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- PDB-3ai3: The crystal structure of L-Sorbose reductase from Gluconobacter f... -

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Basic information

Entry
Database: PDB / ID: 3ai3
TitleThe crystal structure of L-Sorbose reductase from Gluconobacter frateurii complexed with NADPH and L-sorbose
ComponentsNADPH-sorbose reductase
KeywordsOXIDOREDUCTASE / Rossmann-fold / NADPH-dependent reductase / short chain dehydrogenase/reductase
Function / homology
Function and homology information


oxidoreductase activity / nucleotide binding
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
Chem-NDP / alpha-L-sorbopyranose / L-sorbose / NADPH-sorbose reductase
Similarity search - Component
Biological speciesGluconobacter frateurii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsKubota, K. / Nagata, K. / Okai, M. / Miyazono, K. / Tanokura, M.
CitationJournal: J.Mol.Biol. / Year: 2011
Title: The Crystal Structure of l-Sorbose Reductase from Gluconobacter frateurii Complexed with NADPH and l-Sorbose
Authors: Kubota, K. / Nagata, K. / Okai, M. / Miyazono, K. / Soemphol, W. / Ohtsuka, J. / Yamamura, A. / Saichana, N. / Toyama, H. / Matsushita, K. / Tanokura, M.
History
DepositionMay 7, 2010Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 9, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 20, 2013Group: Non-polymer description
Revision 1.3Jul 29, 2020Group: Data collection / Database references / Derived calculations
Category: chem_comp / pdbx_chem_comp_identifier ...chem_comp / pdbx_chem_comp_identifier / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _chem_comp.type / _struct_ref_seq_dif.details / Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.4Nov 1, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: NADPH-sorbose reductase
C: NADPH-sorbose reductase
E: NADPH-sorbose reductase
G: NADPH-sorbose reductase
A: L-sorbose
C: L-sorbose
E: L-sorbose
G: L-sorbose
hetero molecules


Theoretical massNumber of molelcules
Total (without water)117,90917
Polymers113,3064
Non-polymers4,60313
Water6,630368
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13410 Å2
ΔGint-106 kcal/mol
Surface area36880 Å2
MethodPISA
Unit cell
Length a, b, c (Å)61.040, 124.410, 124.540
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
NADPH-sorbose reductase / L-Sorbose Reductase


Mass: 28326.541 Da / Num. of mol.: 4 / Mutation: H116L
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Gluconobacter frateurii (bacteria) / Gene: sboA / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta(DE3) / References: UniProt: A4PB64, EC: 1.1.1.289
#2: Chemical
ChemComp-NDP / NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / Nicotinamide adenine dinucleotide phosphate


Mass: 745.421 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C21H30N7O17P3
#3: Sugar
ChemComp-SOL / L-sorbose / Sorbose


Type: L-saccharide / Mass: 180.156 Da / Num. of mol.: 5
Source method: isolated from a genetically manipulated source
Formula: C6H12O6
#4: Sugar
ChemComp-SOE / alpha-L-sorbopyranose / alpha-L-sorbose / L-sorbose / sorbose / L-sorbose in pyranose form / Sorbose


Type: L-saccharide, alpha linking / Mass: 180.156 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Formula: C6H12O6
IdentifierTypeProgram
LSorpaCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
a-L-sorbopyranoseCOMMON NAMEGMML 1.0
a-L-SorpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
SorSNFG CARBOHYDRATE SYMBOLGMML 1.0
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 368 / 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: 2.09 Å3/Da / Density % sol: 41.06 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4.5
Details: Crystals of the His116Leu mutant of SR containing 10 mM NADPH and 100 mM L-sorbose were obtained under a reservoir solution condition of 30% (w/v) PEG400, 200 mM calcium chloride and 100 mM ...Details: Crystals of the His116Leu mutant of SR containing 10 mM NADPH and 100 mM L-sorbose were obtained under a reservoir solution condition of 30% (w/v) PEG400, 200 mM calcium chloride and 100 mM sodium acetate trihydrate, pH 4.5. The crystals of SR complexed with NADPH and L-sorbose were prepared by soaking the crystals in the reservoir solution supplemented with 2 M L-sorbose and 10 mM NADPH for 12 h at 293 K., VAPOR DIFFUSION, SITTING DROP, temperature 293.0K

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NE3A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Oct 30, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.8→20 Å / Num. obs: 88419 / % possible obs: 99.8 % / Observed criterion σ(F): 1.0001 / Observed criterion σ(I): 1 / Rmerge(I) obs: 0.083 / Net I/σ(I): 21.3
Reflection shellResolution: 1.8→1.85 Å / Rmerge(I) obs: 0.465 / Mean I/σ(I) obs: 5.6 / % possible all: 100

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
REFMAC5.5.0102refinement
XDSdata reduction
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3AI2

3ai2


Resolution: 1.8→19.69 Å / Cor.coef. Fo:Fc: 0.924 / Cor.coef. Fo:Fc free: 0.885 / SU B: 2.367 / SU ML: 0.076 / Cross valid method: THROUGHOUT / ESU R: 0.162 / ESU R Free: 0.146 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24941 4432 5 %RANDOM
Rwork0.2123 ---
obs0.21416 83987 99.84 %-
Solvent computationSolvent model: NONE PARAMETERS FOR MASK CACLULATION
Displacement parametersBiso mean: 12.871 Å2
Baniso -1Baniso -2Baniso -3
1-0.93 Å20 Å20 Å2
2--0.51 Å20 Å2
3----1.44 Å2
Refinement stepCycle: LAST / Resolution: 1.8→19.69 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7956 0 300 368 8624
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0228415
X-RAY DIFFRACTIONr_angle_refined_deg1.4761.99611442
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.58451048
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.16523.951324
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.697151360
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.8291548
X-RAY DIFFRACTIONr_chiral_restr0.0990.21319
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0216156
X-RAY DIFFRACTIONr_mcbond_it0.6931.55192
X-RAY DIFFRACTIONr_mcangle_it1.30828300
X-RAY DIFFRACTIONr_scbond_it2.35833223
X-RAY DIFFRACTIONr_scangle_it3.8314.53142
LS refinement shellResolution: 1.8→1.847 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.297 321 -
Rwork0.267 6131 -
obs--99.91 %

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