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- PDB-4tvu: Crystal structure of trehalose synthase from Deinococcus radiodur... -

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Basic information

Entry
Database: PDB / ID: 4tvu
TitleCrystal structure of trehalose synthase from Deinococcus radiodurans reveals a closed conformation for catalysis of the intramolecular isomerization
ComponentsTrehalose synthase
KeywordsISOMERASE / Trehalose synthase / Glycoside hydrolase family 13 / Tris complex
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 / Oligo-1,6-glucosidase; Domain 2 / Oligo-1,6-glucosidase, domain 2 / Alpha amylase, catalytic domain / Glycosyl hydrolase, family 13, catalytic domain / Alpha-amylase domain / Golgi alpha-mannosidase II ...Trehalose synthase/alpha-amylase, N-terminal / Maltogenic Amylase, C-terminal / Maltogenic Amylase, C-terminal domain / Oligo-1,6-glucosidase; domain 2 / Oligo-1,6-glucosidase; Domain 2 / 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 / Alpha-Beta Complex / Immunoglobulin-like / Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
maltose alpha-D-glucosyltransferase
Similarity search - Component
Biological speciesDeinococcus radiodurans (radioresistant)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsWang, Y.L. / Chow, S.Y. / Lin, Y.T. / Liaw, S.H.
Funding support Taiwan, 1items
OrganizationGrant numberCountry
National Science CouncilNSC 102-2311-B-101-005- Taiwan
Citation
Journal: Acta Crystallogr.,Sect.D / Year: 2014
Title: Structures of trehalose synthase from Deinococcus radiodurans reveal that a closed conformation is involved in catalysis of the intramolecular isomerization.
Authors: Wang, Y.L. / Chow, S.Y. / Lin, Y.T. / Hsieh, Y.C. / Lee, G.C. / Liaw, S.H.
#1: Journal: J. Agric. Food Chem. / Year: 2007
Title: Role of the C-terminal domain of Thermus thermophilus trehalose synthase in the thermophilicity, thermostability, and efficient production of trehalose.
Authors: Wang, J.H. / Tsai, M.Y. / Chen, J.J. / Lee, G.C. / Shaw, J.F.
History
DepositionJun 28, 2014Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Dec 17, 2014Provider: repository / Type: Initial release
Revision 1.1Nov 8, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description / Source and taxonomy
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / entity_src_gen / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_oper_list / refine_hist / struct_conn / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity_src_gen.pdbx_alt_source_flag / _pdbx_database_status.pdb_format_compatible / _pdbx_struct_oper_list.symmetry_operation / _refine_hist.number_atoms_solvent / _refine_hist.pdbx_number_atoms_ligand / _refine_hist.pdbx_number_atoms_nucleic_acid / _refine_hist.pdbx_number_atoms_protein / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _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
E: Trehalose synthase
F: Trehalose synthase
G: Trehalose synthase
H: Trehalose synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)521,39532
Polymers519,9038
Non-polymers1,49224
Water17,637979
1
A: Trehalose synthase
B: Trehalose synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)130,3498
Polymers129,9762
Non-polymers3736
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3960 Å2
ΔGint-32 kcal/mol
Surface area36880 Å2
MethodPISA
2
C: Trehalose synthase
D: Trehalose synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)130,3498
Polymers129,9762
Non-polymers3736
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3950 Å2
ΔGint-18 kcal/mol
Surface area37030 Å2
MethodPISA
3
G: Trehalose synthase
H: Trehalose synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)130,3498
Polymers129,9762
Non-polymers3736
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3900 Å2
ΔGint-34 kcal/mol
Surface area37290 Å2
MethodPISA
4
E: Trehalose synthase
F: Trehalose synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)130,3498
Polymers129,9762
Non-polymers3736
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3970 Å2
ΔGint-33 kcal/mol
Surface area37130 Å2
MethodPISA
Unit cell
Length a, b, c (Å)95.609, 195.896, 130.986
Angle α, β, γ (deg.)90.00, 92.89, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13A
23D
14A
24E
15A
25F
16A
26G
17A
27H
18B
28C
19B
29D
110B
210E
111B
211F
112B
212G
113B
213H
114C
214D
115C
215E
116C
216F
117C
217G
118C
218H
119D
219E
120D
220F
121D
221G
122D
222H
123E
223F
124E
224G
125E
225H
126F
226G
127F
227H
128G
228H

NCS domain segments:

Component-ID: _ / Beg auth comp-ID: PRO / Beg label comp-ID: PRO / End auth comp-ID: SER / End label comp-ID: SER / Refine code: _ / Auth seq-ID: 6 - 553 / Label seq-ID: 8 - 555

Dom-IDEns-IDAuth asym-IDLabel asym-ID
11AA
21BB
12AA
22CC
13AA
23DD
14AA
24EE
15AA
25FF
16AA
26GG
17AA
27HH
18BB
28CC
19BB
29DD
110BB
210EE
111BB
211FF
112BB
212GG
113BB
213HH
114CC
214DD
115CC
215EE
116CC
216FF
117CC
217GG
118CC
218HH
119DD
219EE
120DD
220FF
121DD
221GG
122DD
222HH
123EE
223FF
124EE
224GG
125EE
225HH
126FF
226GG
127FF
227HH
128GG
228HH

