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- PDB-8d3t: Crystal structure of GalS1 from Populus trichocarpas -

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Basic information

Entry
Database: PDB / ID: 8d3t
TitleCrystal structure of GalS1 from Populus trichocarpas
ComponentsGalactan synthase
KeywordsTRANSFERASE / glycosyltransferase galactan synthase
Function / homologyGlycosyltransferase family 92 / Glycosyltransferase family 92 / : / Transferases; Glycosyltransferases; Hexosyltransferases / glycosyltransferase activity / metal ion binding / membrane / cytoplasm / Glycosyltransferase family 92 protein
Function and homology information
Biological speciesPopulus trichocarpa (black cottonwood)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.37 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 23, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature
Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)206,04230
Polymers195,3814
Non-polymers10,66126
Water10,413578
1
A: Galactan synthase
B: Galactan synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)103,00015
Polymers97,6912
Non-polymers5,31013
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11670 Å2
ΔGint86 kcal/mol
Surface area36770 Å2
MethodPISA
2
C: Galactan synthase
D: Galactan synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)103,04215
Polymers97,6912
Non-polymers5,35113
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11180 Å2
ΔGint84 kcal/mol
Surface area36500 Å2
MethodPISA
Unit cell
Length a, b, c (Å)70.398, 83.422, 94.689
Angle α, β, γ (deg.)76.160, 69.670, 88.570
Int Tables number1
Space group name H-MP1
Space group name HallP1
Symmetry operation#1: x,y,z

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Components

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Protein / Non-polymers , 2 types, 582 molecules ABCD

#1: Protein
Galactan synthase


Mass: 48845.289 Da / Num. of mol.: 4
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
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 578 / Source method: isolated from a natural source / Formula: H2O

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Sugars , 4 types, 26 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.: 4
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.: 3
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
#4: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose- ...2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[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: 1276.157 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-2DManpa1-3[DManpa1-3DManpa1-6]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]/1-1-2-3-1-3-3/a4-b1_b4-c1_c3-d1_c6-f1_d2-e1_f3-g1WURCSPDB2Glycan 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)][b-D-GlcpNAc]{}}[(6+1)][a-D-Manp]{[(3+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.: 18 / 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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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: 2.59 Å3/Da / Density % sol: 52.44 %
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: Sep 26, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.37→80.84 Å / Num. obs: 78131 / % possible obs: 98.2 % / Redundancy: 2.6 % / Biso Wilson estimate: 36.67 Å2 / CC1/2: 0.989 / Rmerge(I) obs: 0.103 / Net I/σ(I): 7.18
Reflection shellResolution: 2.37→2.45 Å / Rmerge(I) obs: 1.036 / Num. unique obs: 7586 / CC1/2: 0.506

