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- PDB-3ugg: Crystal structure of a 6-SST/6-SFT from Pachysandra terminalis in... -

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Basic information

Entry
Database: PDB / ID: 3ugg
TitleCrystal structure of a 6-SST/6-SFT from Pachysandra terminalis in complex with 1-kestose
ComponentsSucrose:(Sucrose/fructan) 6-fructosyltransferase
KeywordsTRANSFERASE / fructosyltransferase / glycoside hydrolase family 32
Function / homology
Function and homology information


beta-fructofuranosidase activity / beta-fructofuranosidase / vacuole / transferase activity / carbohydrate metabolic process / membrane
Similarity search - Function
Beta-fructofuranosidase, N-terminal domain / Beta-fructofuranosidase, N-terminal domain / Glycosyl hydrolase family 32, C-terminal / Glycosyl hydrolases family 32 C terminal / Exo-inulinase; domain 1 / Glycoside hydrolase, family 32 / Glycosyl hydrolase family 32, N-terminal / Glycosyl hydrolases family 32 N-terminal domain / Glycosyl hydrolases family 32 / Glycosyl hydrolase domain; family 43 ...Beta-fructofuranosidase, N-terminal domain / Beta-fructofuranosidase, N-terminal domain / Glycosyl hydrolase family 32, C-terminal / Glycosyl hydrolases family 32 C terminal / Exo-inulinase; domain 1 / Glycoside hydrolase, family 32 / Glycosyl hydrolase family 32, N-terminal / Glycosyl hydrolases family 32 N-terminal domain / Glycosyl hydrolases family 32 / Glycosyl hydrolase domain; family 43 / 5 Propeller / Tachylectin-2; Chain A / Glycosyl hydrolase, five-bladed beta-propellor domain superfamily / Concanavalin A-like lectin/glucanase domain superfamily / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
1-kestose / beta-fructofuranosidase
Similarity search - Component
Biological speciesPachysandra terminalis (plant)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.9 Å
AuthorsLammens, W. / Rabijns, A. / Van Laere, A. / Strelkov, S.V. / Van den Ende, W.
CitationJournal: Plant J. / Year: 2012
Title: Crystal structure of 6-SST/6-SFT from Pachysandra terminalis, a plant fructan biosynthesizing enzyme in complex with its acceptor substrate 6-kestose.
Authors: Lammens, W. / Le Roy, K. / Yuan, S. / Vergauwen, R. / Rabijns, A. / Van Laere, A. / Strelkov, S.V. / Van den Ende, W.
History
DepositionNov 2, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 30, 2011Provider: repository / Type: Initial release
Revision 1.1Oct 24, 2012Group: Database references
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Non-polymer description / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp / diffrn_source / 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_assembly_gen / struct_asym / struct_conn / 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 / _atom_site_anisotrop.U[1][1] / _atom_site_anisotrop.U[1][2] / _atom_site_anisotrop.U[1][3] / _atom_site_anisotrop.U[2][2] / _atom_site_anisotrop.U[2][3] / _atom_site_anisotrop.U[3][3] / _atom_site_anisotrop.id / _atom_site_anisotrop.pdbx_auth_asym_id / _atom_site_anisotrop.pdbx_auth_atom_id / _atom_site_anisotrop.pdbx_auth_comp_id / _atom_site_anisotrop.pdbx_auth_seq_id / _atom_site_anisotrop.pdbx_label_asym_id / _atom_site_anisotrop.pdbx_label_atom_id / _atom_site_anisotrop.pdbx_label_comp_id / _atom_site_anisotrop.type_symbol / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.pdbx_synonyms / _chem_comp.type / _diffrn_source.pdbx_synchrotron_site / _pdbx_struct_assembly_gen.asym_id_list
Description: Carbohydrate remediation / Provider: repository / Type: Remediation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Sucrose:(Sucrose/fructan) 6-fructosyltransferase
B: Sucrose:(Sucrose/fructan) 6-fructosyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)128,85816
Polymers122,4312
Non-polymers6,42714
Water57632
1
A: Sucrose:(Sucrose/fructan) 6-fructosyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,3288
Polymers61,2161
Non-polymers3,1127
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Sucrose:(Sucrose/fructan) 6-fructosyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,5318
Polymers61,2161
Non-polymers3,3157
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)88.420, 123.800, 146.390
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1114A1 - 9999
2114B1 - 9999

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Sucrose:(Sucrose/fructan) 6-fructosyltransferase


Mass: 61215.652 Da / Num. of mol.: 2 / Fragment: unp residues 110-655 / Source method: isolated from a natural source / Source: (natural) Pachysandra terminalis (plant) / References: UniProt: E3PQS3

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Sugars , 5 types, 10 molecules

