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- PDB-8h1l: Crystal structure of glucose-2-epimerase in complex with D-Glucit... -

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Basic information

Entry
Database: PDB / ID: 8h1l
TitleCrystal structure of glucose-2-epimerase in complex with D-Glucitol from Runella slithyformis Runsl_4512
ComponentsN-acylglucosamine 2-epimerase
KeywordsISOMERASE / complex form / Runsl
Function / homology
Function and homology information


isomerase activity / carbohydrate metabolic process
Similarity search - Function
N-acylglucosamine 2-epimerase/Cellobiose 2-epimerase / N-acylglucosamine 2-epimerase (GlcNAc 2-epimerase) / Glycosyltransferase - #10 / Six-hairpin glycosidase-like superfamily / Six-hairpin glycosidase superfamily / Glycosyltransferase / Alpha/alpha barrel / Mainly Alpha
Similarity search - Domain/homology
sorbitol / N-acylglucosamine 2-epimerase
Similarity search - Component
Biological speciesRunella slithyformis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.33 Å
AuthorsWang, H. / Sun, X.M. / Saburi, W. / Yu, J. / Yao, M.
Funding support Japan, 5items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)18K05382 Japan
Japan Society for the Promotion of Science (JSPS)21K05388 Japan
Japan Society for the Promotion of Science (JSPS)21H01754 Japan
Japan Agency for Medical Research and Development (AMED)JP18am0101071 (0058) Japan
Japan Agency for Medical Research and Development (AMED)JP19am0101083 Japan
CitationJournal: Acta Crystallogr D Struct Biol / Year: 2023
Title: Structural insights into the substrate specificity and activity of a novel mannose 2-epimerase from Runella slithyformis.
Authors: Wang, H. / Sun, X. / Saburi, W. / Hashiguchi, S. / Yu, J. / Ose, T. / Mori, H. / Yao, M.
History
DepositionOct 3, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 12, 2023Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / diffrn_source / pdbx_initial_refinement_model
Item: _diffrn_source.pdbx_synchrotron_site

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: N-acylglucosamine 2-epimerase
B: N-acylglucosamine 2-epimerase
C: N-acylglucosamine 2-epimerase
D: N-acylglucosamine 2-epimerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)196,6976
Polymers196,3324
Non-polymers3642
Water14,016778
1
A: N-acylglucosamine 2-epimerase
B: N-acylglucosamine 2-epimerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)98,3483
Polymers98,1662
Non-polymers1821
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2710 Å2
ΔGint-4 kcal/mol
Surface area28090 Å2
MethodPISA
2
C: N-acylglucosamine 2-epimerase
D: N-acylglucosamine 2-epimerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)98,3483
Polymers98,1662
Non-polymers1821
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2670 Å2
ΔGint-3 kcal/mol
Surface area28220 Å2
MethodPISA
Unit cell
Length a, b, c (Å)146.242, 172.731, 150.457
Angle α, β, γ (deg.)90.000, 116.964, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z

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Components

#1: Protein
N-acylglucosamine 2-epimerase


Mass: 49083.070 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Runella slithyformis (bacteria) / Gene: Runsl_4512 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A7U4E834
#2: Sugar ChemComp-SOR / sorbitol / D-sorbitol / D-glucitol


Type: D-saccharide / Mass: 182.172 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H14O6
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 778 / 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: 4.33 Å3/Da / Density % sol: 71.57 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / Details: 3.6M sodium formate, 486 mM D-glucitol

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Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-1A / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 4M / Detector: PIXEL / Date: Jun 27, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.33→48.53 Å / Num. obs: 140052 / % possible obs: 99.23 % / Redundancy: 3.6 % / Biso Wilson estimate: 29.85 Å2 / CC1/2: 0.994 / Rmerge(I) obs: 0.1086 / Net I/σ(I): 9.66
Reflection shellResolution: 2.33→2.42 Å / Rmerge(I) obs: 0.5531 / Num. unique obs: 51624 / CC1/2: 0.784

