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- PDB-1ofg: GLUCOSE-FRUCTOSE OXIDOREDUCTASE -

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Basic information

Entry
Database: PDB / ID: 1ofg
TitleGLUCOSE-FRUCTOSE OXIDOREDUCTASE
ComponentsGLUCOSE-FRUCTOSE OXIDOREDUCTASE
KeywordsOXIDOREDUCTASE / NADP BINDING / OSMOTIC PROTECTION / PERIPLASM
Function / homology
Function and homology information


glucose-fructose oxidoreductase / sorbitol biosynthetic process / glucose-fructose oxidoreductase activity / periplasmic space / 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 / Twin arginine translocation (Tat) signal profile. / Twin-arginine translocation pathway, signal sequence / NAD(P)-binding Rossmann-like Domain ...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 / Twin arginine translocation (Tat) signal profile. / Twin-arginine translocation pathway, signal sequence / 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 / Glucose--fructose oxidoreductase
Similarity search - Component
Biological speciesZymomonas mobilis (bacteria)
MethodX-RAY DIFFRACTION / MIR / Resolution: 2.7 Å
AuthorsKingston, R.L. / Scopes, R.K. / Baker, E.N.
Citation
Journal: Structure / Year: 1996
Title: The structure of glucose-fructose oxidoreductase from Zymomonas mobilis: an osmoprotective periplasmic enzyme containing non-dissociable NADP.
Authors: Kingston, R.L. / Scopes, R.K. / Baker, E.N.
#1: Journal: J.Bacteriol. / Year: 1994
Title: Sorbitol Promotes Growth of Zymomonas Mobilis in Environments with High Concentrations of Sugar: Evidence for a Physiological Function of Glucose-Fructose Oxidoreductase in Osmoprotection
Authors: Loos, H. / Kramer, R. / Sahm, H. / Sprenger, G.A.
#2: Journal: J.Bacteriol. / Year: 1992
Title: Cloning, Sequence Analysis, and Expression of the Structural Gene Encoding Glucose-Fructose Oxidoreductase from Zymomonas Mobilis
Authors: Kanagasundaram, V. / Scopes, R.K.
#3: Journal: J.Bacteriol. / Year: 1986
Title: Glucose-Fructose Oxidoreductase, a New Enzyme Isolated from Zymomonas Mobilis that is Responsible for Sorbitol Production
Authors: Zachariou, M. / Scopes, R.K.
History
DepositionOct 17, 1996Processing site: BNL
Revision 1.0Apr 21, 1997Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site / _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

Downloads & links

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Assembly

Deposited unit
A: GLUCOSE-FRUCTOSE OXIDOREDUCTASE
B: GLUCOSE-FRUCTOSE OXIDOREDUCTASE
C: GLUCOSE-FRUCTOSE OXIDOREDUCTASE
D: GLUCOSE-FRUCTOSE OXIDOREDUCTASE
E: GLUCOSE-FRUCTOSE OXIDOREDUCTASE
F: GLUCOSE-FRUCTOSE OXIDOREDUCTASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)257,75612
Polymers253,2846
Non-polymers4,4736
Water15,133840
1
A: GLUCOSE-FRUCTOSE OXIDOREDUCTASE
B: GLUCOSE-FRUCTOSE OXIDOREDUCTASE
C: GLUCOSE-FRUCTOSE OXIDOREDUCTASE
D: GLUCOSE-FRUCTOSE OXIDOREDUCTASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)171,8388
Polymers168,8564
Non-polymers2,9824
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area26830 Å2
ΔGint-124 kcal/mol
Surface area47490 Å2
MethodPISA
2
E: GLUCOSE-FRUCTOSE OXIDOREDUCTASE
F: GLUCOSE-FRUCTOSE OXIDOREDUCTASE
hetero molecules

