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- PDB-8h1m: Crystal structure of glucose-2-epimerase mutant_D254A from Runell... -

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Basic information

Entry
Database: PDB / ID: 8h1m
TitleCrystal structure of glucose-2-epimerase mutant_D254A from Runella slithyformis Runsl_4512
ComponentsN-acylglucosamine 2-epimerase
KeywordsISOMERASE / mutant 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
FORMIC ACID / N-acylglucosamine 2-epimerase
Similarity search - Component
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 1.1May 29, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond / diffrn_source / 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)48,9013
Polymers48,8091
Non-polymers922
Water12,647702
1
A: N-acylglucosamine 2-epimerase
hetero molecules

A: N-acylglucosamine 2-epimerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)97,8026
Polymers97,6172
Non-polymers1844
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_465y-1,x+1,-z1
Unit cell
Length a, b, c (Å)113.219, 113.219, 116.284
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-1138-

HOH

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Components

#1: Protein N-acylglucosamine 2-epimerase


Mass: 48808.738 Da / Num. of mol.: 1 / Mutation: D254A
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


Mass: 46.025 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: CH2O2 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 702 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 3.8 Å3/Da / Density % sol: 67.63 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / Details: 3.6M sodium formate

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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: Oct 7, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.6→47.04 Å / Num. obs: 99920 / % possible obs: 99.94 % / Redundancy: 13.1 % / Biso Wilson estimate: 17.01 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.0826 / Net I/σ(I): 20.83
Reflection shellResolution: 1.6→1.66 Å / Num. unique obs: 9806 / CC1/2: 0.89

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Processing

Software
NameVersionClassification
PHENIX1.17_3644refinement
PHENIX1.17_3644refinement
XDSdata reduction
XDSdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.6→47.04 Å / SU ML: 0.1301 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 14.532
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1662 4990 5 %
Rwork0.144 94899 -
obs0.1451 99889 99.96 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 20.72 Å2
Refinement stepCycle: LAST / Resolution: 1.6→47.04 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3446 0 6 702 4154
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01853570
X-RAY DIFFRACTIONf_angle_d1.52494834
X-RAY DIFFRACTIONf_chiral_restr0.1088488
X-RAY DIFFRACTIONf_plane_restr0.011620
X-RAY DIFFRACTIONf_dihedral_angle_d17.2149468
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6-1.620.24261780.18853081X-RAY DIFFRACTION98.97
1.62-1.640.211610.18683118X-RAY DIFFRACTION99.94
1.64-1.660.22321570.1743123X-RAY DIFFRACTION99.97
1.66-1.680.19111660.16453131X-RAY DIFFRACTION99.97
1.68-1.70.1841590.16713113X-RAY DIFFRACTION100
1.7-1.720.19521670.16273142X-RAY DIFFRACTION100
1.72-1.750.18441750.16083120X-RAY DIFFRACTION100
1.75-1.770.17341660.15813114X-RAY DIFFRACTION100
1.77-1.80.21831740.16093139X-RAY DIFFRACTION100
1.8-1.830.20661700.15493102X-RAY DIFFRACTION100
1.83-1.860.17451640.15563126X-RAY DIFFRACTION99.94
1.86-1.90.16021810.15223107X-RAY DIFFRACTION100
1.9-1.930.1871670.14973170X-RAY DIFFRACTION100
1.93-1.970.17191780.14993100X-RAY DIFFRACTION100
1.97-2.010.17311550.14013158X-RAY DIFFRACTION100
2.01-2.060.15081610.14213157X-RAY DIFFRACTION100
2.06-2.110.16511540.13583153X-RAY DIFFRACTION100
2.11-2.170.15841650.13253140X-RAY DIFFRACTION100
2.17-2.230.15471680.13423163X-RAY DIFFRACTION100
2.23-2.310.15981470.1383161X-RAY DIFFRACTION100
2.31-2.390.18151790.13173161X-RAY DIFFRACTION100
2.39-2.480.15621680.13613155X-RAY DIFFRACTION100
2.48-2.60.14171740.14933166X-RAY DIFFRACTION100
2.6-2.730.18451570.153196X-RAY DIFFRACTION100
2.73-2.90.18061740.16843202X-RAY DIFFRACTION100
2.9-3.130.19471580.16073194X-RAY DIFFRACTION100
3.13-3.440.1551690.14493225X-RAY DIFFRACTION100
3.44-3.940.14061610.11793234X-RAY DIFFRACTION100
3.94-4.960.13461880.10883268X-RAY DIFFRACTION100
4.97-47.040.16811490.16293480X-RAY DIFFRACTION99.94

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