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- PDB-5a03: Crystal structure of aldose-aldose oxidoreductase from Caulobacte... -

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Basic information

Entry
Database: PDB / ID: 5a03
TitleCrystal structure of aldose-aldose oxidoreductase from Caulobacter crescentus complexed with xylose
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 ...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
1,4-DIETHYLENE DIOXIDE / Chem-NDP / beta-D-xylopyranose / alpha-D-xylopyranose / Glucose-fructose oxidoreductase
Similarity search - Component
Biological speciesCAULOBACTER CRESCENTUS CB15 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.848 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 1.1Nov 25, 2015Group: Source and taxonomy
Revision 1.2Dec 9, 2015Group: Database references
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Other / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_chem_comp_identifier / pdbx_database_status / pdbx_entity_nonpoly / pdbx_validate_close_contact / struct_site / struct_site_gen
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_database_status.status_code_sf / _pdbx_entity_nonpoly.name / _pdbx_validate_close_contact.auth_atom_id_1
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Jan 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

Downloads & links

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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)231,50238
Polymers223,7376
Non-polymers7,76532
Water32,6431812
1
A: ALDOSE-ALDOSE OXIDOREDUCTASE
E: ALDOSE-ALDOSE OXIDOREDUCTASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)77,75117
Polymers74,5792
Non-polymers3,17215
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8840 Å2
ΔGint-92.3 kcal/mol
Surface area24580 Å2
MethodPISA
2
B: ALDOSE-ALDOSE OXIDOREDUCTASE
D: ALDOSE-ALDOSE OXIDOREDUCTASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)77,03912
Polymers74,5792
Non-polymers2,46010
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7610 Å2
ΔGint-37.5 kcal/mol
Surface area24640 Å2
MethodPISA
3
C: ALDOSE-ALDOSE OXIDOREDUCTASE
F: ALDOSE-ALDOSE OXIDOREDUCTASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,7129
Polymers74,5792
Non-polymers2,1337
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6750 Å2
ΔGint-43.6 kcal/mol
Surface area24670 Å2
MethodPISA
Unit cell
Length a, b, c (Å)101.059, 153.480, 107.327
Angle α, β, γ (deg.)90.00, 109.42, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(-0.0642, -0.8162, 0.5742), (0.8212, -0.3701, -0.4343), (0.567, 0.4437, 0.694)24.8182, -9.5133, -19.267
2given(0.2251, -0.6745, -0.7032), (-0.7517, -0.5794, 0.315), (-0.6199, 0.4577, -0.6374)70.4611, 25.183, 63.6373
3given(0.1986, 0.7377, -0.6453), (0.6527, -0.5907, -0.4743), (-0.7311, -0.327, -0.5988)58.3762, -2.5822, 67.056
4given(-0.9855, 0.1697, -0.0039), (0.1667, 0.9633, -0.2105), (-0.0319, -0.2081, -0.9776)84.192, -2.1264, 46.7342
5given(-0.3345, 0.5563, 0.7607), (-0.5534, -0.7693, 0.3192), (0.7628, -0.3142, 0.5652)17.9677, 20.4525, -22.4657

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Components

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Protein , 1 types, 6 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) / Production host: SACCHAROMYCES CEREVISIAE (brewer's yeast)
References: UniProt: Q9A8X3*PLUS, Oxidoreductases; Acting on the CH-OH group of donors; With unknown physiological acceptors

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Sugars , 2 types, 15 molecules

#3: Sugar
ChemComp-XYP / beta-D-xylopyranose / beta-D-xylose / D-xylose / xylose


Type: D-saccharide, beta linking / Mass: 150.130 Da / Num. of mol.: 13
Source method: isolated from a genetically manipulated source
Formula: C5H10O5
IdentifierTypeProgram
DXylpbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
b-D-xylopyranoseCOMMON NAMEGMML 1.0
b-D-XylpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
XylSNFG CARBOHYDRATE SYMBOLGMML 1.0
#5: Sugar ChemComp-XYS / alpha-D-xylopyranose / alpha-D-xylose / D-xylose / xylose / XYLOPYRANOSE


