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- PDB-1h6d: Oxidized Precursor Form of Glucose-Fructose Oxidoreductase from Z... -

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Basic information

Entry
Database: PDB / ID: 1h6d
TitleOxidized Precursor Form of Glucose-Fructose Oxidoreductase from Zymomonas mobilis complexed with glycerol
ComponentsPRECURSOR FORM OF GLUCOSE-FRUCTOSE OXIDOREDUCTASE
KeywordsPROTEIN TRANSLOCATION / PERIPLASMIC OXIDOREDUCTASE / SIGNAL PEPTIDE / LIGAND BINDING
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 / Glucose--fructose oxidoreductase
Similarity search - Component
Biological speciesZYMOMONAS MOBILIS (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.05 Å
AuthorsNurizzo, D. / Baker, E.N.
CitationJournal: Biochemistry / Year: 2001
Title: Crystal Structures of the Precursor Form of Glucose-Fructose Oxidoreductase from Zymomonas Mobilis and its Complexes with Bound Ligands
Authors: Nurizzo, D. / Halbig, D. / Sprenger, G. / Baker, E.N.
History
DepositionJun 12, 2001Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 28, 2001Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 13, 2023Group: 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

Downloads & links

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Assembly

Deposited unit
A: PRECURSOR FORM OF GLUCOSE-FRUCTOSE OXIDOREDUCTASE
B: PRECURSOR FORM OF GLUCOSE-FRUCTOSE OXIDOREDUCTASE
C: PRECURSOR FORM OF GLUCOSE-FRUCTOSE OXIDOREDUCTASE
D: PRECURSOR FORM OF GLUCOSE-FRUCTOSE OXIDOREDUCTASE
E: PRECURSOR FORM OF GLUCOSE-FRUCTOSE OXIDOREDUCTASE
F: PRECURSOR FORM OF GLUCOSE-FRUCTOSE OXIDOREDUCTASE
G: PRECURSOR FORM OF GLUCOSE-FRUCTOSE OXIDOREDUCTASE
H: PRECURSOR FORM OF GLUCOSE-FRUCTOSE OXIDOREDUCTASE
I: PRECURSOR FORM OF GLUCOSE-FRUCTOSE OXIDOREDUCTASE
J: PRECURSOR FORM OF GLUCOSE-FRUCTOSE OXIDOREDUCTASE
K: PRECURSOR FORM OF GLUCOSE-FRUCTOSE OXIDOREDUCTASE
L: PRECURSOR FORM OF GLUCOSE-FRUCTOSE OXIDOREDUCTASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)578,16136
Polymers568,11112
Non-polymers10,05024
Water71,1413949
1
A: PRECURSOR FORM OF GLUCOSE-FRUCTOSE OXIDOREDUCTASE
B: PRECURSOR FORM OF GLUCOSE-FRUCTOSE OXIDOREDUCTASE
C: PRECURSOR FORM OF GLUCOSE-FRUCTOSE OXIDOREDUCTASE
D: PRECURSOR FORM OF GLUCOSE-FRUCTOSE OXIDOREDUCTASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)192,72012
Polymers189,3704
Non-polymers3,3508
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
E: PRECURSOR FORM OF GLUCOSE-FRUCTOSE OXIDOREDUCTASE
F: PRECURSOR FORM OF GLUCOSE-FRUCTOSE OXIDOREDUCTASE
G: PRECURSOR FORM OF GLUCOSE-FRUCTOSE OXIDOREDUCTASE
H: PRECURSOR FORM OF GLUCOSE-FRUCTOSE OXIDOREDUCTASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)192,72012
Polymers189,3704
Non-polymers3,3508
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
3
I: PRECURSOR FORM OF GLUCOSE-FRUCTOSE OXIDOREDUCTASE
J: PRECURSOR FORM OF GLUCOSE-FRUCTOSE OXIDOREDUCTASE
K: PRECURSOR FORM OF GLUCOSE-FRUCTOSE OXIDOREDUCTASE
L: PRECURSOR FORM OF GLUCOSE-FRUCTOSE OXIDOREDUCTASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)192,72012
Polymers189,3704
Non-polymers3,3508
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)115.724, 83.752, 279.149
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
PRECURSOR FORM OF GLUCOSE-FRUCTOSE OXIDOREDUCTASE


Mass: 47342.578 Da / Num. of mol.: 12
Source method: isolated from a genetically manipulated source
Details: NADP, GLYCEROL / Source: (gene. exp.) ZYMOMONAS MOBILIS (bacteria) / Production host: ESCHERICHIA COLI (E. coli)
References: UniProt: P75002, UniProt: Q07982*PLUS, glucose-fructose oxidoreductase
#2: Chemical
ChemComp-NDP / NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / Nicotinamide adenine dinucleotide phosphate


Mass: 745.421 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C21H30N7O17P3
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 3949 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsMATURE FORM OF GLUCOSE FRUCTOSE OXIDOREDUCTASE

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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: 2.62 Å3/Da / Density % sol: 53 %
Crystal growpH: 6
Details: 12% PEG6000, 550MM AMMONIUM SULFATE, 20% GLYCEROL, pH 6.00
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
120 mg/mlprotein1drop
240 mMMES/KOH1droppH6.4
312 %PEG60001reservoir
420 %glycerol1reservoir
5550 mMammonium sulfate1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.5418
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Details: DOUBLE FOCUSING MIRRORS
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.05→15 Å / Num. obs: 317883 / % possible obs: 99.9 % / Redundancy: 3.8 % / Biso Wilson estimate: 15.7 Å2 / Rmerge(I) obs: 0.094 / Net I/σ(I): 6.2
Reflection shellResolution: 2.05→2.16 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.388 / Mean I/σ(I) obs: 1.8 / % possible all: 99.9
Reflection shell
*PLUS
% possible obs: 99.9 %

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Processing

Software
NameVersionClassification
CNS1refinement
DENZOdata reduction
SCALAdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1OFG

1ofg


Resolution: 2.05→15 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 4197810.8 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.228 1557 0.5 %RANDOM
Rwork0.197 ---
obs0.197 317883 95.1 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 65.0272 Å2 / ksol: 0.396131 e/Å3
Displacement parametersBiso mean: 23.5 Å2
Baniso -1Baniso -2Baniso -3
1-2.27 Å20 Å20 Å2
2---5.04 Å20 Å2
3---2.77 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.27 Å0.23 Å
Luzzati d res low-5 Å
Luzzati sigma a0.28 Å0.22 Å
Refinement stepCycle: LAST / Resolution: 2.05→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms35555 0 648 3949 40152
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d23.7
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1.88
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it0.631.5
X-RAY DIFFRACTIONc_mcangle_it0.992
X-RAY DIFFRACTIONc_scbond_it1.132
X-RAY DIFFRACTIONc_scangle_it1.642.5
LS refinement shellResolution: 2.05→2.18 Å / Rfactor Rfree error: 0.019 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.31 262 0.5 %
Rwork0.268 51069 -
obs--92.8 %
Refinement
*PLUS
Lowest resolution: 15 Å
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg23.7
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg1.88

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