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- PDB-4lxf: Crystal structure of M. tuberculosis TreS -

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Basic information

Entry
Database: PDB / ID: 4lxf
TitleCrystal structure of M. tuberculosis TreS
ComponentsTrehalose synthase
KeywordsISOMERASE / (alpha/beta) barrel / amylase / trehalose / maltose
Function / homology
Function and homology information


Oligo-1,6-glucosidase; domain 2 / Oligo-1,6-glucosidase; Domain 2 / Golgi alpha-mannosidase II / Glycosidases / TIM Barrel / Alpha-Beta Barrel / Alpha-Beta Complex / Immunoglobulin-like / Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsRoy, R. / Besra, G.S. / Futterer, K.
CitationJournal: Acs Chem.Biol. / Year: 2013
Title: Synthesis of alpha-glucan in mycobacteria involves a hetero-octameric complex of trehalose synthase TreS and Maltokinase Pep2.
Authors: Roy, R. / Usha, V. / Kermani, A. / Scott, D.J. / Hyde, E.I. / Besra, G.S. / Alderwick, L.J. / Futterer, K.
History
DepositionJul 29, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 21, 2013Provider: repository / Type: Initial release
Revision 1.1Sep 11, 2013Group: Database references
Revision 1.2Dec 25, 2013Group: Database references
Revision 1.3Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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.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_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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)142,51115
Polymers141,3942
Non-polymers1,11713
Water82946
1
A: Trehalose synthase
B: Trehalose synthase
hetero molecules

A: Trehalose synthase
B: Trehalose synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)285,02230
Polymers282,7884
Non-polymers2,23426
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_554-y,-x,-z-2/31
Buried area12850 Å2
ΔGint-211 kcal/mol
Surface area76760 Å2
MethodPISA
Unit cell
Length a, b, c (Å)161.640, 161.640, 139.110
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number153
Space group name H-MP3212
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2given(-0.992654, 0.06144, -0.104229), (-0.039932, -0.979566, -0.197118), (-0.11421, -0.191508, 0.974824)78.05856, -57.41048, -1.70678

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Components

#1: Protein Trehalose synthase


Mass: 70696.945 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: ligation sites: NdeI, HindIII / Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Strain: H37Rv / Gene: Rv0126, RVBD_0126 / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: I6X8K8, maltose alpha-D-glucosyltransferase
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 46 / 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: 3.71 Å3/Da / Density % sol: 66.85 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 5.6
Details: 0.1 M NaCitrate, 0.5 M (NH4)2SO4, 1 M Li2SO4, pH 5.6, VAPOR DIFFUSION, SITTING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: May 7, 2012
RadiationMonochromator: double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.6→29.2 Å / Num. all: 63561 / Num. obs: 63561 / % possible obs: 99.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.7 % / Biso Wilson estimate: 70.6 Å2 / Rmerge(I) obs: 0.06 / Rsym value: 0.06 / Net I/σ(I): 16.1
Reflection shellResolution: 2.6→2.74 Å / Redundancy: 4.7 % / Rmerge(I) obs: 0.668 / Mean I/σ(I) obs: 1.7 / Rsym value: 0.668 / % possible all: 99.6

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
PHASERphasing
REFMAC5.6.0117refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 2ZE0, 1UOK, 2PWE, 1WZA

2ze0

1uok

2pwe

1wza


Resolution: 2.6→29.2 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.935 / SU B: 24.115 / SU ML: 0.225 / Cross valid method: THROUGHOUT / ESU R: 0.336 / ESU R Free: 0.244 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.24041 3226 5.1 %RANDOM
Rwork0.21331 ---
all0.21469 60392 --
obs0.21469 60392 99.59 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 69.239 Å2
Baniso -1Baniso -2Baniso -3
1-3.03 Å21.51 Å2-0 Å2
2--3.03 Å2-0 Å2
3----4.54 Å2
Refinement stepCycle: LAST / Resolution: 2.6→29.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8737 0 62 46 8845
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.029063
X-RAY DIFFRACTIONr_angle_refined_deg1.0031.94712398
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.06151112
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.09523.304451
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.292151226
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.3541565
X-RAY DIFFRACTIONr_chiral_restr0.0710.21314
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0217252
LS refinement shellResolution: 2.6→2.668 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.383 222 -
Rwork0.36 4293 -
obs--99.52 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.075-0.1644-0.37940.5086-0.10762.05910.1096-0.0956-0.0920.01640.12420.1566-0.037-0.5823-0.23380.02320.0077-0.01270.28620.15980.174752.814-47.564-23.042
21.9459-0.72051.04060.9675-0.71842.3036-0.0837-0.35470.16570.2220.0458-0.2698-0.08950.30260.03790.11990.0986-0.00810.4419-0.01380.179327.937-6.436-20.221
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A10 - 600
2X-RAY DIFFRACTION2B10 - 600

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