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- PDB-4wlm: Crystal structure of mouse Xyloside xylosyltransferase 1 complexe... -

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Basic information

Entry
Database: PDB / ID: 4wlm
TitleCrystal structure of mouse Xyloside xylosyltransferase 1 complexed with manganese
ComponentsXyloside xylosyltransferase 1
KeywordsTRANSFERASE / glycosyltransferase / manganese binding
Function / homology
Function and homology information


xylosyl alpha-1,3-xylosyltransferase / xylosyl alpha-1,3-xylosyltransferase activity / UDP-xylosyltransferase activity / protein O-linked glycosylation via N-acetyl-galactosamine / manganese ion binding / endoplasmic reticulum membrane / magnesium ion binding
Similarity search - Function
Xyloside xylosyltransferase 1 / Glycosyl transferase, family 8 / Glycosyl transferase family 8 / Nucleotide-diphospho-sugar transferases
Similarity search - Domain/homology
: / Xyloside xylosyltransferase 1
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 3 Å
AuthorsYu, H. / Li, H.
CitationJournal: Nat.Chem.Biol. / Year: 2015
Title: Notch-modifying xylosyltransferase structures support an SNi-like retaining mechanism.
Authors: Yu, H. / Takeuchi, M. / LeBarron, J. / Kantharia, J. / London, E. / Bakker, H. / Haltiwanger, R.S. / Li, H. / Takeuchi, H.
History
DepositionOct 7, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 30, 2015Provider: repository / Type: Initial release
Revision 1.1Apr 20, 2016Group: Database references
Revision 1.2Dec 27, 2023Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_oper_list / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id
Revision 1.3Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Xyloside xylosyltransferase 1
B: Xyloside xylosyltransferase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,1819
Polymers70,5912
Non-polymers5907
Water00
1
A: Xyloside xylosyltransferase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,5434
Polymers35,2961
Non-polymers2473
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Xyloside xylosyltransferase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,6395
Polymers35,2961
Non-polymers3434
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
B: Xyloside xylosyltransferase 1
hetero molecules

A: Xyloside xylosyltransferase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,1819
Polymers70,5912
Non-polymers5907
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_565-y,x-y+1,z+1/31
Buried area3970 Å2
ΔGint-117 kcal/mol
Surface area24450 Å2
MethodPISA
Unit cell
Length a, b, c (Å)89.306, 89.306, 154.303
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

#1: Protein Xyloside xylosyltransferase 1 / UDP-xylose:alpha-xyloside alpha-1 / 3-xylosyltransferase


Mass: 35295.500 Da / Num. of mol.: 2 / Fragment: unp residues 87-392
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Xxylt1 / Production host: Homo sapiens (human)
References: UniProt: Q3U4G3, Transferases; Glycosyltransferases; Pentosyltransferases
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mn
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.52 Å3/Da / Density % sol: 51.12 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 20 mM HEPES, 1.5 M Li2SO4

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1.1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Sep 8, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 3→40 Å / Num. obs: 14806 / % possible obs: 99.8 % / Redundancy: 5.9 % / Rmerge(I) obs: 0.122 / Net I/σ(I): 15.6
Reflection shellResolution: 3→3.11 Å / Redundancy: 6.1 % / Rmerge(I) obs: 0.589 / Mean I/σ(I) obs: 2.8 / % possible all: 99.9

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Processing

SoftwareName: REFMAC / Version: 5.6.0117 / Classification: refinement
RefinementResolution: 3→40 Å / Cor.coef. Fo:Fc: 0.907 / Cor.coef. Fo:Fc free: 0.854 / Cross valid method: THROUGHOUT / ESU R Free: 0.512 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.28698 749 5.1 %RANDOM
Rwork0.23018 ---
obs0.23294 14014 99.71 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 55.948 Å2
Baniso -1Baniso -2Baniso -3
1-1.22 Å20.61 Å20 Å2
2--1.22 Å20 Å2
3----1.84 Å2
Refinement stepCycle: 1 / Resolution: 3→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4747 0 27 0 4774
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.024914
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg0.9171.9446660
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.5465571
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.20223.306248
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.46515818
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.5761530
X-RAY DIFFRACTIONr_chiral_restr0.0630.2702
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.0213768
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_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 3.001→3.079 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.356 60 -
Rwork0.329 1034 -
obs--99.64 %

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