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- PDB-5a04: Crystal structure of aldose-aldose oxidoreductase from Caulobacte... -

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Basic information

Entry
Database: PDB / ID: 5a04
TitleCrystal structure of aldose-aldose oxidoreductase from Caulobacter crescentus complexed with glucose
ComponentsALDOSE-ALDOSE OXIDOREDUCTASE
KeywordsOXIDOREDUCTASE
Function / homology
Function and homology information


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 ...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
beta-D-glucopyranose / 1,4-DIETHYLENE DIOXIDE / Chem-NDP / Glucose-fructose oxidoreductase
Similarity search - Component
Biological speciesCAULOBACTER CRESCENTUS CB15 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.698 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: Data collection / Derived calculations ...Data collection / Derived calculations / Other / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / 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)230,84732
Polymers223,7376
Non-polymers7,11126
Water36,6972037
1
A: ALDOSE-ALDOSE OXIDOREDUCTASE
E: ALDOSE-ALDOSE OXIDOREDUCTASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,97911
Polymers74,5792
Non-polymers2,4009
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3560 Å2
ΔGint-10.2 kcal/mol
Surface area30540 Å2
MethodPQS
2
B: ALDOSE-ALDOSE OXIDOREDUCTASE
D: ALDOSE-ALDOSE OXIDOREDUCTASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,6228
Polymers74,5792
Non-polymers2,0436
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3250 Å2
ΔGint-4 kcal/mol
Surface area30430 Å2
MethodPQS
3
C: ALDOSE-ALDOSE OXIDOREDUCTASE
F: ALDOSE-ALDOSE OXIDOREDUCTASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)77,24713
Polymers74,5792
Non-polymers2,66811
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3160 Å2
ΔGint-5.6 kcal/mol
Surface area30760 Å2
MethodPQS
Unit cell
Length a, b, c (Å)101.154, 153.516, 108.145
Angle α, β, γ (deg.)90.00, 109.35, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(-0.0582, -0.8208, 0.5682), (0.8202, -0.3638, -0.4415), (0.5692, 0.4403, 0.6944)24.7202, -9.0866, -19.2203
2given(0.2317, -0.6735, -0.7019), (-0.7525, -0.5813, 0.3095), (-0.6165, 0.4565, -0.6415)70.7227, 25.4875, 64.1654
3given(0.1894, 0.7466, -0.6377), (0.6548, -0.58, -0.4846), (-0.7317, -0.3258, -0.5988)59.0551, -2.2274, 67.4522
4given(-0.9868, 0.1619, -0.0001), (0.1581, 0.9638, -0.2148), (-0.0347, -0.212, -0.9767)84.7287, -1.6421, 47.5206
5given(-0.3355, 0.5619, 0.7561), (-0.5587, -0.7649, 0.3206), (0.7585, -0.3149, 0.5706)18.1289, 20.5301, -22.4607

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Components

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Protein / Sugars , 2 types, 15 molecules ABCDEF

#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*PLUS, EC: 1.1.99.-
#3: Sugar
ChemComp-BGC / beta-D-glucopyranose / beta-D-glucose / D-glucose / glucose


Type: D-saccharide, beta linking / Mass: 180.156 Da / Num. of mol.: 9
Source method: isolated from a genetically manipulated source
Formula: C6H12O6
IdentifierTypeProgram
DGlcpbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
b-D-glucopyranoseCOMMON NAMEGMML 1.0
b-D-GlcpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 4 types, 2054 molecules

#2: Chemical
ChemComp-NDP / NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE


Mass: 745.421 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C21H30N7O17P3
#4: Chemical
ChemComp-DIO / 1,4-DIETHYLENE DIOXIDE


Mass: 88.105 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C4H8O2
#5: Chemical
ChemComp-SO4 / SULFATE ION


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


Mass: 18.015 Da / Num. of mol.: 2037 / 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: 66 % / Description: NONE
Crystal growpH: 6.5 / Details: MES PH 6.5, AMMONIUM SULPHATE, DIOXANE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.97625
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 27, 2014 / Details: MIRRORS
RadiationMonochromator: CHANNEL-CUT SI / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97625 Å / Relative weight: 1
ReflectionResolution: 1.7→50 Å / Num. obs: 338561 / % possible obs: 99 % / Observed criterion σ(I): 2 / Redundancy: 3.5 % / Biso Wilson estimate: 21.3 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 13
Reflection shellResolution: 1.7→1.8 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.6 / Mean I/σ(I) obs: 2 / % possible all: 97

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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: 1.698→47.591 Å / SU ML: 0.2 / σ(F): 1.36 / Phase error: 17.9 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1811 16929 5 %
Rwork0.1594 --
obs0.1604 338561 99.05 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 24.2 Å2
Refinement stepCycle: LAST / Resolution: 1.698→47.591 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15558 0 456 2037 18051
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00716385
X-RAY DIFFRACTIONf_angle_d1.10922262
X-RAY DIFFRACTIONf_dihedral_angle_d12.726097
X-RAY DIFFRACTIONf_chiral_restr0.0472430
X-RAY DIFFRACTIONf_plane_restr0.0052898
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.698-1.71730.35795080.33439638X-RAY DIFFRACTION89
1.7173-1.73750.31085620.293710688X-RAY DIFFRACTION99
1.7375-1.75860.27955640.267210715X-RAY DIFFRACTION99
1.7586-1.78090.26855640.245510706X-RAY DIFFRACTION99
1.7809-1.80430.25235660.227810757X-RAY DIFFRACTION99
1.8043-1.82910.25725620.216410672X-RAY DIFFRACTION99
1.8291-1.85520.2185640.197410721X-RAY DIFFRACTION99
1.8552-1.88290.21975660.18810749X-RAY DIFFRACTION99
1.8829-1.91230.2295630.190710701X-RAY DIFFRACTION99
1.9123-1.94370.22325630.190610706X-RAY DIFFRACTION99
1.9437-1.97720.2115610.188610653X-RAY DIFFRACTION99
1.9772-2.01310.21875660.186810745X-RAY DIFFRACTION100
2.0131-2.05190.20535640.170110734X-RAY DIFFRACTION99
2.0519-2.09370.17895650.160910727X-RAY DIFFRACTION99
2.0937-2.13930.17515670.159610777X-RAY DIFFRACTION99
2.1393-2.1890.19485690.157410799X-RAY DIFFRACTION100
2.189-2.24380.16965680.152910790X-RAY DIFFRACTION100
2.2438-2.30440.1715640.15310733X-RAY DIFFRACTION100
2.3044-2.37220.18165670.156310772X-RAY DIFFRACTION100
2.3722-2.44880.18785670.154610767X-RAY DIFFRACTION100
2.4488-2.53630.18515650.158310730X-RAY DIFFRACTION99
2.5363-2.63790.19955700.160510831X-RAY DIFFRACTION100
2.6379-2.75790.17255690.155910818X-RAY DIFFRACTION100
2.7579-2.90330.18555670.157910776X-RAY DIFFRACTION100
2.9033-3.08520.18155700.161710822X-RAY DIFFRACTION100
3.0852-3.32330.16835660.148910757X-RAY DIFFRACTION99
3.3233-3.65760.15565660.144810747X-RAY DIFFRACTION99
3.6576-4.18660.13685700.126310838X-RAY DIFFRACTION100
4.1866-5.27360.14125720.121710858X-RAY DIFFRACTION100
5.2736-47.60950.1745740.154910905X-RAY DIFFRACTION99

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