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

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Basic information

Entry
Database: PDB / ID: 8xkd
Titlebeta-1,4-galacosyltransferase
ComponentsGlycosyltransferase family 25 protein
KeywordsTRANSFERASE
Function / homologyGlycosyl transferase, family 25 / Glycosyltransferase family 25 (LPS biosynthesis protein) / nucleotide binding / metal ion binding / DI(HYDROXYETHYL)ETHER / TRIETHYLENE GLYCOL / URIDINE-5'-DIPHOSPHATE / Glycosyltransferase family 25 protein
Function and homology information
Biological speciesAggregatibacter actinomycetemcomitans NUM4039 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.73 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 23, 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

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)60,1866
Polymers59,1212
Non-polymers1,0654
Water3,315184
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6060 Å2
ΔGint-27 kcal/mol
Surface area18960 Å2
MethodPISA
Unit cell
Length a, b, c (Å)82.600, 92.810, 71.320
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11A-455-

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
Details: AUTHORS STATE THAT THE NCBI ACCESSION NUMBER IS BAS48030 FOR THE PROTEIN.
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: Chemical ChemComp-UDP / URIDINE-5'-DIPHOSPHATE


Type: RNA linking / Mass: 404.161 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C9H14N2O12P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: UDP*YM
#3: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O4 / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 184 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
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: 2.31 Å3/Da / Density % sol: 46.8 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop
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: 0.97851 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 11, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97851 Å / Relative weight: 1
ReflectionResolution: 1.73→46.71 Å / Num. obs: 57948 / % possible obs: 100 % / Redundancy: 12.9 % / CC1/2: 0.993 / Net I/σ(I): 11.7
Reflection shellResolution: 1.73→1.76 Å / Num. unique obs: 3113 / CC1/2: 0.804

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.73→46.71 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.947 / SU B: 2.343 / SU ML: 0.076 / Cross valid method: THROUGHOUT / ESU R: 0.108 / ESU R Free: 0.107 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23359 2986 5.2 %RANDOM
Rwork0.20042 ---
obs0.20212 54915 99.97 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 34.59 Å2
Baniso -1Baniso -2Baniso -3
1-1.04 Å2-0 Å20 Å2
2---0.71 Å2-0 Å2
3----0.33 Å2
Refinement stepCycle: 1 / Resolution: 1.73→46.71 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3464 0 67 184 3715
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0193642
X-RAY DIFFRACTIONr_bond_other_d0.0010.023421
X-RAY DIFFRACTIONr_angle_refined_deg1.4461.9654937
X-RAY DIFFRACTIONr_angle_other_deg0.78537877
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9695428
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.06825.436195
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.25715640
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.8371515
X-RAY DIFFRACTIONr_chiral_restr0.0880.2544
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.024096
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_it2.4733.191691
X-RAY DIFFRACTIONr_mcbond_other2.4683.1881690
X-RAY DIFFRACTIONr_mcangle_it3.8444.7652111
X-RAY DIFFRACTIONr_mcangle_other3.8444.7682112
X-RAY DIFFRACTIONr_scbond_it3.0833.6181951
X-RAY DIFFRACTIONr_scbond_other3.0833.6181951
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.995.2962822
X-RAY DIFFRACTIONr_long_range_B_refined7.14638.7344182
X-RAY DIFFRACTIONr_long_range_B_other7.09938.4114121
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Number: 6661 / 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: 1.73→1.775 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.285 228 -
Rwork0.266 3987 -
obs--100 %

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