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- PDB-5a02: Crystal structure of aldose-aldose oxidoreductase from Caulobacte... -

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Basic information

Entry
Database: PDB / ID: 5a02
TitleCrystal structure of aldose-aldose oxidoreductase from Caulobacter crescentus complexed with glycerol
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
NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / Glucose-fructose oxidoreductase
Similarity search - Component
Biological speciesCAULOBACTER CRESCENTUS CB15 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 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 1.3Jan 10, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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)230,43936
Polymers223,7376
Non-polymers6,70230
Water27,9231550
1
B: ALDOSE-ALDOSE OXIDOREDUCTASE
D: ALDOSE-ALDOSE OXIDOREDUCTASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,71811
Polymers74,5792
Non-polymers2,1399
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7140 Å2
ΔGint-28.7 kcal/mol
Surface area24810 Å2
MethodPISA
2
A: ALDOSE-ALDOSE OXIDOREDUCTASE
E: ALDOSE-ALDOSE OXIDOREDUCTASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,90613
Polymers74,5792
Non-polymers2,32811
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7650 Å2
ΔGint-44.5 kcal/mol
Surface area24530 Å2
MethodPISA
3
C: ALDOSE-ALDOSE OXIDOREDUCTASE
F: ALDOSE-ALDOSE OXIDOREDUCTASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,81412
Polymers74,5792
Non-polymers2,23510
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7360 Å2
ΔGint-44.7 kcal/mol
Surface area24700 Å2
MethodPISA
Unit cell
Length a, b, c (Å)101.310, 153.590, 108.010
Angle α, β, γ (deg.)90.00, 109.85, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(0.2224, -0.6761, -0.7024), (-0.7514, -0.5779, 0.3184), (-0.6212, 0.457, -0.6366)70.8567, 24.3916, 63.4217
2given(-0.0593, -0.8198, 0.5696), (0.8286, -0.3586, -0.4299), (0.5567, 0.4464, 0.7006)24.2547, -9.5571, -18.5188
3given(-0.1994, 0.7366, -0.6462), (0.6601, -0.5884, -0.467), (-0.7243, -0.3334, -0.6036)58.4095, -2.9639, 66.6354
4given(-0.9825, 0.1861, -0.0116), (0.1842, 0.9587, -0.2167), (-0.0292, -0.215, -0.9762)83.3943, -2.6301, 47.0997
5given(-0.3348, 0.5438, 0.7696), (-0.5423, -0.7791, 0.3145), (0.7706, -0.3121, 0.5557)16.6268, 19.9138, -21.5036

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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) / Production host: SACCHAROMYCES CEREVISIAE (brewer's yeast) / References: UniProt: Q9A8X3*PLUS, EC: 1.1.99.-
#2: Chemical
ChemComp-NAP / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / 2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE / Nicotinamide adenine dinucleotide phosphate


Mass: 743.405 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C21H28N7O17P3
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1550 / 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, MAGNESIUM SULPHATE, GLYCEROL

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9763
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Aug 7, 2013 / Details: MIRRORS
RadiationMonochromator: DOUBLE CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. obs: 208164 / % possible obs: 99.5 % / Observed criterion σ(I): 2 / Redundancy: 3.2 % / Biso Wilson estimate: 22.74 Å2 / Rmerge(I) obs: 0.11 / Net I/σ(I): 7
Reflection shellResolution: 2→2.07 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.49 / Mean I/σ(I) obs: 2 / % possible all: 99.1

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Processing

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

1h6a


Resolution: 2→48.226 Å / SU ML: 0.18 / σ(F): 1.37 / Phase error: 18.3 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1869 10403 5 %
Rwork0.1595 --
obs0.1609 208065 99.6 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 25.11 Å2
Refinement stepCycle: LAST / Resolution: 2→48.226 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15558 0 424 1550 17532
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00816326
X-RAY DIFFRACTIONf_angle_d1.07322158
X-RAY DIFFRACTIONf_dihedral_angle_d13.3926076
X-RAY DIFFRACTIONf_chiral_restr0.0452384
X-RAY DIFFRACTIONf_plane_restr0.0052884
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.02270.25023390.23696442X-RAY DIFFRACTION98
2.0227-2.04650.25053450.22156556X-RAY DIFFRACTION100
2.0465-2.07150.25133480.20676623X-RAY DIFFRACTION100
2.0715-2.09770.2473440.20546530X-RAY DIFFRACTION100
2.0977-2.12530.22673450.19746548X-RAY DIFFRACTION100
2.1253-2.15440.23553500.19236649X-RAY DIFFRACTION100
2.1544-2.18520.22113460.18266578X-RAY DIFFRACTION100
2.1852-2.21780.20293430.18146526X-RAY DIFFRACTION100
2.2178-2.25250.21543490.18176619X-RAY DIFFRACTION99
2.2525-2.28940.2183460.17346572X-RAY DIFFRACTION100
2.2894-2.32890.21123460.17746579X-RAY DIFFRACTION100
2.3289-2.37120.21053460.17226568X-RAY DIFFRACTION100
2.3712-2.41680.20573470.17276610X-RAY DIFFRACTION100
2.4168-2.46610.21453480.17396594X-RAY DIFFRACTION100
2.4661-2.51980.22213460.17146577X-RAY DIFFRACTION100
2.5198-2.57840.18623450.16466567X-RAY DIFFRACTION100
2.5784-2.64290.20573490.16466629X-RAY DIFFRACTION100
2.6429-2.71430.21333450.16756549X-RAY DIFFRACTION100
2.7143-2.79420.21173470.15816603X-RAY DIFFRACTION99
2.7942-2.88430.18443470.15956594X-RAY DIFFRACTION100
2.8843-2.98740.20283480.16136596X-RAY DIFFRACTION100
2.9874-3.1070.17623460.15086587X-RAY DIFFRACTION100
3.107-3.24840.16823480.14426610X-RAY DIFFRACTION100
3.2484-3.41960.16063480.14126609X-RAY DIFFRACTION100
3.4196-3.63380.17223470.13626592X-RAY DIFFRACTION100
3.6338-3.91420.15453480.136608X-RAY DIFFRACTION99
3.9142-4.30790.13683480.12666606X-RAY DIFFRACTION100
4.3079-4.93080.14773480.13276622X-RAY DIFFRACTION100
4.9308-6.21020.18593480.17246619X-RAY DIFFRACTION99
6.2102-48.24030.17453530.16766700X-RAY DIFFRACTION99

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