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- PDB-6pej: Structure of sorbitol dehydrogenase from Sinorhizobium meliloti 1... -

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Basic information

Entry
Database: PDB / ID: 6pej
TitleStructure of sorbitol dehydrogenase from Sinorhizobium meliloti 1021 bound to sorbitol
ComponentsSorbitol dehydrogenase (L-iditol 2-dehydrogenase)
KeywordsOXIDOREDUCTASE / SmoS / sorbitol / galactitol / dehydrogenase
Function / homology
Function and homology information


L-iditol 2-dehydrogenase / L-iditol 2-dehydrogenase (NAD+) activity
Similarity search - Function
PKS_KR / 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
sorbitol / Probable sorbitol dehydrogenase (L-iditol 2-dehydrogenase)
Similarity search - Component
Biological speciesSinorhizobium meliloti 1021 (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsBailey-Elkin, B.A. / Kohlmeier, M.G. / Oresnik, I.J. / Mark, B.L.
Funding support Canada, 1items
OrganizationGrant numberCountry
Natural Sciences and Engineering Research Council (NSERC, Canada) Canada
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2021
Title: Characterization of the sorbitol dehydrogenase SmoS from Sinorhizobium meliloti 1021
Authors: Kohlmeier, M.G. / Bailey-Elkin, B.A. / Mark, B.L. / Oresnik, I.J.
History
DepositionJun 20, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 24, 2020Provider: repository / Type: Initial release
Revision 1.1Jul 29, 2020Group: Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_entity_nonpoly / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.2Mar 10, 2021Group: Database references / Structure summary / Category: chem_comp / citation
Item: _chem_comp.pdbx_synonyms / _citation.country ..._chem_comp.pdbx_synonyms / _citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.title / _citation.year
Revision 1.3Oct 11, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _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: Sorbitol dehydrogenase (L-iditol 2-dehydrogenase)
B: Sorbitol dehydrogenase (L-iditol 2-dehydrogenase)
C: Sorbitol dehydrogenase (L-iditol 2-dehydrogenase)
D: Sorbitol dehydrogenase (L-iditol 2-dehydrogenase)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)124,0168
Polymers123,2884
Non-polymers7294
Water16,304905
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14370 Å2
ΔGint-67 kcal/mol
Surface area32820 Å2
MethodPISA
Unit cell
Length a, b, c (Å)83.298, 88.298, 87.317
Angle α, β, γ (deg.)90.000, 117.390, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Sorbitol dehydrogenase (L-iditol 2-dehydrogenase)


Mass: 30821.904 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sinorhizobium meliloti 1021 (bacteria) / Strain: 1021 / Gene: smoS, SMc01500 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q92N06, L-iditol 2-dehydrogenase
#2: Sugar
ChemComp-SOR / sorbitol / D-sorbitol / D-glucitol


Type: D-saccharide / Mass: 182.172 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Formula: C6H14O6 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 905 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.31 Å3/Da / Density % sol: 46.81 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 50 mM sodium acetate, 100 mM HEPES pH 7.4, 18% PEG 3000, 20% sorbitol

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Data collection

DiffractionMean temperature: 93 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5419 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Apr 19, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5419 Å / Relative weight: 1
ReflectionResolution: 2→39.6 Å / Num. obs: 74395 / % possible obs: 98 % / Redundancy: 3 % / Rmerge(I) obs: 0.139 / Net I/σ(I): 5.4
Reflection shellResolution: 2→10 Å / Rmerge(I) obs: 0.522 / Num. unique obs: 4478

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Processing

Software
NameVersionClassification
REFMAC5.8.0238refinement
PDB_EXTRACT3.22data extraction
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6PEI

6pei


Resolution: 2→39.08 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.915 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.192 / ESU R Free: 0.177
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2494 3581 4.8 %RANDOM
Rwork0.1941 ---
obs0.1968 70800 97.92 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 74.72 Å2 / Biso mean: 19.442 Å2 / Biso min: 6.03 Å2
Baniso -1Baniso -2Baniso -3
1-0.99 Å2-0 Å2-1.58 Å2
2---0.01 Å2-0 Å2
3---0.43 Å2
Refinement stepCycle: final / Resolution: 2→39.08 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7588 0 48 905 8541
Biso mean--23.84 27.67 -
Num. residues----1026
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0137732
X-RAY DIFFRACTIONr_bond_other_d0.0370.0177351
X-RAY DIFFRACTIONr_angle_refined_deg1.9271.63810468
X-RAY DIFFRACTIONr_angle_other_deg2.4691.58216870
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.25651022
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.74321.222401
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.796151237
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.4881569
X-RAY DIFFRACTIONr_chiral_restr0.10.21078
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.028940
X-RAY DIFFRACTIONr_gen_planes_other0.0150.021671
X-RAY DIFFRACTIONr_mcbond_it1.8481.8864100
X-RAY DIFFRACTIONr_mcbond_other1.8481.8864099
X-RAY DIFFRACTIONr_mcangle_it2.5812.8245118
LS refinement shellResolution: 2→2.052 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.291 317 -
Rwork0.262 5289 -
all-5606 -
obs--99.61 %

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