4.8 %

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASESphasing
PHENIX(phenix.refine: 1.5_2)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3NUG

3nug


Resolution: 1.699→39 Å / SU ML: 0.16 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1662 4427 5.01 %RANDOM
Rwork0.1349 ---
obs0.1365 88381 99.74 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 60.163 Å2 / ksol: 0.4 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-0.0424 Å20 Å2-2.1458 Å2
2---1.0773 Å2-0 Å2
3---1.0348 Å2
Refinement stepCycle: LAST / Resolution: 1.699→39 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7152 0 254 914 8320
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0077797
X-RAY DIFFRACTIONf_angle_d1.19210667
X-RAY DIFFRACTIONf_dihedral_angle_d16.6862811
X-RAY DIFFRACTIONf_chiral_restr0.0781254
X-RAY DIFFRACTIONf_plane_restr0.0041363
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.6991-1.71840.18261240.1255264395
1.7184-1.73860.1681380.12692791100
1.7386-1.75980.17261310.12232769100
1.7598-1.78210.16741360.12582823100
1.7821-1.80560.16851360.12912817100
1.8056-1.83030.1851480.1342750100
1.8303-1.85640.17511500.12882810100
1.8564-1.88420.19251430.12992749100
1.8842-1.91360.16741350.12522830100
1.9136-1.9450.1561420.12272805100
1.945-1.97850.18271480.12582753100
1.9785-2.01450.18431440.12862806100
2.0145-2.05320.17731660.12462766100
2.0532-2.09510.14721610.12922816100
2.0951-2.14070.17471270.1242790100
2.1407-2.19050.16181580.12822785100
2.1905-2.24530.15991480.12092783100
2.2453-2.3060.16031490.13182811100
2.306-2.37380.16261650.1352808100
2.3738-2.45040.17971440.14172747100
2.4504-2.5380.18151680.13272823100
2.538-2.63960.15831510.13322790100
2.6396-2.75970.17251470.13322816100
2.7597-2.90510.14961610.12852779100
2.9051-3.08710.18561550.13022804100
3.0871-3.32530.15361390.12862852100
3.3253-3.65970.13631500.12292826100
3.6597-4.18880.14021560.11532835100
4.1888-5.27530.13241580.12222856100
5.2753-39.07620.19371490.1753292199

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