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- PDB-8glr: FrlB - Deglycase for 6-phosphofructose lysine -

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Basic information

Entry
Database: PDB / ID: 8glr
TitleFrlB - Deglycase for 6-phosphofructose lysine
ComponentsSIS domain-containing protein
KeywordsSUGAR BINDING PROTEIN / deglycase / fructose-lysine metabolism / Amadori compound / sugar isomerase domain
Function / homology
Function and homology information


carbohydrate derivative metabolic process / carbohydrate derivative binding
Similarity search - Function
Fructosamine deglycase FrlB / Fructosamine deglycase FrlB, SIS domain 1 / SIS domain / SIS domain / SIS domain profile. / SIS domain superfamily / Glucose-6-phosphate isomerase like protein; domain 1 / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
SIS domain-containing protein
Similarity search - Component
Biological speciesSalmonella enterica subsp. enterica serovar Typhimurium (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.83 Å
AuthorsBell, C.E. / Gopalan, V. / Kovvali, S.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01-AI140541 United States
CitationJournal: Protein Sci. / Year: 2023
Title: Insights into the catalytic mechanism of a bacterial deglycase essential for utilization of fructose-lysine.
Authors: Kovvali, S. / Gao, Y. / Cool, A. / Lindert, S. / Wysocki, V.H. / Bell, C.E. / Gopalan, V.
History
DepositionMar 22, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 5, 2023Provider: repository / Type: Initial release
Revision 1.1Jul 12, 2023Group: Database references / Category: citation / Item: _citation.journal_volume / _citation.title
Revision 1.2Oct 25, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: SIS domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,5332
Polymers38,4411
Non-polymers921
Water4,288238
1
A: SIS domain-containing protein
hetero molecules

A: SIS domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)77,0664
Polymers76,8822
Non-polymers1842
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_565-x,-y+1,z1
Buried area5910 Å2
ΔGint-15 kcal/mol
Surface area21660 Å2
MethodPISA
Unit cell
Length a, b, c (Å)53.680, 75.223, 82.837
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11A-678-

HOH

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Components

#1: Protein SIS domain-containing protein


Mass: 38440.934 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Salmonella enterica subsp. enterica serovar Typhimurium (bacteria)
Gene: AIT36_19960, BG493_20030, G0K88_001622, G0K89_001219, G0K90_002095, G0K94_001269, G0K95_001240, G0L00_000266, G0L02_001295, G0L86_001412, G0M06_001202, G0M13_000979, G0M18_002254, G0M22_001196, ...Gene: AIT36_19960, BG493_20030, G0K88_001622, G0K89_001219, G0K90_002095, G0K94_001269, G0K95_001240, G0L00_000266, G0L02_001295, G0L86_001412, G0M06_001202, G0M13_000979, G0M18_002254, G0M22_001196, G0M25_001016, G0M29_001211, G0M46_001199, G0M48_001460, G4F88_04075, G4F89_20295, G4F91_19950, G4F92_04075, GXC51_00580, GXC56_00580, GXG40_00580, GYJ28_003810
Production host: Escherichia coli (E. coli) / References: UniProt: A0A564XQZ9
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 238 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.18 Å3/Da / Density % sol: 43.46 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / Details: 0.1 M HEPES (pH 7.5) and 1.0 M ammonium sulfate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SEALED TUBE / Type: RIGAKU MICROMAX-003 / Wavelength: 1.54 Å
DetectorType: DECTRIS PILATUS3 R 200K-A / Detector: PIXEL / Date: Dec 19, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 1.83→45.1 Å / Num. obs: 28584 / % possible obs: 94.3 % / Redundancy: 5.5 % / Biso Wilson estimate: 11.7 Å2 / Rmerge(I) obs: 0.083 / Rpim(I) all: 0.038 / Rrim(I) all: 0.091 / Χ2: 1.279 / Net I/av σ(I): 20.7 / Net I/σ(I): 20.5
Reflection shellResolution: 1.83→1.88 Å / Redundancy: 5.2 % / Rmerge(I) obs: 0.462 / Mean I/σ(I) obs: 3.7 / Num. unique obs: 28564 / Rpim(I) all: 0.214 / Rrim(I) all: 0.511 / Χ2: 1.295 / % possible all: 84.7

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
HKL-3000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2a3n

2a3n


Resolution: 1.83→45.09 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.927 / SU B: 2.349 / SU ML: 0.072 / Cross valid method: THROUGHOUT / ESU R: 0.125 / ESU R Free: 0.123 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.20331 1377 4.8 %RANDOM
Rwork0.16009 ---
obs0.16209 27187 94.28 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 16.357 Å2
Baniso -1Baniso -2Baniso -3
1--0.04 Å2-0 Å20 Å2
2--0.24 Å2-0 Å2
3----0.2 Å2
Refinement stepCycle: 1 / Resolution: 1.83→45.09 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2510 0 6 238 2754
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0132570
X-RAY DIFFRACTIONr_bond_other_d0.0010.0152418
X-RAY DIFFRACTIONr_angle_refined_deg1.6551.6313482
X-RAY DIFFRACTIONr_angle_other_deg1.521.5755545
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.655318
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.31722.18133
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.93415432
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.0111516
X-RAY DIFFRACTIONr_chiral_restr0.0870.2335
X-RAY DIFFRACTIONr_gen_planes_refined0.010.022906
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02606
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.5071.5551275
X-RAY DIFFRACTIONr_mcbond_other1.4651.5541274
X-RAY DIFFRACTIONr_mcangle_it2.2232.3241592
X-RAY DIFFRACTIONr_mcangle_other2.2252.3251593
X-RAY DIFFRACTIONr_scbond_it2.5071.7961295
X-RAY DIFFRACTIONr_scbond_other2.5061.7971296
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.8772.5981891
X-RAY DIFFRACTIONr_long_range_B_refined5.28319.4182987
X-RAY DIFFRACTIONr_long_range_B_other5.28219.4242988
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.83→1.878 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.246 97 -
Rwork0.197 1790 -
obs--85.27 %

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