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
DIALSdata reduction
xia2data scaling
PHASERphasing
RefinementMethod to determine structure: SAD / Resolution: 2.37→80.84 Å / SU ML: 0.3352 / Cross valid method: FREE R-VALUE / σ(F): 1.95 / Phase error: 26.3172
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2521 4011 5.14 %
Rwork0.1947 74073 -
obs0.1976 78084 98.15 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 44.7 Å2
Refinement stepCycle: LAST / Resolution: 2.37→80.84 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12933 0 699 578 14210
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.003214039
X-RAY DIFFRACTIONf_angle_d0.572419063
X-RAY DIFFRACTIONf_chiral_restr0.05352062
X-RAY DIFFRACTIONf_plane_restr0.00352396
X-RAY DIFFRACTIONf_dihedral_angle_d9.23832205
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.37-2.40.32251500.29952316X-RAY DIFFRACTION89.12
2.4-2.430.35841150.30212566X-RAY DIFFRACTION97.24
2.43-2.460.3571350.2832548X-RAY DIFFRACTION97.81
2.46-2.490.35091380.2822524X-RAY DIFFRACTION97.69
2.49-2.520.32511350.26012565X-RAY DIFFRACTION97.76
2.52-2.560.28521260.24332522X-RAY DIFFRACTION97.78
2.56-2.60.32351280.24332573X-RAY DIFFRACTION97.58
2.6-2.640.27691290.23512550X-RAY DIFFRACTION98.13
2.64-2.680.29861490.23482575X-RAY DIFFRACTION98.02
2.68-2.730.30661240.23672514X-RAY DIFFRACTION98.1
2.73-2.780.31261480.23932554X-RAY DIFFRACTION98.15
2.78-2.830.30421510.23852565X-RAY DIFFRACTION98.37
2.83-2.890.27561370.24322545X-RAY DIFFRACTION98.31
2.89-2.950.27891320.23992553X-RAY DIFFRACTION98.35
2.95-3.020.32741270.2322562X-RAY DIFFRACTION98.39
3.02-3.10.27771500.22192579X-RAY DIFFRACTION98.52
3.1-3.180.27171330.2062583X-RAY DIFFRACTION98.58
3.18-3.270.25021350.18982542X-RAY DIFFRACTION98.67
3.27-3.380.25271420.1922565X-RAY DIFFRACTION98.54
3.38-3.50.25461430.18912574X-RAY DIFFRACTION98.76
3.5-3.640.25731700.1842543X-RAY DIFFRACTION98.87
3.64-3.810.23021430.17352572X-RAY DIFFRACTION98.98
3.81-4.010.24031430.15842575X-RAY DIFFRACTION99.05
4.01-4.260.18811220.15172599X-RAY DIFFRACTION99.13
4.26-4.590.19011220.13662585X-RAY DIFFRACTION99.05
4.59-5.050.18651420.13542598X-RAY DIFFRACTION99.38
5.05-5.780.1821420.15992564X-RAY DIFFRACTION99.3
5.78-7.280.25231520.19222587X-RAY DIFFRACTION99.67
7.28-80.840.25681480.20282575X-RAY DIFFRACTION99.31
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.07701841452-0.187930197114-0.8403925325190.753274724941-0.08631663191712.421642763590.109539707092-0.00819574923252-0.700093508913-0.119741040559-0.1043598568370.05588175047060.8591622928270.03354781662680.03595765596760.484477613924-0.0143788971705-0.08799487079230.2173711198380.0008278249834550.5750825968394.697-26.505-27.42
21.39463997215-0.4885394580810.314918257052.77552316773-0.9262642029521.298006519040.1184030443540.245181671215-0.182025596695-0.38072551131-0.143352243354-0.1371878522940.234384585350.2160141868480.03193131911010.2580910812660.0140358172699-0.004950013757410.290791562884-0.02754340241130.1843818143184.431-2.781-44.778
33.88615532880.9698262682120.7537354021675.815031459512.356083088395.809231584060.09109932158740.2394106605410.232677198697-0.082967894769-0.12881979549-0.14981015836-0.1082211247170.416064051584-0.0008901553605490.1843747524650.00640524151074-0.02053135936390.2735524026320.09431755143590.2194893492083.14517.36-46.036
40.74540460498-0.115000509937-1.893569639630.665971961223-0.192093717625.081244763880.06107798946560.05620039936470.145423874415-0.057334729321-0.004055674319440.0879745467413-0.115007072202-0.365748325982-0.08790636483590.199217467093-0.0568891121543-0.05465618044160.2908216564040.05159629148880.39234112009-9.154-13.04-6.582
54.77913566223-1.03691317633-2.491215132371.496206192870.9630466420193.86576733534-0.0534954241920.3725110675570.487885165088-0.2121460145730.0573928059819-0.106650954917-0.171635986316-0.34118326050.04237634045990.269816604862-0.0746756613196-0.06847564788730.2653563523690.08479041176880.35186164786-8.539-11.817-0.851
62.34896301607-0.6234772221650.9426278588270.565805384863-0.4530096023161.63559617229-0.0340824379056-0.201976650769-0.0149234160776-0.01880738590060.08557952998940.1509345973160.194296834257-0.233049146485-0.03493431184280.217282702706-0.07111084621950.001361156451420.3146589255840.08575420806930.298557802871.741-25.82713.827
73.53536368658-1.802321195131.451556225391.80379475843-0.08966184706231.16975009245-0.116909986838-0.09192815627380.495113202092-0.0363084683883-0.0871957518653-0.325160778291-0.01004297333030.2025000635120.2087552026080.287119890531-0.04397361199350.01540205444520.4002588692920.1120599099290.30293429963121.031-22.45321.242
82.00173934141-1.22046634167-1.021582283712.072000274460.6676674294792.22803372384-0.210343515407-0.5014689322660.05844304735720.5259162174930.288694796208-0.3176435307440.1362378198760.177196588216-0.09226433454730.286312944741-0.0107763643195-0.07499601912810.331902069905-0.005630837833250.26708351358917.1995.9133.667
91.96694187465-0.3312190846250.9698285034361.65067393668-0.3025620846551.76957584469-0.0722217649154-0.3854685998670.187918082980.2048133028860.07453139299730.124705687048-0.15629412423-0.301144433733-0.004923730711140.2126591685850.02764813389630.03206649089340.259898277294-0.04175972140510.238842786943-5.21520.181-9.235
102.589717319562.536021384251.099540751576.689287832654.219673477074.19942186735-0.14232890170.03693114853180.298673007819-0.0461784194654-0.03750124150870.349313640766-0.259835195085-0.2452847406080.1740412556340.2429049853630.0731078355566-0.02513863895940.2635138339650.07285010444440.272120558771-16.82722.148-25.65
112.19789647898-1.08598215301-1.457649836991.953661053231.100674841413.221763752180.06629726469780.1054763237760.031471028458-0.252255675523-0.0759523593756-0.06130497727020.0523894158622-0.1384161199690.01983349123950.194809606658-0.05130235329-0.01503084199730.2297729570110.04573437995790.27335353097130.798-4.737-23.536
122.273967505550.745561249068-0.1551044490053.29797614399-1.128900305391.83361911702-0.117269792482-0.0763398422725-0.281283260582-0.3564036569720.05627259375210.09733113446390.323223940778-0.02758373173280.06057438895570.3377331608450.02738631935670.01744437932250.1853129097730.005547767453270.31011829113133.239-35.954-11.033
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 26:136 )A26 - 136
2X-RAY DIFFRACTION2( CHAIN A AND RESID 137:365 )A137 - 365
3X-RAY DIFFRACTION3( CHAIN A AND RESID 366:418 )A366 - 418
4X-RAY DIFFRACTION4( CHAIN B AND RESID 25:91 )B25 - 91
5X-RAY DIFFRACTION5( CHAIN B AND RESID 92:135 )B92 - 135
6X-RAY DIFFRACTION6( CHAIN B AND RESID 136:262 )B136 - 262
7X-RAY DIFFRACTION7( CHAIN B AND RESID 263:418 )B263 - 418
8X-RAY DIFFRACTION8( CHAIN C AND RESID 25:136 )C25 - 136
9X-RAY DIFFRACTION9( CHAIN C AND RESID 137:365 )C137 - 365
10X-RAY DIFFRACTION10( CHAIN C AND RESID 366:418 )C366 - 418
11X-RAY DIFFRACTION11( CHAIN D AND RESID 27:154 )D27 - 154
12X-RAY DIFFRACTION12( CHAIN D AND RESID 155:418 )D155 - 418

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