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- PDB-3n2t: Structure of the glycerol dehydrogenase AKR11B4 from Gluconobacte... -

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Basic information

Entry
Database: PDB / ID: 3n2t
TitleStructure of the glycerol dehydrogenase AKR11B4 from Gluconobacter oxydans
ComponentsPutative oxidoreductase
KeywordsOXIDOREDUCTASE / ALDO/KETO Reductase superfamily / AKR / AKR11B4 / TIM BARREL
Function / homology
Function and homology information


Oxidoreductases; Acting on the CH-OH group of donors; With NAD+ or NADP+ as acceptor / oxidoreductase activity
Similarity search - Function
NADP-dependent oxidoreductase domain / Aldo/keto reductase family signature 2. / Aldo/keto reductase, conserved site / NADP-dependent oxidoreductase domain / Aldo/keto reductase family / NADP-dependent oxidoreductase domain superfamily / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
Putative oxidoreductase
Similarity search - Component
Biological speciesGluconobacter oxydans (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsRichter, N. / Breicha, K. / Hummel, W. / Niefind, K.
Citation
Journal: J.Mol.Biol. / Year: 2010
Title: The Three-Dimensional Structure of AKR11B4, a Glycerol Dehydrogenase from Gluconobacter oxydans, Reveals a Tryptophan Residue as an Accelerator of Reaction Turnover.
Authors: Richter, N. / Breicha, K. / Hummel, W. / Niefind, K.
#1: Journal: Chembiochem / Year: 2009
Title: Characterisation of a recombinant NADP-dependent glycerol dehydrogenase from Gluconobacter oxydans and its application in the production of L-glyceraldehyde.
Authors: Richter, N. / Neumann, M. / Liese, A. / Wohlgemuth, R. / Eggert, T. / Hummel, W.
History
DepositionMay 19, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 21, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 21, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_source / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_source.pdbx_synchrotron_site / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Putative oxidoreductase


Theoretical massNumber of molelcules
Total (without water)39,0761
Polymers39,0761
Non-polymers00
Water2,702150
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)41.250, 62.390, 59.820
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 Putative oxidoreductase


Mass: 39076.410 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Gluconobacter oxydans (bacteria) / Gene: GOX1615 / Plasmid: pET28a (NdeI/SalI) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: Q5FQJ0, Oxidoreductases; Acting on the CH-OH group of donors; With NAD+ or NADP+ as acceptor
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 150 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 1.97 Å3/Da / Density % sol: 37.56 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: protein stock solution: 10 mg/ml AKR11B4 protein, 10 mM Tris/HCl puffer, 150 mM NaCl, 0.5 mM EDTA, pH 8.5. Reservoir solution: 35 % (w/v) poly ethylen glycol 3350 (PEG 3350), 200 mM ...Details: protein stock solution: 10 mg/ml AKR11B4 protein, 10 mM Tris/HCl puffer, 150 mM NaCl, 0.5 mM EDTA, pH 8.5. Reservoir solution: 35 % (w/v) poly ethylen glycol 3350 (PEG 3350), 200 mM potassium nitrate. The crystallization drop contained equal volumes of the reservoir and the protein stock solution before equilibration. The pH-value in the crystallization drop was determined by the buffer of the protein stock solution., VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X11 / Wavelength: 0.9537 Å
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 2→34.5 Å / Num. obs: 26999 / % possible obs: 99.8 % / Redundancy: 5.4 % / Biso Wilson estimate: 29.1 Å2 / Rmerge(I) obs: 0.133 / Rsym value: 0.133 / Net I/σ(I): 10.1

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Processing

Software
NameVersionClassification
MOLREPphasing
PHENIX(phenix.refine: 1.5_2)refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→24.119 Å / SU ML: 0.24 / σ(F): 1.37 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2316 1029 5 %
Rwork0.1885 --
obs0.1907 20591 99.86 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 28.413 Å2 / ksol: 0.344 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-2.2631 Å2-0 Å23.2464 Å2
2---5.1194 Å2-0 Å2
3---2.8563 Å2
Refinement stepCycle: LAST / Resolution: 2→24.119 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2585 0 0 150 2735
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0062645
X-RAY DIFFRACTIONf_angle_d0.9633584
X-RAY DIFFRACTIONf_dihedral_angle_d16.788996
X-RAY DIFFRACTIONf_chiral_restr0.067388
X-RAY DIFFRACTIONf_plane_restr0.005471
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.10540.25771440.2262750X-RAY DIFFRACTION100
2.1054-2.23720.26191470.21422783X-RAY DIFFRACTION100
2.2372-2.40980.27531480.20582811X-RAY DIFFRACTION100
2.4098-2.65210.25531450.21032763X-RAY DIFFRACTION100
2.6521-3.03520.2441470.20082792X-RAY DIFFRACTION100
3.0352-3.82160.22551480.17132814X-RAY DIFFRACTION100
3.8216-24.12070.17691500.15262849X-RAY DIFFRACTION100

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