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- PDB-6bsw: Crystal structure of Xyloglucan Xylosyltransferase 1 ternary form -

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Basic information

Entry
Database: PDB / ID: 6bsw
TitleCrystal structure of Xyloglucan Xylosyltransferase 1 ternary form
ComponentsXyloglucan 6-xylosyltransferase 1
KeywordsTRANSFERASE / Xyloglucan / xylosyltransferase
Function / homology
Function and homology information


xyloglucan 6-xylosyltransferase / xyloglucan 6-xylosyltransferase activity / xyloglucan metabolic process / UDP-xylosyltransferase activity / polysaccharide biosynthetic process / protein glycosylation / Golgi medial cisterna / trans-Golgi network / endosome / Golgi membrane ...xyloglucan 6-xylosyltransferase / xyloglucan 6-xylosyltransferase activity / xyloglucan metabolic process / UDP-xylosyltransferase activity / polysaccharide biosynthetic process / protein glycosylation / Golgi medial cisterna / trans-Golgi network / endosome / Golgi membrane / Golgi apparatus / metal ion binding / cytosol
Similarity search - Function
Glycosyltransferase 34 / galactosyl transferase GMA12/MNN10 family / Nucleotide-diphospho-sugar transferases
Similarity search - Domain/homology
beta-cellohexaose / : / NITRATE ION / URIDINE-5'-DIPHOSPHATE / Xyloglucan 6-xylosyltransferase 1
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.156 Å
AuthorsCulbertson, A.T. / Ehrlich, J.J. / Choe, J. / Honzatko, R.B. / Zabotina, O.A.
Funding support United States, 1items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States)1121163 United States
CitationJournal: Proc. Natl. Acad. Sci. U.S.A. / Year: 2018
Title: Structure of xyloglucan xylosyltransferase 1 reveals simple steric rules that define biological patterns of xyloglucan polymers.
Authors: Culbertson, A.T. / Ehrlich, J.J. / Choe, J.Y. / Honzatko, R.B. / Zabotina, O.A.
History
DepositionDec 4, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 23, 2018Provider: repository / Type: Initial release
Revision 1.1Jun 6, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.pdbx_database_id_PubMed ..._citation.journal_abbrev / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.2Jun 20, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Non-polymer description / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / entity_name_com / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_molecule_features / pdbx_nonpoly_scheme / pdbx_struct_conn_angle / struct_asym / struct_conn / struct_conn_type / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.name / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.src_method / _entity.type / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _struct_asym.entity_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Mar 23, 2022Group: Author supporting evidence / Database references / Structure summary
Category: chem_comp / database_2 / pdbx_audit_support
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_audit_support.funding_organization

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Xyloglucan 6-xylosyltransferase 1
B: Xyloglucan 6-xylosyltransferase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)81,39211
Polymers79,0852
Non-polymers2,3079
Water3,765209
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10060 Å2
ΔGint-78 kcal/mol
Surface area26810 Å2
MethodPISA
Unit cell
Length a, b, c (Å)65.037, 94.889, 145.104
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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Protein / Sugars , 2 types, 3 molecules AB

#1: Protein Xyloglucan 6-xylosyltransferase 1 / / AtXT1


Mass: 39542.250 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: XXT1, XT1, At3g62720, F26K9_150 / Production host: Homo sapiens (human)
References: UniProt: Q9LZJ3, xyloglucan 6-xylosyltransferase
#2: Polysaccharide beta-D-glucopyranose-(1-4)-beta-D-glucopyranose-(1-4)-beta-D-glucopyranose-(1-4)-beta-D- ...beta-D-glucopyranose-(1-4)-beta-D-glucopyranose-(1-4)-beta-D-glucopyranose-(1-4)-beta-D-glucopyranose-(1-4)-beta-D-glucopyranose-(1-4)-beta-D-glucopyranose / beta-cellohexaose


Type: oligosaccharide, Oligosaccharide / Class: Metabolism / Mass: 990.860 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: oligosaccharide / References: beta-cellohexaose
DescriptorTypeProgram
DGlcpb1-4DGlcpb1-4DGlcpb1-4DGlcpb1-4DGlcpb1-4DGlcpb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,6,5/[a2122h-1b_1-5]/1-1-1-1-1-1/a4-b1_b4-c1_c4-d1_d4-e1_e4-f1WURCSPDB2Glycan 1.1.0
[][b-D-Glcp]{[(4+1)][b-D-Glcp]{[(4+1)][b-D-Glcp]{[(4+1)][b-D-Glcp]{[(4+1)][b-D-Glcp]{[(4+1)][b-D-Glcp]{}}}}}}LINUCSPDB-CARE

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Non-polymers , 6 types, 217 molecules

#3: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mn
#4: Chemical ChemComp-UDP / URIDINE-5'-DIPHOSPHATE / Uridine diphosphate


Type: RNA linking / Mass: 404.161 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C9H14N2O12P2 / Comment: UDP*YM
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#6: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER / Tris


Mass: 122.143 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#7: Chemical ChemComp-NO3 / NITRATE ION / Nitrate


Mass: 62.005 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: NO3
#8: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 209 / Source method: isolated from a natural source / Formula: H2O

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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: 2.83 Å3/Da / Density % sol: 56.55 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / Details: Tris-HCl, Na-Nitrate, PEG3350

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Data collection

DiffractionMean temperature: 123 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1.0332 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jun 23, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 2.15→48.43 Å / Num. obs: 45315 / % possible obs: 92.14 % / Redundancy: 5.5 % / CC1/2: 0.995 / Rmerge(I) obs: 0.1144 / Rpim(I) all: 0.05202 / Rrim(I) all: 0.1262 / Net I/σ(I): 10.39
Reflection shellResolution: 2.15→2.234 Å / Redundancy: 4.6 % / Rmerge(I) obs: 0.5292 / Num. unique obs: 3194 / CC1/2: 0.822 / Rpim(I) all: 0.05202 / Rrim(I) all: 0.1262 / % possible all: 65.86

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Processing

Software
NameVersionClassification
PHENIX1.12_2829refinement
PDB_EXTRACT3.24data extraction
HKL-3000data reduction
HKL-3000data scaling
PHENIXphasing
RefinementResolution: 2.156→48.428 Å / SU ML: 0.25 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 25.24 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2285 2000 4.41 %
Rwork0.1825 43308 -
obs0.1845 45308 92.04 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 146.63 Å2 / Biso mean: 51.9324 Å2 / Biso min: 23.2 Å2
Refinement stepCycle: final / Resolution: 2.156→48.428 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5566 0 260 209 6035
Biso mean--63.83 45.31 -
Num. residues----674
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0035911
X-RAY DIFFRACTIONf_angle_d0.528003
X-RAY DIFFRACTIONf_chiral_restr0.038808
X-RAY DIFFRACTIONf_plane_restr0.0021007
X-RAY DIFFRACTIONf_dihedral_angle_d10.1483416
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.1558-2.20970.3365930.24292023211661
2.2097-2.26940.24991160.24542503261976
2.2694-2.33620.27021250.24972689281481
2.3362-2.41160.29541310.2452860299186
2.4116-2.49780.3321380.23072998313691
2.4978-2.59780.26311460.22633134328095
2.5978-2.7160.26021530.22683326347999
2.716-2.85920.26431530.214633073460100
2.8592-3.03830.23851540.206333533507100
3.0383-3.27290.23051560.198633473503100
3.2729-3.60220.21351560.184133823538100
3.6022-4.12320.21411570.154634013558100
4.1232-5.19380.17961570.13334103567100
5.1938-48.440.22171650.166835753740100

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