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- PDB-1evj: CRYSTAL STRUCTURE OF GLUCOSE-FRUCTOSE OXIDOREDUCTASE (GFOR) DELTA... -

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Basic information

Entry
Database: PDB / ID: 1evj
TitleCRYSTAL STRUCTURE OF GLUCOSE-FRUCTOSE OXIDOREDUCTASE (GFOR) DELTA1-22 S64D
ComponentsGLUCOSE-FRUCTOSE OXIDOREDUCTASE
KeywordsOXIDOREDUCTASE / NADP/NAD BINDING / OSMOTIC PROTECTION / PERIPLASM / OLIGOMERIZATION STATE / N-TERMINAL ARM
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
NICOTINAMIDE-ADENINE-DINUCLEOTIDE / Glucose--fructose oxidoreductase
Similarity search - Component
Biological speciesZymomonas mobilis (bacteria)
MethodX-RAY DIFFRACTION / Resolution: 2.7 Å
AuthorsLott, J.S. / Halbig, D. / Baker, H.M. / Hardman, M.J. / Sprenger, G.A. / Baker, E.N.
CitationJournal: J.Mol.Biol. / Year: 2000
Title: Crystal structure of a truncated mutant of glucose-fructose oxidoreductase shows that an N-terminal arm controls tetramer formation.
Authors: Lott, J.S. / Halbig, D. / Baker, H.M. / Hardman, M.J. / Sprenger, G.A. / Baker, E.N.
History
DepositionApr 20, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 4, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 3, 2021Group: Database references / Derived calculations / Category: database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Feb 7, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)159,7128
Polymers157,0584
Non-polymers2,6544
Water2,342130
1
A: GLUCOSE-FRUCTOSE OXIDOREDUCTASE
C: GLUCOSE-FRUCTOSE OXIDOREDUCTASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)79,8564
Polymers78,5292
Non-polymers1,3272
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5210 Å2
ΔGint-23 kcal/mol
Surface area24750 Å2
MethodPISA
2
B: GLUCOSE-FRUCTOSE OXIDOREDUCTASE
D: GLUCOSE-FRUCTOSE OXIDOREDUCTASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)79,8564
Polymers78,5292
Non-polymers1,3272
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5180 Å2
ΔGint-23 kcal/mol
Surface area24660 Å2
MethodPISA
Unit cell
Length a, b, c (Å)47.710, 91.460, 98.920
Angle α, β, γ (deg.)64.53, 84.45, 75.28
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
22
33
/ NCS ensembles :
ID
1
2
3

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Components

#1: Protein
GLUCOSE-FRUCTOSE OXIDOREDUCTASE / GFOR


Mass: 39264.555 Da / Num. of mol.: 4 / Mutation: S64D
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Zymomonas mobilis (bacteria) / Plasmid: PZY470 / Production host: Zymomonas mobilis (bacteria) / References: UniProt: Q07982
#2: Chemical
ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE


Mass: 663.425 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Comment: NAD*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 130 / 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: 2.4 Å3/Da / Density % sol: 48.72 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 0.2 M acetate/KOH, 8.6% PEG6000, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal grow
*PLUS
pH: 6.4
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
116 mg/mlprotein1drop
240 mMMES/KOH1drop
35 mMdithiothreitol1drop
40.1 Msuccinate/KOH1reservoir
58.6 %(w/v)PEG60001reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418
DetectorType: RIGAKU RAXIS IIC / Detector: IMAGE PLATE / Date: Sep 8, 1997
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.7→40 Å / Num. all: 100479 / Num. obs: 38847 / % possible obs: 96.9 % / Observed criterion σ(I): 2 / Redundancy: 2.6 % / Biso Wilson estimate: 55.2 Å2 / Rmerge(I) obs: 0.083 / Net I/σ(I): 14.6
Reflection shellResolution: 2.7→2.8 Å / Redundancy: 1.06 % / Rmerge(I) obs: 0.36 / Mean I/σ(I) obs: 2.8 / Num. unique all: 3803 / % possible all: 94.7
Reflection shell
*PLUS
% possible obs: 94.7 %

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Processing

Software
NameVersionClassification
AMoREphasing
CNS1refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementResolution: 2.7→39.14 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 1832235 / Data cutoff low absF: 0 / Isotropic thermal model: GROUP / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
Details: Used slowcool simulated annealing with torsion-angle molecular dynamics, using a maximum-likelihood target function (MLF)
RfactorNum. reflection% reflectionSelection details
Rfree0.284 3897 10 %RANDOM
Rwork0.241 ---
obs0.241 38846 96.8 %-
all-100479 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 64.78 Å2 / ksol: 0.38 e/Å3
Displacement parametersBiso mean: 55.3 Å2
Baniso -1Baniso -2Baniso -3
1-17.85 Å2-3.68 Å25.24 Å2
2---19.14 Å23.53 Å2
3---1.3 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.46 Å0.37 Å
Luzzati d res low-5 Å
Luzzati sigma a0.52 Å0.43 Å
Refinement stepCycle: LAST / Resolution: 2.7→39.14 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10303 0 176 130 10609
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d23
X-RAY DIFFRACTIONc_improper_angle_d0.77
Refine LS restraints NCS
Ens-IDDom-IDNCS model detailsRefine-IDWeight Biso Weight position
11RESTRAINEDX-RAY DIFFRACTION21000
22X-RAY DIFFRACTION21000
33X-RAY DIFFRACTION21000
LS refinement shellResolution: 2.7→2.8 Å / Rfactor Rfree error: 0.02 / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.387 388 10.3 %
Rwork0.335 3392 -
obs--94.3 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
Software
*PLUS
Name: CNS / Version: 1 / Classification: refinement
Refinement
*PLUS
Num. reflection obs: 34948
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg23
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.77

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