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- PDB-4wf7: Crystal structures of trehalose synthase from Deinococcus radiodu... -

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Basic information

Entry
Database: PDB / ID: 4wf7
TitleCrystal structures of trehalose synthase from Deinococcus radiodurans reveal that a closed conformation is involved in the intramolecular isomerization catalysis
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 R1 (radioresistant)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.21 Å
AuthorsWang, Y.L. / Chow, S.Y. / Lin, Y.T. / Hsieh, Y.C. / Lee, G.C. / 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
DepositionSep 13, 2014Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Dec 24, 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_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / pdbx_struct_conn_angle / pdbx_struct_oper_list / refine_hist / struct_conn
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_assembly.oligomeric_details / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_assembly_prop.type / _pdbx_struct_assembly_prop.value / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _pdbx_struct_oper_list.symmetry_operation / _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

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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)260,64817
Polymers259,7794
Non-polymers86813
Water20,6991149
1
A: Trehalose synthase
D: Trehalose synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)130,3859
Polymers129,8902
Non-polymers4957
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4270 Å2
ΔGint-40 kcal/mol
Surface area37020 Å2
MethodPISA
2
B: Trehalose synthase
C: Trehalose synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)130,2638
Polymers129,8902
Non-polymers3736
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4050 Å2
ΔGint-45 kcal/mol
Surface area37040 Å2
MethodPISA
Unit cell
Length a, b, c (Å)96.250, 133.705, 196.614
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
Trehalose synthase


Mass: 64944.820 Da / Num. of mol.: 4 / Fragment: UNP residues 2-552
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Deinococcus radiodurans R1 (radioresistant)
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.: 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: Chemical
ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER / Tris


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


Mass: 18.015 Da / Num. of mol.: 1149 / 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: 51.72 %
Crystal growTemperature: 288 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 11% PEG 4000, 0.2M sodium acetate trihydrate, 0.3M Tris-HCl (pH 8.5), 5% glycerol

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: BL13B1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 22, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.21→20 Å / Num. obs: 129348 / % possible obs: 99.9 % / Redundancy: 5.9 % / Rmerge(I) obs: 0.151 / Rpim(I) all: 0.066 / Rrim(I) all: 0.165 / Χ2: 0.918 / Net I/av σ(I): 12.594 / Net I/σ(I): 5.3 / Num. measured all: 759037
Reflection shell

Diffraction-ID: 1 / Rejects: 0

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.21-2.295.60.787126950.7840.3450.8620.83199.7
2.29-2.385.60.646128050.8410.2830.7070.85599.7
2.38-2.495.70.508128240.8930.2220.5560.86799.8
2.49-2.625.80.409128190.9260.1780.4470.889100
2.62-2.785.90.319128630.9530.1390.3490.929100
2.78-36.10.239128900.9730.1030.2610.919100
3-3.36.20.163129370.9850.070.1770.946100
3.3-3.776.10.116129630.9910.0510.1271.12100
3.77-4.7460.068130870.9960.030.0741.031100
4.74-205.80.048134650.9980.0210.0530.77100

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Processing

Software
NameVersionClassificationNB
SCALEPACKdata reduction
REFMAC5.8.0049refinement
PDB_EXTRACT3.15data extraction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4TVU

4tvu


Resolution: 2.21→20 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.948 / SU B: 5.409 / SU ML: 0.133 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.234 / ESU R Free: 0.178 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1996 6336 5 %RANDOM
Rwork0.1601 119863 --
obs0.1621 119863 99.09 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 93.49 Å2 / Biso mean: 32.96 Å2 / Biso min: 8.9 Å2
Baniso -1Baniso -2Baniso -3
1--0.03 Å20 Å2-0 Å2
2--0.02 Å2-0 Å2
3---0.01 Å2
Refinement stepCycle: final / Resolution: 2.21→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms17604 0 48 1149 18801
Biso mean--34.34 37.28 -
Num. residues----2192
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.01918171
X-RAY DIFFRACTIONr_bond_other_d0.0010.0216570
X-RAY DIFFRACTIONr_angle_refined_deg1.4141.95524757
X-RAY DIFFRACTIONr_angle_other_deg0.807338066
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.24852188
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.11523.262932
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.979152756
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.74515152
X-RAY DIFFRACTIONr_chiral_restr0.0840.22561
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.02120840
X-RAY DIFFRACTIONr_gen_planes_other0.0010.024464
X-RAY DIFFRACTIONr_mcbond_it1.7183.1618769
X-RAY DIFFRACTIONr_mcbond_other1.7173.168767
X-RAY DIFFRACTIONr_mcangle_it2.5764.73410948
LS refinement shellResolution: 2.21→2.267 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.263 459 -
Rwork0.226 8156 -
all-8615 -
obs--93.55 %

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