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- PDB-5a06: Crystal structure of aldose-aldose oxidoreductase from Caulobacte... -

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Basic information

Entry
Database: PDB / ID: 5a06
TitleCrystal structure of aldose-aldose oxidoreductase from Caulobacter crescentus complexed with sorbitol
ComponentsALDOSE-ALDOSE OXIDOREDUCTASE
KeywordsOXIDOREDUCTASE
Function / homology
Function and homology information


oxidoreductase activity / nucleotide binding
Similarity search - Function
Glucose-fructose oxidoreductase, bacterial / : / Gfo/Idh/MocA-like oxidoreductase, C-terminal / Oxidoreductase family, C-terminal alpha/beta domain / Gfo/Idh/MocA-like oxidoreductase, N-terminal / Oxidoreductase family, NAD-binding Rossmann fold / Dihydrodipicolinate Reductase; domain 2 / Dihydrodipicolinate Reductase; domain 2 / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily ...Glucose-fructose oxidoreductase, bacterial / : / Gfo/Idh/MocA-like oxidoreductase, C-terminal / Oxidoreductase family, C-terminal alpha/beta domain / Gfo/Idh/MocA-like oxidoreductase, N-terminal / Oxidoreductase family, NAD-binding Rossmann fold / Dihydrodipicolinate Reductase; domain 2 / Dihydrodipicolinate Reductase; domain 2 / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Rossmann fold / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-NDP / sorbitol / Glucose-fructose oxidoreductase
Similarity search - Component
Biological speciesCAULOBACTER CRESCENTUS CB15 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.841 Å
AuthorsTaberman, H. / Rouvinen, J. / Parkkinen, T.
CitationJournal: Biochem.J. / Year: 2015
Title: Structure and Function of Caulobacter Crescentus Aldose-Aldose Oxidoreductase.
Authors: Taberman, H. / Andberg, M. / Koivula, A. / Hakulinen, N. / Penttila, M. / Rouvinen, J. / Parkkinen, T.
History
DepositionApr 17, 2015Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 21, 2015Provider: repository / Type: Initial release
Revision 1.1Dec 9, 2015Group: Database references
Revision 1.2Jul 29, 2020Group: Derived calculations / Other / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_database_status / 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_database_status.status_code_sf / _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: ALDOSE-ALDOSE OXIDOREDUCTASE
B: ALDOSE-ALDOSE OXIDOREDUCTASE
C: ALDOSE-ALDOSE OXIDOREDUCTASE
D: ALDOSE-ALDOSE OXIDOREDUCTASE
E: ALDOSE-ALDOSE OXIDOREDUCTASE
F: ALDOSE-ALDOSE OXIDOREDUCTASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)232,24737
Polymers223,7376
Non-polymers8,51031
Water37,6692091
1
C: ALDOSE-ALDOSE OXIDOREDUCTASE
F: ALDOSE-ALDOSE OXIDOREDUCTASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)77,35512
Polymers74,5792
Non-polymers2,77610
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8140 Å2
ΔGint-26.9 kcal/mol
Surface area24660 Å2
MethodPISA
2
A: ALDOSE-ALDOSE OXIDOREDUCTASE
E: ALDOSE-ALDOSE OXIDOREDUCTASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)77,35512
Polymers74,5792
Non-polymers2,77610
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8120 Å2
ΔGint-19.4 kcal/mol
Surface area24660 Å2
MethodPISA
3
B: ALDOSE-ALDOSE OXIDOREDUCTASE
D: ALDOSE-ALDOSE OXIDOREDUCTASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)77,53713
Polymers74,5792
Non-polymers2,95811
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8320 Å2
ΔGint-23.3 kcal/mol
Surface area24780 Å2
MethodPISA
Unit cell
Length a, b, c (Å)101.189, 154.088, 107.776
Angle α, β, γ (deg.)90.00, 110.02, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(-0.0504, -0.8182, 0.5727), (0.8302, -0.3531, -0.4314), (0.5552, 0.4537, 0.6971)128.2613, -96.1354, -73.5539
2given(0.224, -0.678, -0.7001), (-0.7594, -0.5716, 0.3107), (-0.6108, 0.4621, -0.643)147.6676, 99.0205, 126.1692
3given(0.1936, 0.7368, -0.6478), (0.6551, -0.5886, -0.4737), (-0.7303, -0.3327, -0.5966)141.7895, -71.8772, 139.8335
4given(-0.9824, 0.1864, -0.0093), (0.1837, 0.9572, -0.2237), (-0.0327, -0.2215, -0.9746)284.1524, -21.115, 50.0351
5given(-0.3401, 0.5495, 0.7631), (-0.5485, -0.7751, 0.3137), (0.7639, -0.3119, 0.565)153.8143, 72.4079, -99.909

