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

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Basic information

Entry
Database: PDB / ID: 8xlz
Titlebeta-1,4-galacosyltransferase
ComponentsGlycosyltransferase family 25 protein
KeywordsTRANSFERASE
Function / homologyURIDINE-5'-DIPHOSPHATE
Function and homology information
Biological speciesAggregatibacter actinomycetemcomitans NUM4039 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.84 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 26, 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)60,0339
Polymers59,1032
Non-polymers9307
Water3,567198
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6090 Å2
ΔGint-87 kcal/mol
Surface area19470 Å2
MethodPISA
Unit cell
Length a, b, c (Å)139.747, 53.210, 77.550
Angle α, β, γ (deg.)90.00, 116.42, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-509-

HOH

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Components

#1: Protein Glycosyltransferase family 25 protein


Mass: 29551.660 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)
Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
#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-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 198 / 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: 2.18 Å3/Da / Density % sol: 43.69 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: 0.2M Magnesium acetate tetrahydrate, 0.1M Sodium cacodylate trihydrate, 20% PEG 8000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.97853 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Oct 22, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97853 Å / Relative weight: 1
ReflectionResolution: 1.84→43.81 Å / Num. obs: 43884 / % possible obs: 99.3 % / Redundancy: 3.3 % / CC1/2: 0.986 / Net I/σ(I): 7.5
Reflection shellResolution: 1.84→1.88 Å / Num. unique obs: 2517 / CC1/2: 0.835

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
XDSFebryary 5, 2021data reduction
Aimlessdata scaling
Cootmodel building
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.84→43.81 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.943 / SU B: 5.075 / SU ML: 0.138 / Cross valid method: THROUGHOUT / ESU R: 0.146 / ESU R Free: 0.137 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24223 2228 5.1 %RANDOM
Rwork0.20666 ---
obs0.20849 41656 99.24 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 34.657 Å2
Baniso -1Baniso -2Baniso -3
1--0.86 Å20 Å2-1.08 Å2
2--7.46 Å20 Å2
3----3.7 Å2
Refinement stepCycle: 1 / Resolution: 1.84→43.81 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3495 0 55 198 3748
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0193665
X-RAY DIFFRACTIONr_bond_other_d0.0010.023401
X-RAY DIFFRACTIONr_angle_refined_deg1.481.964955
X-RAY DIFFRACTIONr_angle_other_deg0.78337827
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3245429
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.49925.515194
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.32815638
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.6681514
X-RAY DIFFRACTIONr_chiral_restr0.0840.2548
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.024116
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02854
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_it2.2543.2681704
X-RAY DIFFRACTIONr_mcbond_other2.2543.2661703
X-RAY DIFFRACTIONr_mcangle_it3.5124.8852128
X-RAY DIFFRACTIONr_mcangle_other3.5114.8872129
X-RAY DIFFRACTIONr_scbond_it2.6793.5911961
X-RAY DIFFRACTIONr_scbond_other2.6463.5931951
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.3395.2722825
X-RAY DIFFRACTIONr_long_range_B_refined6.12638.434195
X-RAY DIFFRACTIONr_long_range_B_other6.05138.0744118
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Number: 6459 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.14 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 1.845→1.893 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.382 158 -
Rwork0.375 2873 -
obs--92.89 %

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