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- PDB-5ykb: The N253F mutant structure of trehalose synthase from Deinococcus... -

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Basic information

Entry
Database: PDB / ID: 5ykb
TitleThe N253F mutant structure of trehalose synthase from Deinococcus radiodurans reveals an open active-site conformation
ComponentsTrehalose synthase
KeywordsISOMERASE / trehalose synthase / glycoside hydrolase family 13
Function / homology
Function and homology information


maltose alpha-D-glucosyltransferase / maltose alpha-D-glucosyltransferase activity / carbohydrate metabolic process / metal ion binding
Similarity search - Function
Trehalose synthase/alpha-amylase, N-terminal / Maltogenic Amylase, C-terminal / Maltogenic Amylase, C-terminal domain / Oligo-1,6-glucosidase, domain 2 / Alpha amylase, catalytic domain / Glycosyl hydrolase, family 13, catalytic domain / Alpha-amylase domain / Golgi alpha-mannosidase II / Glycosyl hydrolase, all-beta / Glycosidases ...Trehalose synthase/alpha-amylase, N-terminal / Maltogenic Amylase, C-terminal / Maltogenic Amylase, C-terminal domain / Oligo-1,6-glucosidase, domain 2 / Alpha amylase, catalytic domain / Glycosyl hydrolase, family 13, catalytic domain / Alpha-amylase domain / Golgi alpha-mannosidase II / Glycosyl hydrolase, all-beta / Glycosidases / Glycoside hydrolase superfamily / TIM Barrel / Alpha-Beta Barrel / Immunoglobulin-like / Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
maltose alpha-D-glucosyltransferase
Similarity search - Component
Biological speciesDeinococcus radiodurans str. R1 (radioresistant)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.76 Å
AuthorsChow, S.Y. / Hsieh, Y.C. / Liaw, S.H.
Funding support Taiwan, 1items
OrganizationGrant numberCountry
Ministry of Science and TechnologyNSC 102-2311-B-010-005 Taiwan
CitationJournal: Acta Crystallogr F Struct Biol Commun / Year: 2017
Title: The N253F mutant structure of trehalose synthase from Deinococcus radiodurans reveals an open active-site topology
Authors: Chow, S.Y. / Wang, Y.L. / Hsieh, Y.C. / Lee, G.C. / Liaw, S.H.
History
DepositionOct 13, 2017Deposition site: PDBJ / Processing site: PDBJ
SupersessionOct 25, 2017ID: 5GTV
Revision 1.0Oct 25, 2017Provider: repository / Type: Initial release
Revision 1.1Nov 1, 2017Group: Database references / Category: citation / Item: _citation.pdbx_database_id_DOI
Revision 1.2Nov 15, 2017Group: Database references / Category: citation
Item: _citation.journal_abbrev / _citation.journal_volume ..._citation.journal_abbrev / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed
Revision 1.3Nov 22, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)260,34112
Polymers260,0844
Non-polymers2588
Water4,270237
1
A: Trehalose synthase
D: Trehalose synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)130,1716
Polymers130,0422
Non-polymers1294
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3190 Å2
ΔGint-27 kcal/mol
Surface area37450 Å2
MethodPISA
2
B: Trehalose synthase
C: Trehalose synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)130,1716
Polymers130,0422
Non-polymers1294
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3200 Å2
ΔGint-26 kcal/mol
Surface area37450 Å2
MethodPISA
Unit cell
Length a, b, c (Å)100.401, 132.422, 196.013
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
12A
22C
13A
23D
14B
24C
15B
25D
16C
26D

NCS domain segments:

Component-ID: 0 / Beg auth comp-ID: PRO / Beg label comp-ID: PRO / End auth comp-ID: ASN / End label comp-ID: ASN / Refine code: 0 / Auth seq-ID: 6 - 552 / Label seq-ID: 8 - 554

Dom-IDEns-IDAuth asym-IDLabel asym-ID
11AA
21BB
12AA
22CC
13AA
23DD
14BB
24CC
15BB
25DD
16CC
26DD

NCS ensembles :
ID
1
2
3
4
5
6

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Components

#1: Protein
Trehalose synthase


Mass: 65020.914 Da / Num. of mol.: 4 / Mutation: R97W,N253F,T313I,I380V
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Deinococcus radiodurans str. R1 (radioresistant)
Strain: R1 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: I3NX86, maltose alpha-D-glucosyltransferase
#2: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca
#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 237 / 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: 2.55 Å3/Da / Density % sol: 51.78 %
Crystal growTemperature: 288 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 7% PEG 4000, 0.2M sodium acetate trihydrate, 0.3M Tris-HCl (pH 7.0)

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: BL15A1 / Wavelength: 1 Å
DetectorType: RAYONIX MX300HE / Detector: CCD / Date: May 10, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.76→30 Å / Num. obs: 67645 / % possible obs: 99.9 % / Redundancy: 4.5 % / CC1/2: 0.993 / Net I/σ(I): 12.3
Reflection shellResolution: 2.76→2.86 Å / Redundancy: 4.4 % / Mean I/σ(I) obs: 1.8 / Num. unique obs: 6642 / CC1/2: 0.606 / % possible all: 99.3

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Processing

Software
NameVersionClassification
REFMAC5.8.0073refinement
PDB_EXTRACT3.22data extraction
HKL-2000data reduction
HKL-2000data scaling
HKL-2000phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4TVU

4tvu


Resolution: 2.76→30 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.884 / SU B: 14.965 / SU ML: 0.298 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.374
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.251 3231 4.9 %RANDOM
Rwork0.192 ---
obs0.1949 62376 96.72 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 136.58 Å2 / Biso mean: 50.759 Å2 / Biso min: 2 Å2
Baniso -1Baniso -2Baniso -3
1--0.56 Å20 Å20 Å2
2--0.92 Å20 Å2
3----0.36 Å2
Refinement stepCycle: final / Resolution: 2.76→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms16951 0 8 237 17196
Biso mean--51.24 34.86 -
Num. residues----2104
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.01917468
X-RAY DIFFRACTIONr_bond_other_d0.0060.0215936
X-RAY DIFFRACTIONr_angle_refined_deg1.2981.95223791
X-RAY DIFFRACTIONr_angle_other_deg1.238336582
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1752094
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.48323.178903
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.007152647
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.4715148
X-RAY DIFFRACTIONr_chiral_restr0.0730.22449
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.02120041
X-RAY DIFFRACTIONr_gen_planes_other0.0050.024343
Refine LS restraints NCS

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

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A299470.16
12B299470.16
21A299740.16
22C299740.16
31A299220.16
32D299220.16
41B296420.16
42C296420.16
51B291530.17
52D291530.17
61C298500.16
62D298500.16
LS refinement shellResolution: 2.761→2.832 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.331 150 -
Rwork0.265 3030 -
all-3180 -
obs--65 %

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