#2: Polysaccharide alpha-L-fucopyranose-(1-3)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 367.349 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
LFucpa1-3DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,2,1/[a2122h-1b_1-5_2*NCC/3=O][a1221m-1a_1-5]/1-2/a3-b1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(3+1)][a-L-Fucp]{}}}LINUCSPDB-CARE
#3: Polysaccharide
beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1- ...beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-3)]2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 732.682 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpb1-4DGlcpNAcb1-4[LFucpa1-3]DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/3,4,3/[a2122h-1b_1-5_2*NCC/3=O][a1221m-1a_1-5][a1122h-1b_1-5]/1-2-1-3/a3-b1_a4-c1_c4-d1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(3+1)][a-L-Fucp]{}[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{}}}}LINUCSPDB-CARE
#4: Polysaccharide beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta- ...beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 586.542 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5]/1-1-2/a4-b1_b4-c1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{}}}}LINUCSPDB-CARE
#5: Polysaccharide alpha-L-fucopyranose-(1-3)-[2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)]2-acetamido-2-deoxy-beta- ...alpha-L-fucopyranose-(1-3)-[2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)]2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 570.542 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
LFucpa1-3[DGlcpNAcb1-4]DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1221m-1a_1-5]/1-2-1/a3-b1_a4-c1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(3+1)][a-L-Fucp]{}[(4+1)][b-D-GlcpNAc]{}}}LINUCSPDB-CARE
#6: Polysaccharide beta-D-fructofuranose-(2-1)-beta-D-fructofuranose-(2-1)-alpha-D-glucopyranose / 1-kestose


Type: oligosaccharide, Oligosaccharide / Class: Nutrient / Mass: 504.438 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: oligosaccharide with reducing-end-to-reducing-end glycosidic bond
References: 1-kestose
DescriptorTypeProgram
DFrufb2-1DFrufb2-1DGlcpaGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1a_1-5][ha122h-2b_2-5]/1-2-2/a1-b2_b1-c2WURCSPDB2Glycan 1.1.0
[][b-D-Fruf]{[(2+1)][a-D-Glcp]{}}LINUCSPDB-CARE

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Non-polymers , 3 types, 36 molecules

#7: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#8: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#9: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 32 / Source method: isolated from a natural source / Formula: H2O

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Details

Sequence detailsTHE AUTHORS STATE THAT THE DISCREPANCIES ARISE FROM AN INCORRECT DEPOSITED SEQUENCE OF THE UNP ENTRY E3PQS3

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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: 3.27 Å3/Da / Density % sol: 62.41 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: 0.1M citrate, 0.7M ammonium sulfate, 1M Li-sulfate, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: BW7A / Wavelength: 1.0332 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Nov 23, 2006
RadiationMonochromator: Fixed exit double crystal Si [111], horizontally focusing
Protocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 2.9→32.287 Å / Num. all: 36335 / Num. obs: 36295 / % possible obs: 99.9 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 1.41 / Redundancy: 7.2 % / Rsym value: 0.156 / Net I/σ(I): 12.3
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
2.9-3.0670.4461.63673452430.446100
3.06-3.247.10.3342.23497249320.334100
3.24-3.477.10.22433335246680.224100
3.47-3.747.30.1654.33162943550.165100
3.74-4.17.30.1285.42948540280.128100
4.1-4.597.30.0937.72688136690.093100
4.59-5.297.30.0818.72361532350.081100
5.29-6.487.20.1046.92005927760.104100
6.48-9.177.10.0759.71550221950.075100
9.17-32.626.20.0639.3765912340.06396.9

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation3.11 Å28.19 Å
Translation3.11 Å28.19 Å

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Processing

Software
NameVersionClassificationNB
SCALA3.3.9data scaling
MOLREPphasing
REFMACrefinement
PDB_EXTRACT3.1data extraction
HKL-2000data collection
MOSFLMdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.9→28.49 Å / Cor.coef. Fo:Fc: 0.912 / Cor.coef. Fo:Fc free: 0.873 / WRfactor Rfree: 0.2126 / WRfactor Rwork: 0.1738 / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.866 / SU B: 26.827 / SU ML: 0.242 / SU R Cruickshank DPI: 0.2915 / SU Rfree: 0.3483 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.348 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2338 1810 5 %RANDOM
Rwork0.1956 ---
all0.1975 36264 --
obs0.1975 36264 99.97 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 60.67 Å2 / Biso mean: 17.6789 Å2 / Biso min: 2 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 2.9→28.49 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8328 0 426 32 8786
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0229029
X-RAY DIFFRACTIONr_angle_refined_deg1.1361.99812350
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.86951042
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.94924.084382
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.929151352
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.751536
X-RAY DIFFRACTIONr_chiral_restr0.0690.21405
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0216691
X-RAY DIFFRACTIONr_mcbond_it0.2431.55214
X-RAY DIFFRACTIONr_mcangle_it0.48228426
X-RAY DIFFRACTIONr_scbond_it0.78933815
X-RAY DIFFRACTIONr_scangle_it1.4754.53924
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Number: 4198 / Refine-ID: X-RAY DIFFRACTION

TypeRms dev position (Å)Weight position
MEDIUM POSITIONAL0.230.5
MEDIUM THERMAL0.182
LS refinement shellResolution: 2.9→2.975 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.362 126 -
Rwork0.273 2480 -
all-2606 -
obs--100 %
Refinement TLS params.

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

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
10.23770.3213-0.00471.10960.30020.8270.0256-0.0247-0.00150.0447-0.05130.05410.0272-0.08780.02560.00660.004-0.00040.0442-0.00330.014239.906-10.111-4.324
21.34210.1276-0.16640.35570.06570.5781-0.0099-0.0253-0.0352-0.02940.009-0.0029-0.02220.02980.00090.035-0.0051-0.00020.00310.00330.010749.961-21.913-47.196
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A7 - 545
2X-RAY DIFFRACTION2B7 - 545

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