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- PDB-5jo9: Structural characterization of the thermostable Bradyrhizobium ja... -

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Basic information

Entry
Database: PDB / ID: 5jo9
TitleStructural characterization of the thermostable Bradyrhizobium japonicum d-sorbitol dehydrogenase
ComponentsRibitol 2-dehydrogenase
KeywordsOXIDOREDUCTASE / glucitol dehydrogenase
Function / homology
Function and homology information


oxidoreductase activity
Similarity search - Function
short chain dehydrogenase / Short-chain dehydrogenase/reductase, conserved site / Short-chain dehydrogenases/reductases family signature. / 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
PHOSPHATE ION / sorbitol / Ribitol 2-dehydrogenase
Similarity search - Component
Biological speciesBradyrhizobium japonicum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.894 Å
AuthorsFredslund, F. / Otten, H. / Navarro Poulsen, J.-C. / Lo Leggio, L.
CitationJournal: Acta Crystallogr F Struct Biol Commun / Year: 2016
Title: Structural characterization of the thermostable Bradyrhizobium japonicumD-sorbitol dehydrogenase.
Authors: Fredslund, F. / Otten, H. / Gemperlein, S. / Poulsen, J.C. / Carius, Y. / Kohring, G.W. / Lo Leggio, L.
History
DepositionMay 2, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 9, 2016Provider: repository / Type: Initial release
Revision 1.1Apr 18, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.pdbx_database_id_PubMed ..._citation.journal_abbrev / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.2Jul 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 1.3Jan 10, 2024Group: 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: Ribitol 2-dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,3963
Polymers26,1181
Non-polymers2772
Water0
1
A: Ribitol 2-dehydrogenase
hetero molecules

A: Ribitol 2-dehydrogenase
hetero molecules

A: Ribitol 2-dehydrogenase
hetero molecules

A: Ribitol 2-dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)105,58212
Polymers104,4734
Non-polymers1,1098
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_885-x+3,-y+3,z1
crystal symmetry operation7_557y,x,-z+8/31
crystal symmetry operation10_887-y+3,-x+3,-z+8/31
Buried area15710 Å2
ΔGint-110 kcal/mol
Surface area32400 Å2
MethodPISA
Unit cell
Length a, b, c (Å)100.879, 100.879, 88.600
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number180
Space group name H-MP6222

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Components

#1: Protein Ribitol 2-dehydrogenase /


Mass: 26118.359 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bradyrhizobium japonicum (bacteria) / Gene: rdh, bll6662 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Gold / References: UniProt: Q89FN7
#2: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#3: Sugar ChemComp-SOR / sorbitol / D-sorbitol / D-glucitol / Sorbitol


Type: D-saccharide / Mass: 182.172 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C6H14O6

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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: 2.49 Å3/Da / Density % sol: 50.63 % / Description: Disc shaped
Crystal growTemperature: 294 K / Method: evaporation / pH: 5.6 / Details: 1.4 M NaH2PO4/K2HPO4 pH 5.6

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.8999 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 24, 2011
RadiationMonochromator: Si111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8999 Å / Relative weight: 1
ReflectionResolution: 2.894→43.87 Å / Num. obs: 6287 / % possible obs: 99.5 % / Redundancy: 10.32 % / CC1/2: 0.996 / Rrim(I) all: 0.247 / Net I/σ(I): 12.4
Reflection shellResolution: 2.894→3.07 Å / Redundancy: 10.17 % / Mean I/σ(I) obs: 1.14 / Rrim(I) all: 2.485 / % possible all: 98

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4NBU

4nbu


Resolution: 2.894→43.834 Å / SU ML: 0.46 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 33.54 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2951 312 4.96 %
Rwork0.27 --
obs0.2713 6284 99.19 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.894→43.834 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1800 0 17 0 1817
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0041846
X-RAY DIFFRACTIONf_angle_d0.7652514
X-RAY DIFFRACTIONf_dihedral_angle_d14.8321125
X-RAY DIFFRACTIONf_chiral_restr0.045306
X-RAY DIFFRACTIONf_plane_restr0.004322
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.8944-3.64640.37791520.32942882X-RAY DIFFRACTION99
3.6464-43.8390.26621600.24963090X-RAY DIFFRACTION100

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