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- PDB-8h1k: Crystal structure of glucose-2-epimerase from Runella slithyformi... -

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Basic information

Entry
Database: PDB / ID: 8h1k
TitleCrystal structure of glucose-2-epimerase from Runella slithyformis Runsl_4512
ComponentsN-acylglucosamine 2-epimerase
KeywordsISOMERASE / Apo form / Runsl
Function / homologyN-acylglucosamine 2-epimerase/Cellobiose 2-epimerase / N-acylglucosamine 2-epimerase (GlcNAc 2-epimerase) / Six-hairpin glycosidase-like superfamily / Six-hairpin glycosidase superfamily / isomerase activity / carbohydrate metabolic process / FORMIC ACID / N-acylglucosamine 2-epimerase
Function and homology information
Biological speciesRunella slithyformis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 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

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Assembly

Deposited unit
A: N-acylglucosamine 2-epimerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,4055
Polymers49,0831
Non-polymers3224
Water9,674537
1
A: N-acylglucosamine 2-epimerase
hetero molecules

A: N-acylglucosamine 2-epimerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)98,81110
Polymers98,1662
Non-polymers6458
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_465y-1,x+1,-z1
Buried area4120 Å2
ΔGint-7 kcal/mol
Surface area28720 Å2
MethodPISA
Unit cell
Length a, b, c (Å)113.366, 113.366, 116.031
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212
Space group name HallP4nw2abw
Symmetry operation#1: x,y,z
#2: -y+1/2,x+1/2,z+3/4
#3: y+1/2,-x+1/2,z+1/4
#4: x+1/2,-y+1/2,-z+1/4
#5: -x+1/2,y+1/2,-z+3/4
#6: -x,-y,z+1/2
#7: y,x,-z
#8: -y,-x,-z+1/2
Components on special symmetry positions
IDModelComponents
11A-854-

HOH

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Components

#1: Protein N-acylglucosamine 2-epimerase /


Mass: 49083.070 Da / Num. of mol.: 1
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: Chemical ChemComp-FMT / FORMIC ACID / Formic acid


Mass: 46.025 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CH2O2
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Formula: C3H8O3
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 537 / 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: 3.79 Å3/Da / Density % sol: 67.51 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / Details: 3.4 M sodium formate, 20 mM glucose

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Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL45XU / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 5, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.6→47 Å / Num. obs: 99680 / % possible obs: 99.97 % / Redundancy: 13.2 % / Biso Wilson estimate: 15.18 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.1499 / Net I/σ(I): 14.15
Reflection shellResolution: 1.6→1.7 Å / Rmerge(I) obs: 0.8708 / Num. unique obs: 9841 / CC1/2: 0.923

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
PHENIX1.20.1_4487refinement
XDSdata reduction
XDSdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3vw5

3vw5


Resolution: 1.6→47 Å / SU ML: 0.13 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 13.6912
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1616 4979 5 %
Rwork0.1419 94690 -
obs0.1428 99669 99.97 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 18.33 Å2
Refinement stepCycle: LAST / Resolution: 1.6→47 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3449 0 21 537 4007
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01843687
X-RAY DIFFRACTIONf_angle_d1.56975001
X-RAY DIFFRACTIONf_chiral_restr0.1078500
X-RAY DIFFRACTIONf_plane_restr0.0134647
X-RAY DIFFRACTIONf_dihedral_angle_d15.0923495
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6-1.620.23491630.19923122X-RAY DIFFRACTION99.61
1.62-1.640.18651770.17763113X-RAY DIFFRACTION99.97
1.64-1.660.17721490.1583116X-RAY DIFFRACTION100
1.66-1.680.15721470.14613127X-RAY DIFFRACTION99.97
1.68-1.70.15651750.14213104X-RAY DIFFRACTION99.97
1.7-1.720.15921750.13723118X-RAY DIFFRACTION99.97
1.72-1.750.15511660.13443111X-RAY DIFFRACTION100
1.75-1.770.16381630.13423107X-RAY DIFFRACTION100
1.77-1.80.15211660.1373147X-RAY DIFFRACTION100
1.8-1.830.17821670.13543112X-RAY DIFFRACTION100
1.83-1.860.14861440.143145X-RAY DIFFRACTION99.97
1.86-1.90.1571570.14053117X-RAY DIFFRACTION99.97
1.9-1.930.17041580.13923141X-RAY DIFFRACTION100
1.93-1.970.1611550.13543139X-RAY DIFFRACTION100
1.97-2.020.14171540.13123140X-RAY DIFFRACTION100
2.02-2.060.14861640.12773152X-RAY DIFFRACTION100
2.06-2.110.161770.13293101X-RAY DIFFRACTION100
2.11-2.170.15511650.1293159X-RAY DIFFRACTION100
2.17-2.240.14171570.13373138X-RAY DIFFRACTION99.97
2.24-2.310.14481550.13633171X-RAY DIFFRACTION100
2.31-2.390.16881750.13333137X-RAY DIFFRACTION100
2.39-2.490.18231750.14223151X-RAY DIFFRACTION100
2.49-2.60.1861850.15493137X-RAY DIFFRACTION100
2.6-2.740.17371840.15523166X-RAY DIFFRACTION99.97
2.74-2.910.17741620.16113210X-RAY DIFFRACTION100
2.91-3.130.16861750.15573167X-RAY DIFFRACTION100
3.13-3.450.17551600.14423217X-RAY DIFFRACTION100
3.45-3.950.14431720.12523220X-RAY DIFFRACTION100
3.95-4.970.12041880.1173263X-RAY DIFFRACTION100
4.97-470.18891690.17093442X-RAY DIFFRACTION99.81
Refinement TLS params.Method: refined / Origin x: -21.4049654101 Å / Origin y: 59.1785975754 Å / Origin z: 7.09916815636 Å
111213212223313233
T0.107681880315 Å2-0.014700248035 Å2-0.000839670048872 Å2-0.0993881657047 Å20.00524118423328 Å2--0.100859401635 Å2
L0.544253418327 °2-0.20000518311 °20.130203605594 °2-0.602092506681 °2-0.106629038803 °2--0.592878439401 °2
S0.000461413713251 Å °0.0062094944726 Å °-0.0528909228609 Å °0.00131593647661 Å °0.0271668136761 Å °0.0391576698017 Å °0.0433291217937 Å °-0.0334546991086 Å °-0.0266134376593 Å °
Refinement TLS groupSelection details: all

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