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- PDB-5jio: Structure of Mycobacterium thermoresistibile trehalose-6-phosphat... -

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Basic information

Entry
Database: PDB / ID: 5jio
TitleStructure of Mycobacterium thermoresistibile trehalose-6-phosphate synthase ternary complex with ADP and Glucose-6-phosphate.
ComponentsAlpha,alpha-trehalose-phosphate synthase
KeywordsTRANSFERASE / OtsA trehalose-6-phosphate synthase Trehalose
Function / homology
Function and homology information


alpha,alpha-trehalose-phosphate synthase (ADP-forming) / trehalose biosynthetic process / hexosyltransferase activity / nucleotide binding
Similarity search - Function
Glycosyl transferase, family 20 / Glycosyltransferase family 20 / Glycogen Phosphorylase B; / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / 6-O-phosphono-alpha-D-glucopyranose / alpha,alpha-trehalose-phosphate synthase (ADP-forming) / alpha,alpha-trehalose-phosphate synthase (ADP-forming)
Similarity search - Component
Biological speciesMycobacterium thermoresistibile (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.711 Å
AuthorsMendes, V. / Verma, N. / Blaszczyk, M. / Blundell, T.L.
Funding support United States, 1items
OrganizationGrant numberCountry
Bill & Melinda Gates Foundation United States
CitationJournal: Mbio / Year: 2019
Title: Mycobacterial OtsA Structures Unveil Substrate Preference Mechanism and Allosteric Regulation by 2-Oxoglutarate and 2-Phosphoglycerate.
Authors: Mendes, V. / Acebron-Garcia-de-Eulate, M. / Verma, N. / Blaszczyk, M. / Dias, M.V.B. / Blundell, T.L.
History
DepositionApr 22, 2016Deposition site: RCSB / Processing site: PDBE
Revision 1.0May 10, 2017Provider: repository / Type: Initial release
Revision 1.1Sep 13, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 2.0Jan 22, 2020Group: Atomic model / Database references / Category: atom_site / citation / citation_author
Item: _atom_site.occupancy / _citation.country ..._atom_site.occupancy / _citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 2.1Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_site / struct_site_gen
Item: _chem_comp.mon_nstd_flag / _chem_comp.name ..._chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.2Jan 10, 2024Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Alpha,alpha-trehalose-phosphate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,4935
Polymers54,6811
Non-polymers8114
Water5,909328
1
A: Alpha,alpha-trehalose-phosphate synthase
hetero molecules

A: Alpha,alpha-trehalose-phosphate synthase
hetero molecules

A: Alpha,alpha-trehalose-phosphate synthase
hetero molecules

A: Alpha,alpha-trehalose-phosphate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)221,97020
Polymers218,7244
Non-polymers3,24616
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_785-x+2,-y+3,z1
crystal symmetry operation9_767-x+2,-x+y+1,-z+7/31
crystal symmetry operation12_577x,x-y+2,-z+7/31
Buried area14410 Å2
ΔGint-28 kcal/mol
Surface area63990 Å2
MethodPISA
Unit cell
Length a, b, c (Å)105.357, 105.357, 158.866
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number180
Space group name H-MP6222
Components on special symmetry positions
IDModelComponents
11A-845-

HOH

21A-917-

HOH

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Components

#1: Protein Alpha,alpha-trehalose-phosphate synthase


Mass: 54681.047 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium thermoresistibile (bacteria)
Gene: RMCT_1906 / Production host: Escherichia coli Bl21(DE3) (bacteria) / References: UniProt: A0A117IMA6, UniProt: G7CGT2*PLUS
#2: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE / Adenosine diphosphate


Mass: 427.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#3: Sugar ChemComp-G6P / 6-O-phosphono-alpha-D-glucopyranose / ALPHA-D-GLUCOSE-6-PHOSPHATE / 6-O-phosphono-alpha-D-glucose / 6-O-phosphono-D-glucose / 6-O-phosphono-glucose


Type: D-saccharide, alpha linking / Mass: 260.136 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C6H13O9P
IdentifierTypeProgram
a-D-Glcp6PO3IUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 328 / 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: 2.33 Å3/Da / Density % sol: 47.15 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 8.5 / Details: 1M Ammonium Phosphate dibasic 0.1M Tris

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.916 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Apr 25, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.916 Å / Relative weight: 1
ReflectionResolution: 1.71→91.24 Å / Num. obs: 56816 / % possible obs: 100 % / Redundancy: 18.1 % / Biso Wilson estimate: 22.76 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.098 / Rpim(I) all: 0.023 / Rrim(I) all: 0.101 / Net I/σ(I): 19.1 / Num. measured all: 1030194
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsDiffraction-ID% possible all
1.71-1.8714.50.8211100
4.19-91.2417.90.0581100

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation7.04 Å91.24 Å
Translation7.04 Å91.24 Å

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Processing

Software
NameVersionClassification
Aimless0.3.11data scaling
PHASER2.5.6phasing
PHENIXrefinement
PDB_EXTRACT3.2data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5JIJ

5jij


Resolution: 1.711→91 Å / SU ML: 0.15 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 16.23
RfactorNum. reflection% reflection
Rfree0.1786 2793 4.92 %
Rwork0.1523 --
obs0.1535 56756 99.99 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 98.66 Å2 / Biso mean: 31.8127 Å2 / Biso min: 12.92 Å2
Refinement stepCycle: final / Resolution: 1.711→91 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3685 0 51 328 4064
Biso mean--25.77 39.77 -
Num. residues----467
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0073834
X-RAY DIFFRACTIONf_angle_d1.0925221
X-RAY DIFFRACTIONf_chiral_restr0.048581
X-RAY DIFFRACTIONf_plane_restr0.005679
X-RAY DIFFRACTIONf_dihedral_angle_d12.7231403
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
1.7105-1.740.28181520.233126222774
1.74-1.77170.22191550.208526412796
1.7717-1.80570.21931180.190726662784
1.8057-1.84260.18911370.174126482785
1.8426-1.88270.24741320.173626712803
1.8827-1.92650.20041410.173426332774
1.9265-1.97460.19221500.17126442794
1.9746-2.0280.21341370.155626952832
2.028-2.08770.20441510.152826132764
2.0877-2.15510.18041370.149226932830
2.1551-2.23210.15941320.147126732805
2.2321-2.32150.17261210.146327012822
2.3215-2.42720.20721420.154526772819
2.4272-2.55520.20381380.156126952833
2.5552-2.71530.18221610.155526812842
2.7153-2.92490.17451400.157527192859
2.9249-3.21930.17261170.154427492866
3.2193-3.68510.15641330.147827642897
3.6851-4.64290.14661460.125128022948
4.6429-91.37190.17381530.15129763129
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)
11.49440.1544-0.1482.32930.40651.9804-0.06450.099-0.1696-0.1488-0.0430.31830.3841-0.28260.06590.2718-0.05210.03590.1521-0.01470.225120.2224103.9118177.8176
20.7713-0.005-0.16271.3778-0.07371.1908-0.05250.0781-0.0911-0.1971-0.0057-0.02530.20790.04320.03360.24360.01970.03450.1091-0.0190.142734.6104116.3691162.4237
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 7 through 213 )A7 - 213
2X-RAY DIFFRACTION2chain 'A' and (resid 214 through 477 )A214 - 477

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