NCS ensembles :
ID
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28

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Components

#1: Protein
Trehalose synthase


Mass: 64987.844 Da / Num. of mol.: 8 / Mutation: R99W, T315I, I382V
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Deinococcus radiodurans (radioresistant)
Strain: ATCC 13939 / DSM 20539 / JCM 16871 / LMG 4051 / NBRC 15346 / NCIMB 9279 / R1 / VKM B-1422
Production host: Escherichia coli (E. coli)
References: UniProt: I3NX86, maltose alpha-D-glucosyltransferase
#2: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Ca
#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Mg
#4: Chemical
ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 979 / 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: 2.46 Å3/Da / Density % sol: 49.94 %
Crystal growTemperature: 288 K / Method: vapor diffusion, hanging drop
Details: 15 % PEG 4000, 0.2 M sodium acetate trihydrate, 0.1 M Tris-HCl (pH 8.5)

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: BL13B1 / Wavelength: 1 Å
DetectorType: RAYONIX MX300HE / Detector: CCD / Date: Mar 24, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.7→30 Å / Num. obs: 128557 / % possible obs: 97.7 % / Redundancy: 3.6 % / Rmerge(I) obs: 0.096 / Χ2: 1.113 / Net I/av σ(I): 13.104 / Net I/σ(I): 9.2 / Num. measured all: 462831
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
2.7-2.83.30.408117711.07689.4
2.8-2.913.30.331123611.194.2
2.91-3.043.30.26127101.12297.3
3.04-3.23.50.201130191.18998.9
3.2-3.43.70.156130301.18399.4
3.4-3.663.80.113130631.18699.4
3.66-4.033.80.077130651.12299.6
4.03-4.613.80.054131231.00899.6
4.61-5.83.80.051131541.0199.8
5.8-303.70.033132611.13599.5

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Processing

Software
NameVersionClassificationNB
REFMAC5.8.0049refinement
SCALEPACKdata reduction
PDB_EXTRACT3.14data extraction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3ZOA

3zoa


Resolution: 2.7→30 Å / Cor.coef. Fo:Fc: 0.931 / Cor.coef. Fo:Fc free: 0.894 / SU B: 14.459 / SU ML: 0.284 / Cross valid method: THROUGHOUT / ESU R Free: 0.357 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23626 6455 5 %RANDOM
Rwork0.19372 ---
obs0.19586 122065 97.62 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 37.461 Å2
Baniso -1Baniso -2Baniso -3
1-3.01 Å20 Å22.54 Å2
2---1.9 Å2-0 Å2
3----1.36 Å2
Refinement stepCycle: final / Resolution: 2.7→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms35232 0 80 979 36291
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.01936352
X-RAY DIFFRACTIONr_bond_other_d0.0070.0233128
X-RAY DIFFRACTIONr_angle_refined_deg1.4161.95549528
X-RAY DIFFRACTIONr_angle_other_deg1.313376104
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.954376
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.22823.2911872
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.439155520
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.07715304
X-RAY DIFFRACTIONr_chiral_restr0.0830.25120
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.02141728
X-RAY DIFFRACTIONr_gen_planes_other0.0060.028944
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_it2.4913.67917536
X-RAY DIFFRACTIONr_mcbond_other2.4893.67917534
X-RAY DIFFRACTIONr_mcangle_it4.0055.51421896
X-RAY DIFFRACTIONr_mcangle_other4.0055.51421897
X-RAY DIFFRACTIONr_scbond_it2.5283.85518816
X-RAY DIFFRACTIONr_scbond_other2.5283.85518816
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.1675.70927633
X-RAY DIFFRACTIONr_long_range_B_refined6.5529.16142141
X-RAY DIFFRACTIONr_long_range_B_other6.53829.18442008
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

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

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A339370.08
12B339370.08
21A340310.07
22C340310.07
31A338620.08
32D338620.08
41A340170.07
42E340170.07
51A337370.08
52F337370.08
61A341360.07
62G341360.07
71A330260.1
72H330260.1
81B339370.08
82C339370.08
91B340260.07
92D340260.07
101B340480.08
102E340480.08
111B339790.08
112F339790.08
121B339280.08
122G339280.08
131B333530.09
132H333530.09
141C340120.07
142D340120.07
151C343910.07
152E343910.07
161C340380.08
162F340380.08
171C340700.07
172G340700.07
181C333410.09
182H333410.09
191D344500.06
192E344500.06
201D343580.07
202F343580.07
211D343440.07
212G343440.07
221D338440.08
222H338440.08
231E343940.07
232F343940.07
241E346460.06
242G346460.06
251E337460.08
252H337460.08
261F342660.07
262G342660.07
271F338040.08
272H338040.08
281G335460.09
282H335460.09
LS refinement shellResolution: 2.701→2.771 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.319 463 -
Rwork0.282 8113 -
obs--88.81 %

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