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- PDB-3zo9: The structure of Trehalose Synthase (TreS) of Mycobacterium smegmatis -

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Basic information

Entry
Database: PDB / ID: 3zo9
TitleThe structure of Trehalose Synthase (TreS) of Mycobacterium smegmatis
ComponentsTREHALOSE SYNTHASE/AMYLASE TRES
KeywordsHYDROLASE / GLYCOHYDROLASE / DRUG DESIGN / TUBERCULOSIS
Function / homology
Function and homology information


maltose alpha-D-glucosyltransferase / maltose alpha-D-glucosyltransferase activity / maltose metabolic process / trehalose metabolic process / alpha-amylase / glycogen biosynthetic process / alpha-amylase activity / glycogen metabolic process / polysaccharide catabolic process / calcium 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
Trehalose synthase/amylase TreS
Similarity search - Component
Biological speciesMYCOBACTERIUM SMEGMATIS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.84 Å
AuthorsCaner, S. / Nguyen, N. / Aguda, A. / Zhang, R. / Pan, Y.T. / Withers, S.G. / Brayer, G.D.
CitationJournal: Glycobiology / Year: 2013
Title: The Structure of the Mycobacterium Smegmatis Trehalose Synthase Reveals an Unusual Active Site Configuration and Acarbose-Binding Mode.
Authors: Caner, S. / Nguyen, N. / Aguda, A. / Zhang, R. / Pan, Y.T. / Withers, S.G. / Brayer, G.D.
History
DepositionFeb 21, 2013Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 17, 2013Provider: repository / Type: Initial release
Revision 1.1Aug 7, 2013Group: Database references
Revision 1.2Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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_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_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 700 SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AA" IN EACH CHAIN ON SHEET RECORDS BELOW ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 8-STRANDED BARREL THIS IS REPRESENTED BY A 9-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEETS PRESENTED AS "BA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 8-STRANDED BARREL THIS IS REPRESENTED BY A 9-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: TREHALOSE SYNTHASE/AMYLASE TRES
B: TREHALOSE SYNTHASE/AMYLASE TRES
hetero molecules


Theoretical massNumber of molelcules
Total (without water)136,92113
Polymers136,5442
Non-polymers37711
Water18,9701053
1
A: TREHALOSE SYNTHASE/AMYLASE TRES
B: TREHALOSE SYNTHASE/AMYLASE TRES
hetero molecules

A: TREHALOSE SYNTHASE/AMYLASE TRES
B: TREHALOSE SYNTHASE/AMYLASE TRES
hetero molecules


Theoretical massNumber of molelcules
Total (without water)273,84226
Polymers273,0894
Non-polymers75422
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_555-x,-y,z1
Buried area10530 Å2
ΔGint-267.7 kcal/mol
Surface area78190 Å2
MethodPISA
Unit cell
Length a, b, c (Å)127.550, 127.550, 217.760
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number80
Space group name H-MI41
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.9758, 0.2179, 0.0196), (0.2179, 0.976, -0.0005), (-0.0192, 0.0038, -0.9998)
Vector: -26.7093, -17.8822, -51.2172)

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Components

#1: Protein TREHALOSE SYNTHASE/AMYLASE TRES / MALTOSE ALPHA-D-GLUCOSYLTRANSFERASE / MTASE


Mass: 68272.133 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) MYCOBACTERIUM SMEGMATIS (bacteria)
References: UniProt: A0R6E0, alpha-amylase, maltose alpha-D-glucosyltransferase
#2: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1053 / 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: 3.22 Å3/Da / Density % sol: 62 % / Description: NONE
Crystal growDetails: 0.1 M SODIUM CACODYLATE BUFFER PH 6.5, 0.2 M MGCL2, 10% PEG 1000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.9795
DetectorType: DECTRIS PILATUS / Detector: PIXEL / Date: Jul 21, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.84→35 Å / Num. obs: 139127 / % possible obs: 93 % / Observed criterion σ(I): 2 / Redundancy: 4.4 % / Biso Wilson estimate: 27.82 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 14.4
Reflection shellResolution: 1.84→1.89 Å / Redundancy: 4.5 % / Rmerge(I) obs: 0.52 / Mean I/σ(I) obs: 3.05 / % possible all: 96.4

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE: 1.8.1_1168)refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2ZE0

2ze0


Resolution: 1.84→34.918 Å / SU ML: 0.17 / σ(F): 1.99 / Phase error: 19.39 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1954 3479 2.5 %
Rwork0.163 --
obs0.1638 139122 92.85 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.84→34.918 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9157 0 11 1053 10221
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0079504
X-RAY DIFFRACTIONf_angle_d1.10512974
X-RAY DIFFRACTIONf_dihedral_angle_d13.7263479
X-RAY DIFFRACTIONf_chiral_restr0.081335
X-RAY DIFFRACTIONf_plane_restr0.0061725
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.84-1.86520.24911450.21215626X-RAY DIFFRACTION96
1.8652-1.89180.26881430.20785592X-RAY DIFFRACTION96
1.8918-1.920.2431440.20385620X-RAY DIFFRACTION96
1.92-1.950.21971450.19445632X-RAY DIFFRACTION96
1.95-1.9820.2471430.19615588X-RAY DIFFRACTION96
1.982-2.01620.23821430.19745570X-RAY DIFFRACTION96
2.0162-2.05280.24851440.19015621X-RAY DIFFRACTION96
2.0528-2.09230.21551410.18465527X-RAY DIFFRACTION95
2.0923-2.1350.24291420.18595537X-RAY DIFFRACTION95
2.135-2.18140.21651410.18885475X-RAY DIFFRACTION93
2.1814-2.23220.22741410.18415517X-RAY DIFFRACTION94
2.2322-2.2880.21721400.17515458X-RAY DIFFRACTION94
2.288-2.34980.23481400.18145467X-RAY DIFFRACTION93
2.3498-2.4190.24441390.17735410X-RAY DIFFRACTION93
2.419-2.4970.21261400.17515445X-RAY DIFFRACTION93
2.497-2.58620.23711380.17325393X-RAY DIFFRACTION93
2.5862-2.68980.18261390.1715416X-RAY DIFFRACTION92
2.6898-2.81210.19361340.17035238X-RAY DIFFRACTION90
2.8121-2.96030.21431360.16735296X-RAY DIFFRACTION91
2.9603-3.14570.21091370.17215331X-RAY DIFFRACTION91
3.1457-3.38840.19711340.1635243X-RAY DIFFRACTION90
3.3884-3.7290.17991340.14865201X-RAY DIFFRACTION89
3.729-4.26780.16031300.13315103X-RAY DIFFRACTION87
4.2678-5.37380.1421330.12795187X-RAY DIFFRACTION89
5.3738-34.92450.16631330.15545150X-RAY DIFFRACTION87

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