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- PDB-8xc8: beta-1,4-galacosyltransferase -

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Basic information

Entry
Database: PDB / ID: 8xc8
Titlebeta-1,4-galacosyltransferase
ComponentsGlycosyltransferase family 25 protein
KeywordsTRANSFERASE
Function / homologyGlycosyl transferase, family 25 / Glycosyltransferase family 25 (LPS biosynthesis protein) / transferase activity / Glycosyltransferase family 25 protein
Function and homology information
Biological speciesAggregatibacter actinomycetemcomitans NUM4039 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.51 Å
AuthorsLuo, G. / Huang, Z. / Chen, J. / Hou, X. / Zhu, Y. / Ni, D. / Xu, W. / Zhang, W. / Rao, Y. / Mu, W.
Funding support China, 3items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)2022YFC2104900 China
National Natural Science Foundation of China (NSFC)32302010 China
Other privateBK20231043
CitationJournal: Int.J.Biol.Macromol. / Year: 2024
Title: Crystal structure and structure-guided tunnel engineering in a bacterial beta-1,4-galactosyltransferase.
Authors: Luo, G. / Huang, Z. / Zhu, Y. / Chen, J. / Hou, X. / Ni, D. / Xu, W. / Zhang, W. / Rao, Y. / Mu, W.
History
DepositionDec 8, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 11, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Glycosyltransferase family 25 protein
B: Glycosyltransferase family 25 protein


Theoretical massNumber of molelcules
Total (without water)59,6842
Polymers59,6842
Non-polymers00
Water1086
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)84.393, 84.393, 257.495
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein Glycosyltransferase family 25 protein


Mass: 29842.023 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aggregatibacter actinomycetemcomitans NUM4039 (bacteria)
Gene: FXB68_02155 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: A0A5D0ENI3
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationY

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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: 3.84 Å3/Da / Density % sol: 67.98 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: 1.26M Sodium phosphate monobasic monohydrate, 0.14M Potassium phosphate dibasic

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97852 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 14, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97852 Å / Relative weight: 1
ReflectionResolution: 2.507→80.2 Å / Num. obs: 13430 / % possible obs: 99.8 % / Redundancy: 15.8 % / Rmerge(I) obs: 0.142 / Net I/σ(I): 16.5
Reflection shellResolution: 2.51→2.87 Å / Num. unique obs: 672 / CC1/2: 0.731

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
XDSFebruary 5, 2021data reduction
Aimlessdata scaling
Cootmodel building
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.51→80.2 Å / Cor.coef. Fo:Fc: 0.916 / Cor.coef. Fo:Fc free: 0.888 / SU B: 16.297 / SU ML: 0.328 / Cross valid method: THROUGHOUT / ESU R Free: 0.527 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.27882 663 4.9 %RANDOM
Rwork0.23649 ---
obs0.23863 12767 40.71 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 73.854 Å2
Baniso -1Baniso -2Baniso -3
1-0.67 Å20 Å20 Å2
2--0.67 Å20 Å2
3----1.34 Å2
Refinement stepCycle: 1 / Resolution: 2.51→80.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3842 0 0 6 3848
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0040.0133921
X-RAY DIFFRACTIONr_bond_other_d0.0010.0163720
X-RAY DIFFRACTIONr_angle_refined_deg1.341.6455306
X-RAY DIFFRACTIONr_angle_other_deg1.0891.5768556
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.4885466
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.70924.646226
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.31815681
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.4051515
X-RAY DIFFRACTIONr_chiral_restr0.0510.2521
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.024477
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02933
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_it3.6717.6821870
X-RAY DIFFRACTIONr_mcbond_other3.6727.681869
X-RAY DIFFRACTIONr_mcangle_it6.1911.5222334
X-RAY DIFFRACTIONr_mcangle_other6.18911.5242335
X-RAY DIFFRACTIONr_scbond_it3.3168.0492051
X-RAY DIFFRACTIONr_scbond_other3.3168.0512052
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.84511.9432973
X-RAY DIFFRACTIONr_long_range_B_refined9.75291.5074329
X-RAY DIFFRACTIONr_long_range_B_other9.75191.524330
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Number: 6672 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.16 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 2.51→2.58 Å
RfactorNum. reflection% reflection
Rfree0.284 1 -
Rwork0.678 34 -
obs--1.47 %

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