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

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Basic information

Entry
Database: PDB / ID: 8xgx
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: 2.41 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 15, 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)59,1212
Polymers59,1212
Non-polymers00
Water1,51384
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)87.840, 87.840, 140.240
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number94
Space group name H-MP42212
Components on special symmetry positions
IDModelComponents
11B-313-

HOH

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Components

#1: Protein Glycosyltransferase family 25 protein


Mass: 29560.652 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.: 84 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationN

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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: 2.29 Å3/Da / Density % sol: 46.24 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop
Details: 1.26M Sodium phosphate monobasic monohydrate, 0.14M Potassium phosphate monobasic

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17B1 / Wavelength: 0.97628 Å
DetectorType: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Dec 29, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97628 Å / Relative weight: 1
ReflectionResolution: 2.41→46.75 Å / Num. obs: 21910 / % possible obs: 100 % / Redundancy: 25.7 % / CC1/2: 0.999 / Net I/σ(I): 13.8
Reflection shellResolution: 2.41→2.5 Å / CC1/2: 0.786

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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: 2.41→46.54 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.917 / SU B: 8.771 / SU ML: 0.198 / Cross valid method: THROUGHOUT / ESU R: 0.375 / ESU R Free: 0.256 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25261 1070 4.9 %RANDOM
Rwork0.2083 ---
obs0.21057 20838 99.95 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 41.343 Å2
Baniso -1Baniso -2Baniso -3
1--0.32 Å2-0 Å2-0 Å2
2---0.32 Å2-0 Å2
3---0.63 Å2
Refinement stepCycle: 1 / Resolution: 2.41→46.54 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3466 0 0 84 3550
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.0133559
X-RAY DIFFRACTIONr_bond_other_d0.0010.0173364
X-RAY DIFFRACTIONr_angle_refined_deg1.3291.6414821
X-RAY DIFFRACTIONr_angle_other_deg1.1571.5767740
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.3215423
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.624.293205
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.4515635
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.6131514
X-RAY DIFFRACTIONr_chiral_restr0.0570.2473
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.024053
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02855
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_it2.8024.1981686
X-RAY DIFFRACTIONr_mcbond_other2.8014.1971685
X-RAY DIFFRACTIONr_mcangle_it4.5696.2922105
X-RAY DIFFRACTIONr_mcangle_other4.5686.2942106
X-RAY DIFFRACTIONr_scbond_it2.844.5261873
X-RAY DIFFRACTIONr_scbond_other2.8394.5281874
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.8296.6522715
X-RAY DIFFRACTIONr_long_range_B_refined7.47547.7283781
X-RAY DIFFRACTIONr_long_range_B_other7.4847.7173775
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Number: 6645 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.09 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 2.41→2.473 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.386 64 -
Rwork0.298 1517 -
obs--100 %

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