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- PDB-8wex: Crystal structure of N-acetyl sugar amidotransferase from Legione... -

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Basic information

Entry
Database: PDB / ID: 8wex
TitleCrystal structure of N-acetyl sugar amidotransferase from Legionella pneumophila
ComponentsN-acetyl sugar amidotransferase
KeywordsTRANSFERASE / N-acetyl sugar amidotransferase / Rossmanoid fold / PP-loop / LPS biosynthesis
Function / homologyN-acetyl sugar amidotransferase / transferase activity / N-acetyl sugar amidotransferase
Function and homology information
Biological speciesLegionella pneumophila (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.33 Å
AuthorsGao, J. / Xu, W. / Ge, H.
Funding support China, 2items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)32370196 China
National Natural Science Foundation of China (NSFC)31970103 China
CitationJournal: Int J Mol Sci / Year: 2023
Title: Structural Characterization of an N-Acetyl Sugar Amidotransferase Involved in the Lipopolysaccharide Biosynthesis in Bacteria.
Authors: Gao, J. / Xu, W. / Liu, T. / Sun, W. / Wang, N. / Ma, J. / Ge, H.
History
DepositionSep 19, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 22, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: N-acetyl sugar amidotransferase
B: N-acetyl sugar amidotransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)109,4404
Polymers109,3092
Non-polymers1312
Water4,179232
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)74.722, 74.722, 319.678
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number153
Space group name H-MP3212
Components on special symmetry positions
IDModelComponents
11A-632-

HOH

21B-652-

HOH

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Components

#1: Protein N-acetyl sugar amidotransferase


Mass: 54654.359 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Legionella pneumophila (bacteria) / Gene: D1H98_00335 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A3A6V1D8
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 232 / 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: 2.36 Å3/Da / Density % sol: 47.81 %
Crystal growTemperature: 287 K / Method: vapor diffusion / Details: 20% (w/v) PEG 3350, 0.2 M ammonium acetate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.97914 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 29, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97914 Å / Relative weight: 1
ReflectionResolution: 2.33→45.67 Å / Num. obs: 44179 / % possible obs: 100 % / Redundancy: 17.2 % / CC1/2: 0.998 / Net I/σ(I): 19.8
Reflection shellResolution: 2.33→2.39 Å / Num. unique obs: 3210 / CC1/2: 0.602

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Processing

Software
NameVersionClassification
REFMAC5.8.0238refinement
autoPXdata reduction
pointlessdata scaling
MR-Rosettaphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.33→20 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.934 / Cross valid method: THROUGHOUT / ESU R: 0.314 / ESU R Free: 0.231 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24687 2141 4.9 %RANDOM
Rwork0.2079 ---
obs0.20986 41846 99.51 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 51.194 Å2
Baniso -1Baniso -2Baniso -3
1-0.17 Å20.08 Å20 Å2
2--0.17 Å2-0 Å2
3----0.55 Å2
Refinement stepCycle: 1 / Resolution: 2.33→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6236 0 2 232 6470
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0136418
X-RAY DIFFRACTIONr_bond_other_d0.0350.0175638
X-RAY DIFFRACTIONr_angle_refined_deg1.2341.6498689
X-RAY DIFFRACTIONr_angle_other_deg2.2731.57913070
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4775760
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.11421.989377
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.37151028
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.1731542
X-RAY DIFFRACTIONr_chiral_restr0.0640.2788
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.027250
X-RAY DIFFRACTIONr_gen_planes_other0.0080.021488
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_it3.5775.4073064
X-RAY DIFFRACTIONr_mcbond_other3.5775.4063063
X-RAY DIFFRACTIONr_mcangle_it5.3298.0933816
X-RAY DIFFRACTIONr_mcangle_other5.3298.0943817
X-RAY DIFFRACTIONr_scbond_it3.7835.6693353
X-RAY DIFFRACTIONr_scbond_other3.7835.673354
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.9798.3584873
X-RAY DIFFRACTIONr_long_range_B_refined8.17760.7157354
X-RAY DIFFRACTIONr_long_range_B_other8.16760.6197301
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Number: 12396 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.11 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 2.332→2.392 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.352 142 -
Rwork0.309 2909 -
obs--96.67 %

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