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- PDB-8d3z: Crystal structure of GalS1 in complex with Manganese from Populus... -

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Basic information

Entry
Database: PDB / ID: 8d3z
TitleCrystal structure of GalS1 in complex with Manganese from Populus trichocarpas
ComponentsGalactan synthase
KeywordsTRANSFERASE / glycosyltransferase galactan synthase
Function / homology
Function and homology information


glycosylation / Transferases; Glycosyltransferases; Hexosyltransferases / glycosyltransferase activity / metal ion binding / membrane / cytoplasm
Similarity search - Function
Glycosyltransferase family 92 / Glycosyltransferase family 92
Similarity search - Domain/homology
: / Glycosyltransferase family 92 protein
Similarity search - Component
Biological speciesPopulus trichocarpa (black cottonwood)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.56 Å
AuthorsPereira, J.H. / Prabhakar, P.K. / Urbanowicz, B.R. / Adams, P.D.
Funding support United States, 1items
OrganizationGrant numberCountry
Department of Energy (DOE, United States) United States
CitationJournal: Nat.Plants / Year: 2023
Title: Structural and biochemical insight into a modular beta-1,4-galactan synthase in plants.
Authors: Prabhakar, P.K. / Pereira, J.H. / Taujale, R. / Shao, W. / Bharadwaj, V.S. / Chapla, D. / Yang, J.Y. / Bomble, Y.J. / Moremen, K.W. / Kannan, N. / Hammel, M. / Adams, P.D. / Scheller, H.V. / Urbanowicz, B.R.
History
DepositionJun 1, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 15, 2023Provider: repository / Type: Initial release
Revision 1.1Apr 5, 2023Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.2Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.3Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Galactan synthase
B: Galactan synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)102,88916
Polymers97,6912
Non-polymers5,19914
Water66737
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: SAXS
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11760 Å2
ΔGint69 kcal/mol
Surface area36920 Å2
MethodPISA
Unit cell
Length a, b, c (Å)169.982, 169.982, 73.960
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121
Space group name HallP312"
Symmetry operation#1: x,y,z
#2: -y,x-y,z+1/3
#3: -x+y,-x,z+2/3
#4: x-y,-y,-z+2/3
#5: -x,-x+y,-z+1/3
#6: y,x,-z

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Galactan synthase


Mass: 48845.289 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Populus trichocarpa (black cottonwood) / Production host: Escherichia coli (E. coli)
References: UniProt: A0A2K2AMS7, Transferases; Glycosyltransferases; Hexosyltransferases

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Sugars , 3 types, 12 molecules

#2: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}}LINUCSPDB-CARE
#3: Polysaccharide alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D- ...alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 1235.105 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-2DManpa1-2DManpa1-3[DManpa1-6]DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/3,7,6/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3-3-3-3/a4-b1_b4-c1_c3-d1_c6-g1_d2-e1_e2-f1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{[(2+1)][a-D-Manp]{[(2+1)][a-D-Manp]{}}}[(6+1)][a-D-Manp]{}}}}}LINUCSPDB-CARE
#5: Sugar
ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C8H15NO6 / Feature type: SUBJECT OF INVESTIGATION
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 2 types, 39 molecules

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


Mass: 54.938 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mn
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 37 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Has protein modificationY

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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: 3.16 Å3/Da / Density % sol: 61.04 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.1 M sodium citrate tribasic dihydrate pH 5.0 10 % PEG 6,000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 24, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.56→49.07 Å / Num. obs: 79592 / % possible obs: 99.9 % / Redundancy: 2 % / Biso Wilson estimate: 68.99 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.018 / Net I/σ(I): 20.3
Reflection shellResolution: 2.56→2.65 Å / Rmerge(I) obs: 0.35 / Num. unique obs: 7908 / CC1/2: 0.755

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
DIALSdata reduction
xia2data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 8D3T

8d3t


Resolution: 2.56→49.07 Å / SU ML: 0.4108 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 31.2787
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2639 2005 5.04 %
Rwork0.2297 37788 -
obs0.2314 39793 99.98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 107.46 Å2
Refinement stepCycle: LAST / Resolution: 2.56→49.07 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6556 0 335 37 6928
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00727094
X-RAY DIFFRACTIONf_angle_d1.01299632
X-RAY DIFFRACTIONf_chiral_restr0.05411038
X-RAY DIFFRACTIONf_plane_restr0.01041212
X-RAY DIFFRACTIONf_dihedral_angle_d19.55442622
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.56-2.620.38491430.32262652X-RAY DIFFRACTION99.96
2.62-2.690.33691420.29172676X-RAY DIFFRACTION100
2.7-2.770.33551470.31972674X-RAY DIFFRACTION99.96
2.77-2.860.42781410.33732693X-RAY DIFFRACTION99.96
2.86-2.970.35361400.3112673X-RAY DIFFRACTION99.96
2.97-3.080.36211430.27022692X-RAY DIFFRACTION99.96
3.09-3.220.30061410.26852661X-RAY DIFFRACTION100
3.23-3.40.2941400.25342682X-RAY DIFFRACTION100
3.4-3.610.32151480.25612686X-RAY DIFFRACTION100
3.61-3.890.26781410.21452720X-RAY DIFFRACTION100
3.89-4.280.24941420.21492692X-RAY DIFFRACTION100
4.28-4.90.20161390.17852747X-RAY DIFFRACTION100
4.9-6.170.21981450.20782727X-RAY DIFFRACTION99.97
6.17-49.070.22921530.2152813X-RAY DIFFRACTION99.93

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