E: GLUCOSE-FRUCTOSE OXIDOREDUCTASE
F: GLUCOSE-FRUCTOSE OXIDOREDUCTASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)171,8388
Polymers168,8564
Non-polymers2,9824
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-x+1,-y+1,z1
Unit cell
Length a, b, c (Å)84.490, 283.690, 116.990
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(-0.53678, -0.84348, -0.02025), (-0.8432, 0.53545, 0.04813), (-0.02975, 0.04291, -0.99864)104.44364, 56.12222, 42.87604
2given(0.53653, 0.84362, 0.0209), (0.84359, -0.53683, 0.01306), (0.02224, 0.01062, -0.9997)-20.4112, 35.93366, 42.16801
3given(-1, -0.00057, 0.00116), (0.00051, -0.99849, -0.05491), (0.00119, -0.05491, 0.99849)84.08351, 94.41982, 2.56472
4given(0.99996, 0.00836, -0.00189), (-0.00831, 0.99963, 0.02587), (0.0021, -0.02585, 0.99966)-0.17853, 94.97285, 3.17754
5given(-0.54566, -0.83778, -0.01939), (-0.83799, 0.54537, 0.01842), (-0.00485, 0.0263, -0.99964)104.76831, 151.27325, 44.63948
DetailsNON-CRYSTALLOGRAPHIC SYMMETRY CONSTRAINTS WERE APPLIED THROUGHOUT THE REFINEMENT. THUS THE SIX MODELLED SUBUNITS (A, B, C, D, E, F) ARE ALL IDENTICAL. CORRELATION COEFFICIENTS CALCULATED DURING MAP AVERAGING PROCEDURES SUGGEST THERE MAY BE SMALL DIFFERENCES BETWEEN SUBUNITS. THESE HAVE NOT BEEN MODELLED DUE TO THE LIMITED RESOLUTION OF THE DATA.

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Components

#1: Protein
GLUCOSE-FRUCTOSE OXIDOREDUCTASE


Mass: 42213.957 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Source: (natural) Zymomonas mobilis (bacteria) / Cellular location: PERIPLASM
References: UniProt: Q07982, glucose-fructose oxidoreductase
#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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 840 / 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: 4

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Sample preparation

CrystalDensity Matthews: 2.7 Å3/Da / Density % sol: 54 %
Crystal growpH: 5.5 / Details: pH 5.5
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
110 mg/mlprotein1drop
25-15 %(w/v)PEG60001reservoir
30.2 Msuccinic acid/KOH1reservoiror 0.2 M citric acid/KOH

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Data collection

DiffractionMean temperature: 277 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418
DetectorType: RIGAKU / Detector: IMAGE PLATE / Date: Apr 1, 1996
RadiationMonochromator: GRAPHITE(002) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.7→50 Å / Num. obs: 71500 / % possible obs: 91 % / Observed criterion σ(I): 0 / Redundancy: 4.8 % / Biso Wilson estimate: 44 Å2 / Rmerge(I) obs: 0.09
Reflection shellResolution: 2.7→2.87 Å / Redundancy: 2 % / Rmerge(I) obs: 0.265 / % possible all: 60
Reflection
*PLUS
Num. measured all: 353200
Reflection shell
*PLUS
% possible obs: 60 % / Num. unique obs: 7701 / Num. measured obs: 15509

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Processing

Software
NameClassification
TNTrefinement
DENZOdata reduction
CCP4data scaling
RefinementMethod to determine structure: MIR / Resolution: 2.7→50 Å / σ(F): 0 / Stereochemistry target values: ENGH AND HUBER (1991)
Details: THE OCCUPANCIES OF SOLVENT MOLECULES WITH HIGH TEMPERATURE FACTORS WERE REDUCED TO 0.5 IN THE COURSE OF STRUCTURE REFINEMENT. THERE ARE CLEAR INDICATIONS OF ALTERNATE CONFORMATIONS FOR THE ...Details: THE OCCUPANCIES OF SOLVENT MOLECULES WITH HIGH TEMPERATURE FACTORS WERE REDUCED TO 0.5 IN THE COURSE OF STRUCTURE REFINEMENT. THERE ARE CLEAR INDICATIONS OF ALTERNATE CONFORMATIONS FOR THE FOLLOWING RESIDUES (NOT YET MODELLED): GLN 256, MET 314
RfactorNum. reflection% reflection
Rwork0.203 --
all-71500 -
obs-71500 91 %
Refinement stepCycle: LAST / Resolution: 2.7→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms17370 0 288 840 18498
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONt_bond_d0.013
X-RAY DIFFRACTIONt_angle_deg1.596
X-RAY DIFFRACTIONt_dihedral_angle_d22.9
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes
X-RAY DIFFRACTIONt_it
X-RAY DIFFRACTIONt_nbd
Software
*PLUS
Name: TNT / Classification: refinement
Refinement
*PLUS
Rfactor obs: 0.203
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d
X-RAY DIFFRACTIONt_dihedral_angle_deg22.9

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