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- PDB-1ryd: Crystal Structure of Glucose-Fructose Oxidoreductase from Zymomon... -

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Basic information

Entry
Database: PDB / ID: 1ryd
TitleCrystal Structure of Glucose-Fructose Oxidoreductase from Zymomonas mobilis
Componentsglucose-fructose oxidoreductase
KeywordsOXIDOREDUCTASE / Glucose / Fructose / NADP / Zymomonas mobilis
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
ACETATE ION / BETA-MERCAPTOETHANOL / alpha-D-glucopyranose / Chem-NDP / Glucose--fructose oxidoreductase
Similarity search - Component
Biological speciesZymomonas mobilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsKim, Y. / Arora, M. / Straza, M. / Joachimiak, A.
CitationJournal: To be Published
Title: Crystal Structure of Glucose-Fructose Oxidoreductase from Zymomonas mobilis
Authors: Kim, Y. / Arora, M. / Straza, M. / Joachimiak, A.
History
DepositionDec 22, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 15, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Jul 29, 2020Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / pdbx_unobs_or_zero_occ_atoms / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _pdbx_unobs_or_zero_occ_atoms.label_asym_id / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.4Aug 23, 2023Group: 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: glucose-fructose oxidoreductase
B: glucose-fructose oxidoreductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)88,0129
Polymers86,0862
Non-polymers1,9267
Water9,962553
1
A: glucose-fructose oxidoreductase
B: glucose-fructose oxidoreductase
hetero molecules

A: glucose-fructose oxidoreductase
B: glucose-fructose oxidoreductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)176,02418
Polymers172,1714
Non-polymers3,85314
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-x+1,-y+1,z1
Buried area29370 Å2
ΔGint-133 kcal/mol
Surface area49870 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)84.525, 91.382, 115.473
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
DetailsTetramer (dimer of dimers), the second part (dimer) of the assembly is generated by the two fold axis:1-x,1-y,z

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Components

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Protein / Sugars , 2 types, 3 molecules AB

#1: Protein glucose-fructose oxidoreductase


Mass: 43042.836 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Zymomonas mobilis (bacteria) / Production host: Escherichia coli (E. coli)
References: UniProt: Q07982, glucose-fructose oxidoreductase
#4: Sugar ChemComp-GLC / alpha-D-glucopyranose / alpha-D-glucose / D-glucose / glucose


Type: D-saccharide, alpha linking / Mass: 180.156 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C6H12O6
IdentifierTypeProgram
DGlcpaCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
a-D-glucopyranoseCOMMON NAMEGMML 1.0
a-D-GlcpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 4 types, 559 molecules

#2: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H3O2
#3: Chemical ChemComp-NDP / NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE


Mass: 745.421 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H30N7O17P3
#5: Chemical ChemComp-BME / BETA-MERCAPTOETHANOL


Mass: 78.133 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6OS
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 553 / 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: 2.59 Å3/Da / Density % sol: 52.49 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: PEG 4000, ammonium acetate, sodium citrate, glucose, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9793 Å
DetectorType: SBC-2 / Detector: CCD / Date: Aug 22, 2002 / Details: mirror
RadiationMonochromator: double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 2.2→50 Å / Num. all: 47681 / Num. obs: 45279 / % possible obs: 98.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.7 % / Biso Wilson estimate: 26.6 Å2 / Rmerge(I) obs: 0.122 / Net I/σ(I): 7.2
Reflection shellResolution: 2.2→2.28 Å / Rmerge(I) obs: 0.56 / Mean I/σ(I) obs: 2.7 / % possible all: 94.1

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Processing

Software
NameVersionClassification
CNS1.1refinement
d*TREKdata reduction
HKL-2000data reduction
HKL-2000data scaling
EPMRphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1OFG

1ofg


Resolution: 2.2→47.68 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 375413.17 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.253 4340 10.1 %RANDOM
Rwork0.204 ---
obs0.209 42851 92.9 %-
all-46140 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 46.3952 Å2 / ksol: 0.33555 e/Å3
Displacement parametersBiso mean: 34.9 Å2
Baniso -1Baniso -2Baniso -3
1--12.09 Å20 Å20 Å2
2--3.77 Å20 Å2
3---8.32 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.34 Å0.26 Å
Luzzati d res low-5 Å
Luzzati sigma a0.31 Å0.24 Å
Refinement stepCycle: LAST / Resolution: 2.2→47.68 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5920 0 123 553 6596
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.008
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_d23.6
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.88
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.281.5
X-RAY DIFFRACTIONc_mcangle_it1.922
X-RAY DIFFRACTIONc_scbond_it2.192
X-RAY DIFFRACTIONc_scangle_it3.072.5
LS refinement shellResolution: 2.2→2.34 Å / Rfactor Rfree error: 0.013 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.322 634 10.5 %
Rwork0.271 5223 -
obs-5458 80.5 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION3NDP.PARAMNDP1.TOP
X-RAY DIFFRACTION4LIGAND.PARAMGOL.TOP

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