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- PDB-3nug: Crystal structure of wild type tetrameric pyridoxal 4-dehydrogena... -

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Basic information

Entry
Database: PDB / ID: 3nug
TitleCrystal structure of wild type tetrameric pyridoxal 4-dehydrogenase from Mesorhizobium loti
Components3-oxoacyl-(Acyl-carrier protein) reductase
KeywordsOXIDOREDUCTASE / PYRIDOXAL / tPLDH / 4-PYRIDOXOLACTONE / SHORT CHAIN DEHYDROGENASE/REDUCTASE
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
ACETIC ACID / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / Pyridoxal 4-dehydrogenase
Similarity search - Component
Biological speciesMesorhizobium loti (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.788 Å
AuthorsChu, H.N.
Citation
Journal: Biosci.Biotechnol.Biochem. / Year: 2011
Title: The crystal structure of SDR-type pyridoxal 4-dehydrogenase of Mesorhizobium loti
Authors: Chu, H.N. / Kobayashi, J. / Mikami, B. / Yagi, T.
#1: Journal: Acta Crystallogr.,Sect.F / Year: 2010
Title: Crystallization and preliminary X-ray analysis of SDR-type pyridoxal dehydrogenase from Mesorhizobium loti.
Authors: Chu, H.N. / Kobayashi, J. / Yoshikane, Y. / Mikami, B. / Yagi, T.
History
DepositionJul 6, 2010Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Apr 20, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 8, 2017Group: Advisory / Refinement description / Category: pdbx_unobs_or_zero_occ_atoms / software
Revision 1.3Nov 1, 2023Group: Advisory / Data collection ...Advisory / 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_unobs_or_zero_occ_atoms / 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: 3-oxoacyl-(Acyl-carrier protein) reductase
B: 3-oxoacyl-(Acyl-carrier protein) reductase
C: 3-oxoacyl-(Acyl-carrier protein) reductase
D: 3-oxoacyl-(Acyl-carrier protein) reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)104,4219
Polymers101,7084
Non-polymers2,7145
Water16,736929
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14030 Å2
ΔGint-58 kcal/mol
Surface area30320 Å2
MethodPISA
Unit cell
Length a, b, c (Å)85.638, 50.695, 94.551
Angle α, β, γ (deg.)90.00, 89.29, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
3-oxoacyl-(Acyl-carrier protein) reductase / Pyridoxal 4-dehydrogenase


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-ACY / ACETIC ACID


Mass: 60.052 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H4O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 929 / 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: 2.02 Å3/Da / Density % sol: 39.04 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.1M Sodium acetate, 0.1M Tris-HCl, 30% PEG4000, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 289.0K

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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: Jun 29, 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: 1.788→50 Å / Num. obs: 73944 / % possible obs: 96.5 % / Redundancy: 6.3 % / Net I/σ(I): 18.3
Reflection shellResolution: 1.8→1.86 Å / Redundancy: 5.4 % / Num. unique all: 6986 / % possible all: 92.3

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Processing

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

3ndr


Resolution: 1.788→34.573 Å / SU ML: 0.2 / Cross valid method: THROUGHOUT / σ(F): 0.12 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2016 3540 5.05 %RANDOM
Rwork0.1524 ---
obs0.1549 70095 90.85 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 39.048 Å2 / ksol: 0.323 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--3.866 Å20 Å21.0941 Å2
2--6.6524 Å20 Å2
3----2.7864 Å2
Refinement stepCycle: LAST / Resolution: 1.788→34.573 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7152 0 180 929 8261
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0067581
X-RAY DIFFRACTIONf_angle_d1.12710348
X-RAY DIFFRACTIONf_dihedral_angle_d17.2072707
X-RAY DIFFRACTIONf_chiral_restr0.0731230
X-RAY DIFFRACTIONf_plane_restr0.0041326
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7882-1.81270.28721150.18821848X-RAY DIFFRACTION63
1.8127-1.83860.22561420.17442383X-RAY DIFFRACTION84
1.8386-1.86610.24881250.17332461X-RAY DIFFRACTION83
1.8661-1.89520.2605920.19412114X-RAY DIFFRACTION72
1.8952-1.92630.24921460.21772742X-RAY DIFFRACTION95
1.9263-1.95950.26521200.19152438X-RAY DIFFRACTION83
1.9595-1.99510.27961360.1712497X-RAY DIFFRACTION87
1.9951-2.03350.24091360.16552665X-RAY DIFFRACTION90
2.0335-2.0750.24321300.15812667X-RAY DIFFRACTION92
2.075-2.12010.21171470.15592618X-RAY DIFFRACTION90
2.1201-2.16940.2371470.15962659X-RAY DIFFRACTION91
2.1694-2.22370.21731190.17332438X-RAY DIFFRACTION84
2.2237-2.28380.25831530.18442710X-RAY DIFFRACTION93
2.2838-2.3510.2431530.16392482X-RAY DIFFRACTION86
2.351-2.42680.23141550.16152760X-RAY DIFFRACTION94
2.4268-2.51350.20771400.15262801X-RAY DIFFRACTION96
2.5135-2.61410.25021440.15182871X-RAY DIFFRACTION97
2.6141-2.73310.17431430.14772836X-RAY DIFFRACTION97
2.7331-2.87710.21531540.15552891X-RAY DIFFRACTION98
2.8771-3.05730.17361260.1512934X-RAY DIFFRACTION99
3.0573-3.29310.19511600.15132918X-RAY DIFFRACTION99
3.2931-3.62420.19161580.14232929X-RAY DIFFRACTION99
3.6242-4.14790.14391620.12372949X-RAY DIFFRACTION99
4.1479-5.2230.14331570.11222949X-RAY DIFFRACTION100
5.223-34.57960.15841800.13292995X-RAY DIFFRACTION98

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