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- PDB-8wy1: The structure of cyclization domain in cyclic beta-1,2-glucan syn... -

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Basic information

Entry
Database: PDB / ID: 8wy1
TitleThe structure of cyclization domain in cyclic beta-1,2-glucan synthase from Thermoanaerobacter italicus
ComponentsGlycosyltransferase 36
KeywordsTRANSFERASE / Cyclization / glycosyltransferase / cyclic beta-1 / 2-glucan
Function / homology
Function and homology information


glycosyltransferase activity / carbohydrate binding / carbohydrate metabolic process / membrane
Similarity search - Function
Protein of unknown function DUF3131 / Protein of unknown function (DUF3131) / NdvB, GH94N domain 1 / NdvB, GH94N domain 2 / Glycoamylase-like, conserved domain / Putative glucoamylase / Putative carbohydrate binding domain / Putative carbohydrate binding domain / : / Glycosyl hydrolase 94 ...Protein of unknown function DUF3131 / Protein of unknown function (DUF3131) / NdvB, GH94N domain 1 / NdvB, GH94N domain 2 / Glycoamylase-like, conserved domain / Putative glucoamylase / Putative carbohydrate binding domain / Putative carbohydrate binding domain / : / Glycosyl hydrolase 94 / Glycosyl hydrolase 94, supersandwich domain / Glycosyl hydrolase 36, catalytic domain / Glycosyl hydrolase 94 superfamily, catalytic domain / Glycoside hydrolase family 65, N-terminal domain superfamily / Galactose mutarotase-like domain superfamily / Six-hairpin glycosidase-like superfamily / Six-hairpin glycosidase superfamily
Similarity search - Domain/homology
Glycosyltransferase 36
Similarity search - Component
Biological speciesThermoanaerobacter italicus Ab9 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.9 Å
AuthorsTanaka, N. / Saito, R. / Kobayashi, K. / Nakai, H. / Kamo, S. / Kuramochi, K. / Taguchi, H. / Nakajima, M. / Masaike, T.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Appl.Microbiol.Biotechnol. / Year: 2024
Title: Functional and structural analysis of a cyclization domain in a cyclic beta-1,2-glucan synthase.
Authors: Tanaka, N. / Saito, R. / Kobayashi, K. / Nakai, H. / Kamo, S. / Kuramochi, K. / Taguchi, H. / Nakajima, M. / Masaike, T.
History
DepositionOct 30, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 14, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Glycosyltransferase 36
B: Glycosyltransferase 36
C: Glycosyltransferase 36
D: Glycosyltransferase 36


Theoretical massNumber of molelcules
Total (without water)278,5164
Polymers278,5164
Non-polymers00
Water00
1
A: Glycosyltransferase 36


Theoretical massNumber of molelcules
Total (without water)69,6291
Polymers69,6291
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Glycosyltransferase 36


Theoretical massNumber of molelcules
Total (without water)69,6291
Polymers69,6291
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Glycosyltransferase 36


Theoretical massNumber of molelcules
Total (without water)69,6291
Polymers69,6291
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Glycosyltransferase 36


Theoretical massNumber of molelcules
Total (without water)69,6291
Polymers69,6291
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)172.719, 172.719, 395.599
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13A
23D
14B
24C
15B
25D
16C
26D

NCS domain segments:

Component-ID: _ / Beg auth comp-ID: THR / Beg label comp-ID: THR / Refine code: _

Dom-IDEns-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11THRTHRAA1011 - 15828 - 579
21THRTHRBB1011 - 15828 - 579
12THRTHRAA1011 - 15828 - 579
22THRTHRCC1011 - 15828 - 579
13GLUGLUAA1011 - 15848 - 581
23GLUGLUDD1011 - 15848 - 581
14ARGARGBB1011 - 15838 - 580
24ARGARGCC1011 - 15838 - 580
15THRTHRBB1011 - 15828 - 579
25THRTHRDD1011 - 15828 - 579
16THRTHRCC1011 - 15828 - 579
26THRTHRDD1011 - 15828 - 579

NCS ensembles :
ID
1
2
3
4
5
6

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Components

#1: Protein
Glycosyltransferase 36


Mass: 69628.906 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermoanaerobacter italicus Ab9 (bacteria)
Gene: Thit_1831 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): Rosetta2 (DE3) / References: UniProt: D3T4C1

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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: 5.3 Å3/Da / Density % sol: 76.78 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: 0.1M sodium cacodylate, 1.3M sodium acetate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Oct 23, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.9→89.6 Å / Num. obs: 55512 / % possible obs: 100 % / Redundancy: 25 % / CC1/2: 0.992 / Net I/σ(I): 9.8
Reflection shellResolution: 3.9→4.01 Å / Num. unique obs: 4497 / CC1/2: 0.851

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
BUCCANEERmodel building
MOLREPphasing
Aimlessdata scaling
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.9→89.6 Å / Cor.coef. Fo:Fc: 0.935 / Cor.coef. Fo:Fc free: 0.915 / SU B: 36.199 / SU ML: 0.456 / Cross valid method: THROUGHOUT / ESU R Free: 0.551 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23237 2738 4.9 %RANDOM
Rwork0.19819 ---
obs0.19991 52696 99.96 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--0.01 Å20 Å20 Å2
2---0.01 Å20 Å2
3---0.03 Å2
Refinement stepCycle: 1 / Resolution: 3.9→89.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms18842 0 0 0 18842
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.01319238
X-RAY DIFFRACTIONr_bond_other_d0.0020.01618648
X-RAY DIFFRACTIONr_angle_refined_deg1.5971.64725916
X-RAY DIFFRACTIONr_angle_other_deg1.1671.58243086
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.88152290
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.53623.4261010
X-RAY DIFFRACTIONr_dihedral_angle_3_deg22.671153704
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.8871592
X-RAY DIFFRACTIONr_chiral_restr0.0660.22446
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0221294
X-RAY DIFFRACTIONr_gen_planes_other0.0020.024338
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_it9.07311.5759172
X-RAY DIFFRACTIONr_mcbond_other9.06711.5759171
X-RAY DIFFRACTIONr_mcangle_it14.25117.37111458
X-RAY DIFFRACTIONr_mcangle_other14.25117.37111459
X-RAY DIFFRACTIONr_scbond_it8.9512.36910066
X-RAY DIFFRACTIONr_scbond_other8.94812.36810064
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other14.88418.22114458
X-RAY DIFFRACTIONr_long_range_B_refined20.28822868
X-RAY DIFFRACTIONr_long_range_B_other20.28822869
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A194310.13
12B194310.13
21A194150.14
22C194150.14
31A191520.15
32D191520.15
41B193280.14
42C193280.14
51B190770.15
52D190770.15
61C192750.14
62D192750.14
LS refinement shellResolution: 3.9→4.001 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.345 207 -
Rwork0.319 3833 -
obs--99.95 %

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