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Processing

Software
NameVersionClassification
PHENIX1.17_3644refinement
XDSdata reduction
XDSdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3vw5

3vw5


Resolution: 2.33→48.53 Å / SU ML: 0.2395 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 21.3378
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2077 7032 5.02 %
Rwork0.1792 132977 -
obs0.1806 140009 99.24 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 33.25 Å2
Refinement stepCycle: LAST / Resolution: 2.33→48.53 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13788 0 24 778 14590
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.007614212
X-RAY DIFFRACTIONf_angle_d0.868219242
X-RAY DIFFRACTIONf_chiral_restr0.05021954
X-RAY DIFFRACTIONf_plane_restr0.00552456
X-RAY DIFFRACTIONf_dihedral_angle_d19.04695068
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.33-2.360.2672220.23764399X-RAY DIFFRACTION97.26
2.36-2.390.27582470.23244349X-RAY DIFFRACTION98.82
2.39-2.420.25232310.22864414X-RAY DIFFRACTION98.87
2.42-2.450.27192470.22924390X-RAY DIFFRACTION99.1
2.45-2.480.26612210.23294392X-RAY DIFFRACTION99.03
2.48-2.510.2792050.23414482X-RAY DIFFRACTION99.03
2.51-2.550.25822530.22954344X-RAY DIFFRACTION99.09
2.55-2.590.26482350.22714429X-RAY DIFFRACTION99.15
2.59-2.630.26732530.23024436X-RAY DIFFRACTION99.3
2.63-2.670.27542520.2254376X-RAY DIFFRACTION99.16
2.67-2.720.24992210.23914395X-RAY DIFFRACTION99.12
2.72-2.770.25492480.23454463X-RAY DIFFRACTION99.26
2.77-2.820.26992180.2384424X-RAY DIFFRACTION99.42
2.82-2.880.25352320.22014404X-RAY DIFFRACTION99.34
2.88-2.940.22542320.22044460X-RAY DIFFRACTION99.36
2.94-3.010.22772210.22294445X-RAY DIFFRACTION99.47
3.01-3.080.24972280.22354431X-RAY DIFFRACTION99.49
3.08-3.170.24072590.21484411X-RAY DIFFRACTION99.34
3.17-3.260.25372250.21754450X-RAY DIFFRACTION99.13
3.26-3.360.23062560.19784389X-RAY DIFFRACTION99.08
3.36-3.490.20932390.17234404X-RAY DIFFRACTION99.02
3.49-3.620.18642190.16434474X-RAY DIFFRACTION99.13
3.62-3.790.18462170.15044464X-RAY DIFFRACTION99.49
3.79-3.990.16412250.13544440X-RAY DIFFRACTION99.76
3.99-4.240.15892550.12134447X-RAY DIFFRACTION99.79
4.24-4.570.13582360.11784509X-RAY DIFFRACTION99.85
4.57-5.020.14692350.11594447X-RAY DIFFRACTION99.85
5.03-5.750.17442130.13684523X-RAY DIFFRACTION99.92
5.75-7.240.18362540.15984468X-RAY DIFFRACTION99.81
7.24-48.530.16572330.15594518X-RAY DIFFRACTION98.9
Refinement TLS params.Method: refined / Origin x: -18.516638157 Å / Origin y: 32.3710003478 Å / Origin z: 34.3883789893 Å
111213212223313233
T0.243684711569 Å2-0.0209433190612 Å20.0123651252069 Å2-0.266639135539 Å2-0.0184589138535 Å2--0.237940137086 Å2
L0.0641020517487 °2-0.03606175342 °20.0346930720671 °2-0.286572803213 °2-0.138812053248 °2--0.130031777964 °2
S-0.0150805788647 Å °0.0205027347518 Å °0.0118926432335 Å °-0.0131505136177 Å °0.0020934562488 Å °-0.0310553735708 Å °-0.0225585458826 Å °0.0291534770442 Å °0.0173475632145 Å °
Refinement TLS groupSelection details: all

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