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- PDB-5zoi: Crystal Structure of alpha1,3-Fucosyltransferase -

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Basic information

Entry
Database: PDB / ID: 5zoi
TitleCrystal Structure of alpha1,3-Fucosyltransferase
ComponentsAlpha-(1,3)-fucosyltransferase FucT
KeywordsTRANSFERASE / enzyme
Function / homology
Function and homology information


4-galactosyl-N-acetylglucosaminide 3-alpha-L-fucosyltransferase / 4-galactosyl-N-acetylglucosaminide 3-alpha-L-fucosyltransferase activity / fucosylation / fucose binding / lipopolysaccharide biosynthetic process / protein glycosylation / identical protein binding / membrane / cytoplasm
Similarity search - Function
Glycosyl transferase family 10, N-terminal domain / Glycosyl transferase family 10, C-terminal domain / Alpha-(1, 3)-fucosyltransferase/alpha-(1, 4)-fucosyltransferase, Helicobacter / Alpha-(1,3)-fucosyltransferase FucT, N-terminal / Alpha-(1,3)-fucosyltransferase FucT N-terminal domain / Glycosyl transferase family 10 / GT10-like, C-terminal domain superfamily / Glycosyltransferase family 10 (fucosyltransferase) C-term / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-C06 / Alpha-(1,3)-fucosyltransferase FucT
Similarity search - Component
Biological speciesHelicobacter pylori (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.19 Å
AuthorsTan, Y. / Yang, G.
CitationJournal: Sci Adv / Year: 2019
Title: Directed evolution of an alpha 1,3-fucosyltransferase using a single-cell ultrahigh-throughput screening method.
Authors: Tan, Y. / Zhang, Y. / Han, Y. / Liu, H. / Chen, H. / Ma, F. / Withers, S.G. / Feng, Y. / Yang, G.
History
DepositionApr 13, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 26, 2019Provider: repository / Type: Initial release
Revision 1.1Jan 22, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Mar 27, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Alpha-(1,3)-fucosyltransferase FucT
B: Alpha-(1,3)-fucosyltransferase FucT
hetero molecules


Theoretical massNumber of molelcules
Total (without water)99,5884
Polymers98,4102
Non-polymers1,1792
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1870 Å2
ΔGint-5 kcal/mol
Surface area32870 Å2
Unit cell
Length a, b, c (Å)121.664, 121.664, 64.718
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number145
Space group name H-MP32
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: MET / Beg label comp-ID: MET / End auth comp-ID: PHE / End label comp-ID: PHE / Refine code: _ / Auth seq-ID: 1 - 352 / Label seq-ID: 1 - 352

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

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Components

#1: Protein Alpha-(1,3)-fucosyltransferase FucT / 4-galactosyl-N-acetylglucosaminide 3-alpha-L-fucosyltransferase


Mass: 49204.809 Da / Num. of mol.: 2 / Fragment: UNP residues 1-412 / Mutation: S45F, D127N, R128E, H131I, Y199N, D340D, V368A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Helicobacter pylori (bacteria) / Gene: fucT / Production host: Escherichia coli (E. coli)
References: UniProt: O30511, 4-galactosyl-N-acetylglucosaminide 3-alpha-L-fucosyltransferase
#2: Chemical ChemComp-C06 / [[(2S,3R,4S,5R)-5-(2-azanyl-6-oxidanylidene-1H-purin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl] [(2S,3S,4S,5R,6R)-6-methyl-3,4,5-tris(oxidanyl)oxan-2-yl] hydrogen phosphate


Mass: 589.342 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C16H25N5O15P2

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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: 2.81 Å3/Da / Density % sol: 56.23 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: peg4000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.988 Å
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Jun 27, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.988 Å / Relative weight: 1
Reflection twin
Crystal-IDIDOperatorDomain-IDFraction
11H, K, L10.435
11K, H, -L20.431
11-K, -H, -L30.069
11-h,-k,l40.065
ReflectionResolution: 3.18→39.8 Å / Num. obs: 17862 / % possible obs: 99.8 % / Redundancy: 11 % / Net I/σ(I): 10
Reflection shellResolution: 3.18→3.34 Å / Num. unique obs: 3213

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Processing

Software
NameVersionClassification
REFMAC5.8.0218refinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.19→39.8 Å / Cor.coef. Fo:Fc: 0.726 / Cor.coef. Fo:Fc free: 0.633 / SU B: 23.45 / SU ML: 0.439 / Cross valid method: THROUGHOUT / ESU R Free: 0.126
RfactorNum. reflection% reflectionSelection details
Rfree0.316 893 5 %RANDOM
Rwork0.287 ---
obs0.288 16955 99.8 %-
Solvent computationIon probe radii: 0.9 Å / Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å
Displacement parametersBiso mean: 33.85 Å2
Baniso -1Baniso -2Baniso -3
1-2.3 Å20 Å20 Å2
2--2.3 Å20 Å2
3----4.6 Å2
Refinement stepCycle: LAST / Resolution: 3.19→39.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5642 0 76 0 5718
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0195896
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.3971.9578016
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.0655682
X-RAY DIFFRACTIONr_dihedral_angle_2_deg41.95724.903310
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.31215930
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.5981514
X-RAY DIFFRACTIONr_chiral_restr0.0930.2832
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0214604
X-RAY DIFFRACTIONr_gen_planes_other
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_it2.313.352740
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it3.9195.0173418
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.0873.4243156
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined10.23762.25923705
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Number: 9422 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.24 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 3.19→3.27 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.291 74 -
Rwork0.257 1221 -
obs--97.81 %

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