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

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Basic information

Entry
Database: PDB / ID: 8sxy
TitleX-ray crystal structure of UDP- 2,3-diacetamido-2,3-dideoxy-glucuronic acid-2-epimerase from Thermus thermophilus strain HB27 in complex with its product UDP-2,3-diacetamido-2,3-dideoxy-d-mannuronic acid at pH 5
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-MJ3 / UDP-N-acetylglucosamine 2-epimerase
Similarity search - Component
Biological speciesThermus thermophilus HB27 (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsMcKnight, J.O. / 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 24, 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)85,4217
Polymers83,9902
Non-polymers1,4315
Water8,773487
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3140 Å2
ΔGint-42 kcal/mol
Surface area27120 Å2
MethodPISA
Unit cell
Length a, b, c (Å)56.455, 128.796, 58.663
Angle α, β, γ (deg.)90.00, 111.09, 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: 41995.070 Da / Num. of mol.: 2
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-MJ3 / (2~{S},3~{S},4~{R},5~{S},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-mannuronic acid


Mass: 662.389 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C19H28N4O18P2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 487 / 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: 2.37 Å3/Da / Density % sol: 48.08 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5
Details: Protein incubated with 5 mM UDP-2,3-diacetamido-2,3-dideoxy-glucuronic acid. Precipitant solution: 22-27% pentaerythritol propoxylate (5/4 PO/OH), 100 mM homopipes (pH 5)

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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: Dec 16, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.8→50 Å / Num. obs: 71545 / % possible obs: 99 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.4 % / Rsym value: 0.056 / Net I/σ(I): 17.5
Reflection shellResolution: 1.8→1.9 Å / Redundancy: 4.4 % / Mean I/σ(I) obs: 3.5 / Num. unique obs: 10677 / Rsym value: 0.3 / % possible all: 98.7

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Processing

Software
NameVersionClassification
REFMAC5.8.0403refinement
SAINTdata reduction
SADABSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.8→41.71 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.936 / SU B: 3.272 / SU ML: 0.095 / Cross valid method: THROUGHOUT / ESU R: 0.126 / ESU R Free: 0.122 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21819 3515 4.9 %RANDOM
Rwork0.1796 ---
obs0.1815 68030 99.01 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 20.549 Å2
Baniso -1Baniso -2Baniso -3
1--0 Å2-0 Å2-0 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: 1 / Resolution: 1.8→41.71 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5643 0 89 487 6219
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0125929
X-RAY DIFFRACTIONr_bond_other_d0.0010.0165755
X-RAY DIFFRACTIONr_angle_refined_deg1.5631.6738070
X-RAY DIFFRACTIONr_angle_other_deg0.5311.58213220
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1945741
X-RAY DIFFRACTIONr_dihedral_angle_2_deg9.049556
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.369101023
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0760.2921
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.026988
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021348
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_it1.9731.9662895
X-RAY DIFFRACTIONr_mcbond_other1.9731.9662895
X-RAY DIFFRACTIONr_mcangle_it3.0313.523620
X-RAY DIFFRACTIONr_mcangle_other3.033.5213621
X-RAY DIFFRACTIONr_scbond_it2.8162.3553034
X-RAY DIFFRACTIONr_scbond_other2.8192.3573029
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.554.1474433
X-RAY DIFFRACTIONr_long_range_B_refined6.40622.246776
X-RAY DIFFRACTIONr_long_range_B_other6.33121.866654
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.8→1.846 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.37 286 -
Rwork0.339 4967 -
obs--98.22 %

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