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- PDB-8syd: X-ray crystal structure of UDP-2,3-diacetamido-2,3-dideoxy-glucur... -

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Basic information

Entry
Database: PDB / ID: 8syd
TitleX-ray crystal structure of UDP-2,3-diacetamido-2,3-dideoxy-glucuronic acid-2-epimerase from Thermus thermophilus strain HB27, D98N variant in the presence of UDP-2,3-diacetamido-2,3-dideoxy-glucuronic acid and UDP-N-acetylglucosamine at pH 6
ComponentsUDP-2,3-diacetamido-2,3-dideoxy-glucuronic acid-2-epimerase
KeywordsISOMERASE / lipopolysaccharide / O-antigen / 2-epimerase
Function / homology
Function and homology information


UDP-N-acetylglucosamine 2-epimerase (non-hydrolysing) / UDP-N-acetylglucosamine 2-epimerase activity / nucleotide binding
Similarity search - Function
UDP-N-acetylglucosamine 2-epimerase WecB-like / UDP-N-acetylglucosamine 2-epimerase domain / UDP-N-acetylglucosamine 2-epimerase / Glycogen Phosphorylase B; / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-MJL / URIDINE-DIPHOSPHATE-N-ACETYLGLUCOSAMINE / UDP-N-acetylglucosamine 2-epimerase
Similarity search - Component
Biological speciesThermus thermophilus HB27 (bacteria)
MethodX-RAY DIFFRACTION / FOURIER SYNTHESIS / Resolution: 2.2 Å
AuthorsKroft, C.W. / Thoden, J.B. / Holden, H.M.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35 GM134643 United States
CitationJournal: J.Biol.Chem. / Year: 2023
Title: Structural analysis of a bacterial UDP-sugar 2-epimerase reveals the active site architecture before and after catalysis.
Authors: Thoden, J.B. / McKnight, J.O. / Kroft, C.W. / Jast, J.D.T. / Holden, H.M.
History
DepositionMay 25, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 13, 2023Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2023Group: Database references / Category: citation / Item: _citation.journal_volume

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: UDP-2,3-diacetamido-2,3-dideoxy-glucuronic acid-2-epimerase
B: UDP-2,3-diacetamido-2,3-dideoxy-glucuronic acid-2-epimerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)89,1678
Polymers86,5572
Non-polymers2,6106
Water4,936274
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5180 Å2
ΔGint-45 kcal/mol
Surface area27190 Å2
MethodPISA
Unit cell
Length a, b, c (Å)56.272, 128.436, 58.135
Angle α, β, γ (deg.)90.00, 114.06, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein UDP-2,3-diacetamido-2,3-dideoxy-glucuronic acid-2-epimerase


Mass: 43278.422 Da / Num. of mol.: 2 / Mutation: D98N
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus thermophilus HB27 (bacteria) / Strain: ATCC BAA-163 / DSM 7039 / HB27 / Gene: TT_C0285 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Rosetta2 / References: UniProt: Q72KY0
#2: Chemical ChemComp-MJL / (2~{S},3~{S},4~{R},5~{R},6~{R})-4,5-diacetamido-6-[[[(2~{R},3~{S},4~{R},5~{R})-5-[2,4-bis(oxidanylidene)pyrimidin-1-yl]-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl]oxy-oxidanyl-phosphoryl]oxy-3-oxidanyl-oxane-2-carboxylic acid / UDP-2,3-diacetamido-2,3-dideoxy-alpha-D-glucuronate


Mass: 662.389 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C19H28N4O18P2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-UD1 / URIDINE-DIPHOSPHATE-N-ACETYLGLUCOSAMINE


Mass: 607.354 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C17H27N3O17P2 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 274 / 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: 2.22 Å3/Da / Density % sol: 44.5 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6
Details: Protein incubated with 5 mM UDP-2,3-diacetamido-2,3-dideoxy-glucuronic acid and 5 mM UDP-N-acetylglucosamine. Precipitant used was 22-27% pentaerythritol ethoxylate (3/4 EO/OH), 100 mM MES (pH 6)

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SEALED TUBE / Type: BRUKER D8 QUEST / Wavelength: 1.5418 Å
DetectorType: Bruker PHOTON II / Detector: PIXEL / Date: Feb 24, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.2→50 Å / Num. obs: 38022 / % possible obs: 99.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.9 % / Rsym value: 0.085 / Net I/σ(I): 12.8
Reflection shellResolution: 2.2→2.3 Å / Redundancy: 3.7 % / Mean I/σ(I) obs: 3.2 / Num. unique obs: 4649 / Rsym value: 0.38 / % possible all: 97.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0403refinement
SAINTdata reduction
SADABSdata scaling
REFMACphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 2.2→40.12 Å / Cor.coef. Fo:Fc: 0.936 / Cor.coef. Fo:Fc free: 0.884 / SU B: 7.114 / SU ML: 0.17 / Cross valid method: THROUGHOUT / ESU R: 0.285 / ESU R Free: 0.212 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22914 1822 4.8 %RANDOM
Rwork0.17248 ---
obs0.17517 36200 99.47 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 16.035 Å2
Baniso -1Baniso -2Baniso -3
1-0.01 Å20 Å20.02 Å2
2---0.03 Å20 Å2
3----0 Å2
Refinement stepCycle: 1 / Resolution: 2.2→40.12 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5747 0 166 274 6187
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0126047
X-RAY DIFFRACTIONr_bond_other_d0.0010.0165786
X-RAY DIFFRACTIONr_angle_refined_deg1.5951.6778227
X-RAY DIFFRACTIONr_angle_other_deg0.5351.58413285
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6195733
X-RAY DIFFRACTIONr_dihedral_angle_2_deg8.251557
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.127101014
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0730.2941
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.027049
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021367
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_it1.3621.512926
X-RAY DIFFRACTIONr_mcbond_other1.3621.512926
X-RAY DIFFRACTIONr_mcangle_it2.2612.7043655
X-RAY DIFFRACTIONr_mcangle_other2.2612.7063656
X-RAY DIFFRACTIONr_scbond_it2.1751.7643121
X-RAY DIFFRACTIONr_scbond_other2.1771.7663115
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.5943.0984571
X-RAY DIFFRACTIONr_long_range_B_refined4.85515.876835
X-RAY DIFFRACTIONr_long_range_B_other4.83615.836793
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.2→2.257 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.281 121 -
Rwork0.27 2631 -
obs--97.31 %

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