Type: D-saccharide, alpha linking / Mass: 150.130 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C5H10O5
IdentifierTypeProgram
DXylpaCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
a-D-xylopyranoseCOMMON NAMEGMML 1.0
a-D-XylpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
XylSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 4 types, 1829 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-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: SO4
#6: Chemical ChemComp-DIO / 1,4-DIETHYLENE DIOXIDE


Mass: 88.105 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H8O2
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1812 / 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: 3.5 Å3/Da / Density % sol: 65 % / Description: NONE
Crystal growpH: 6.5 / Details: MES PH 6.5, AMMONIUM SULPHATE, 1,4-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: 1.84→50 Å / Num. obs: 256258 / % possible obs: 97 % / Observed criterion σ(I): 2 / Redundancy: 3.4 % / Biso Wilson estimate: 21.4 Å2 / Rmerge(I) obs: 0.1 / Net I/σ(I): 11
Reflection shellResolution: 1.84→1.9 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.56 / Mean I/σ(I) obs: 2 / % possible all: 92

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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: 1.848→49.995 Å / SU ML: 0.19 / σ(F): 1.36 / Phase error: 19.86 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1945 12799 5 %
Rwork0.1671 --
obs0.1684 256037 97.39 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 24.1 Å2
Refinement stepCycle: LAST / Resolution: 1.848→49.995 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15562 0 495 1812 17869
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00716414
X-RAY DIFFRACTIONf_angle_d1.09822306
X-RAY DIFFRACTIONf_dihedral_angle_d13.0486101
X-RAY DIFFRACTIONf_chiral_restr0.0462443
X-RAY DIFFRACTIONf_plane_restr0.0052896
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8478-1.86880.30953900.27727408X-RAY DIFFRACTION89
1.8688-1.89080.27064270.23948097X-RAY DIFFRACTION97
1.8908-1.91390.27034250.23338090X-RAY DIFFRACTION97
1.9139-1.93810.26364220.238020X-RAY DIFFRACTION97
1.9381-1.96360.24324150.22127878X-RAY DIFFRACTION95
1.9636-1.99050.24834290.20978142X-RAY DIFFRACTION97
1.9905-2.0190.23844270.2098123X-RAY DIFFRACTION98
2.019-2.04910.25074280.20198118X-RAY DIFFRACTION98
2.0491-2.08110.2544290.19428155X-RAY DIFFRACTION98
2.0811-2.11520.22484250.19278074X-RAY DIFFRACTION97
2.1152-2.15170.20744280.18188142X-RAY DIFFRACTION97
2.1517-2.19080.22944250.18358075X-RAY DIFFRACTION97
2.1908-2.2330.21414260.1748104X-RAY DIFFRACTION98
2.233-2.27850.21734290.1718151X-RAY DIFFRACTION98
2.2785-2.32810.21074300.17828174X-RAY DIFFRACTION98
2.3281-2.38220.20634290.17068148X-RAY DIFFRACTION98
2.3822-2.44180.1974300.16218168X-RAY DIFFRACTION98
2.4418-2.50780.20374250.17058052X-RAY DIFFRACTION97
2.5078-2.58160.21314250.17238125X-RAY DIFFRACTION98
2.5816-2.6650.18544350.16128260X-RAY DIFFRACTION99
2.665-2.76020.19664290.1618170X-RAY DIFFRACTION99
2.7602-2.87070.19714340.16488253X-RAY DIFFRACTION99
2.8707-3.00130.22194310.17418188X-RAY DIFFRACTION99
3.0013-3.15950.18054320.16388220X-RAY DIFFRACTION98
3.1595-3.35750.17664320.15648193X-RAY DIFFRACTION98
3.3575-3.61660.16634280.1528116X-RAY DIFFRACTION97
3.6166-3.98040.1594280.13988123X-RAY DIFFRACTION98
3.9804-4.55610.14124270.1248136X-RAY DIFFRACTION97
4.5561-5.73890.16094290.14668170X-RAY DIFFRACTION97
5.7389-50.01310.184300.16578165X-RAY DIFFRACTION96

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