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Components

#1: Protein
ALDOSE-ALDOSE OXIDOREDUCTASE


Mass: 37289.438 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) CAULOBACTER CRESCENTUS CB15 (bacteria) / Strain: CB15 / Production host: SACCHAROMYCES CEREVISIAE (brewer's yeast)
References: UniProt: Q9A8X3, Oxidoreductases; Acting on the CH-OH group of donors; With unknown physiological acceptors
#2: Chemical
ChemComp-NDP / NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE


Mass: 745.421 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C21H30N7O17P3
#3: Sugar
ChemComp-SOR / sorbitol / D-sorbitol / D-glucitol


Type: D-saccharide / Mass: 182.172 Da / Num. of mol.: 19
Source method: isolated from a genetically manipulated source
Formula: C6H14O6
#4: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2091 / 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: 3.6 Å3/Da / Density % sol: 65 % / Description: NONE
Crystal growpH: 6.5 / Details: MES PH 6.5, AMMONIUM SULPHATE, 2-PROPANOL

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.8726
DetectorType: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Feb 7, 2015 / Details: MIRRORS
RadiationMonochromator: SI-CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8726 Å / Relative weight: 1
ReflectionResolution: 1.84→50 Å / Num. obs: 264019 / % possible obs: 98.6 % / Observed criterion σ(I): 2 / Redundancy: 4.3 % / Biso Wilson estimate: 22.19 Å2 / Rmerge(I) obs: 0.1 / Net I/σ(I): 11
Reflection shellResolution: 1.84→1.95 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.68 / Mean I/σ(I) obs: 2 / % possible all: 93

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1H6A

1h6a


Resolution: 1.841→48.101 Å / SU ML: 0.23 / σ(F): 1.36 / Phase error: 18.6 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1867 13201 5 %
Rwork0.1594 --
obs0.1607 264020 98.69 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 24.6 Å2
Refinement stepCycle: LAST / Resolution: 1.841→48.101 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15566 0 546 2091 18203
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00816478
X-RAY DIFFRACTIONf_angle_d1.1322374
X-RAY DIFFRACTIONf_dihedral_angle_d12.5596086
X-RAY DIFFRACTIONf_chiral_restr0.0512462
X-RAY DIFFRACTIONf_plane_restr0.0052903
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8405-1.86150.4622920.41735555X-RAY DIFFRACTION66
1.8615-1.88340.32924430.3018409X-RAY DIFFRACTION100
1.8834-1.90630.30914430.28628425X-RAY DIFFRACTION100
1.9063-1.93050.3184420.27128393X-RAY DIFFRACTION100
1.9305-1.95590.28924450.25118459X-RAY DIFFRACTION100
1.9559-1.98270.26854450.22418454X-RAY DIFFRACTION100
1.9827-2.0110.23574410.20888379X-RAY DIFFRACTION100
2.011-2.0410.23514470.19978484X-RAY DIFFRACTION100
2.041-2.07290.23244430.18668416X-RAY DIFFRACTION100
2.0729-2.10690.22244440.1868450X-RAY DIFFRACTION100
2.1069-2.14320.21184460.18098468X-RAY DIFFRACTION100
2.1432-2.18220.21734420.18388393X-RAY DIFFRACTION100
2.1822-2.22420.224470.18018486X-RAY DIFFRACTION100
2.2242-2.26960.23054450.18238455X-RAY DIFFRACTION100
2.2696-2.31890.20574440.16558442X-RAY DIFFRACTION100
2.3189-2.37280.18254450.16098457X-RAY DIFFRACTION100
2.3728-2.43220.18994460.15558481X-RAY DIFFRACTION100
2.4322-2.49790.19264450.16048456X-RAY DIFFRACTION100
2.4979-2.57140.2084460.16228474X-RAY DIFFRACTION100
2.5714-2.65440.19374450.15838453X-RAY DIFFRACTION100
2.6544-2.74930.17684450.15128444X-RAY DIFFRACTION100
2.7493-2.85940.18014460.14828479X-RAY DIFFRACTION100
2.8594-2.98950.1814470.15478487X-RAY DIFFRACTION100
2.9895-3.14710.17684460.15098476X-RAY DIFFRACTION100
3.1471-3.34420.16754450.14098462X-RAY DIFFRACTION100
3.3442-3.60230.16194460.13838481X-RAY DIFFRACTION100
3.6023-3.96470.13354450.12288449X-RAY DIFFRACTION100
3.9647-4.5380.13324460.11218475X-RAY DIFFRACTION100
4.538-5.71590.15024500.1258536X-RAY DIFFRACTION100
5.7159-48.11710.15674490.14998541X-RAY DIFFRACTION99

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