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- PDB-5k5c: Structure of Mycobacterium thermoresistibile trehalose-6-phosphat... -

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Basic information

Entry
Database: PDB / ID: 5k5c
TitleStructure of Mycobacterium thermoresistibile trehalose-6-phosphate synthase in a complex with Trehalose.
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) / alpha,alpha-trehalose-phosphate synthase (UDP-forming) activity / trehalose biosynthetic process / 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
trehalose / alpha,alpha-trehalose-phosphate synthase (ADP-forming)
Similarity search - Component
Biological speciesMycobacterium thermoresistibile (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.848 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
DepositionMay 23, 2016Deposition site: RCSB / Processing site: PDBE
Revision 1.0Jun 7, 2017Provider: repository / Type: Initial release
Revision 1.1Sep 13, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Jan 22, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._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 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Non-polymer description / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / entity_name_com / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_molecule_features / pdbx_nonpoly_scheme / struct_conn / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.type_symbol / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.pdbx_synonyms / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.src_method / _entity.type
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Jan 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)55,93412
Polymers54,6811
Non-polymers1,25311
Water6,684371
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)223,73848
Polymers218,7244
Non-polymers5,01444
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_545y+1/2,x-1/2,-z+1/21
crystal symmetry operation10_875-x+3,-y+2,z1
crystal symmetry operation16_775-y+5/2,-x+5/2,-z+1/21
Unit cell
Length a, b, c (Å)127.318, 127.318, 207.387
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number98
Space group name H-MI4122
Components on special symmetry positions
IDModelComponents
11A-886-

HOH

21A-942-

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, OtsA / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A117IMA6
#2: Polysaccharide alpha-D-glucopyranose-(1-1)-alpha-D-glucopyranose / trehalose


Type: oligosaccharide, Oligosaccharide / Class: Nutrient / Mass: 342.297 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: oligosaccharide with reducing-end-to-reducing-end glycosidic bond
References: trehalose
DescriptorTypeProgram
DGlcpa1-1DGlcpaGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1a_1-5]/1-1/a1-b1WURCSPDB2Glycan 1.1.0
[][a-D-Glcp]{[(1+1)][a-D-Glcp]{}}LINUCSPDB-CARE
#3: Chemical ChemComp-NHE / 2-[N-CYCLOHEXYLAMINO]ETHANE SULFONIC ACID / N-CYCLOHEXYLTAURINE / CHES


Mass: 207.290 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H17NO3S / Comment: pH buffer*YM
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 371 / 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: 3.84 Å3/Da / Density % sol: 67.99 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 10
Details: 0.1M CHES pH 10 0.7M sodium potassium tartrate 10% v/v ethylene glycol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.96862 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Mar 9, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.96862 Å / Relative weight: 1
ReflectionResolution: 1.848→103.69 Å / Num. obs: 72774 / % possible obs: 100 % / Redundancy: 12.7 % / Biso Wilson estimate: 28.44 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.078 / Net I/σ(I): 20.1
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsDiffraction-ID% possible all
1.85-2.0210.70.81100
4.53-103.6912.40.0391100

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation7.45 Å90.03 Å
Translation7.45 Å90.03 Å

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
Aimless0.2.17data scaling
PHASER2.5.3phasing
PDB_EXTRACT3.2data extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5JIJ

5jij


Resolution: 1.848→41.578 Å / SU ML: 0.17 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 18.27
RfactorNum. reflection% reflection
Rfree0.1747 3595 4.95 %
Rwork0.1509 --
obs0.152 72668 99.89 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.848→41.578 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3645 0 81 371 4097
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0073864
X-RAY DIFFRACTIONf_angle_d1.0285256
X-RAY DIFFRACTIONf_dihedral_angle_d14.0221442
X-RAY DIFFRACTIONf_chiral_restr0.043586
X-RAY DIFFRACTIONf_plane_restr0.004684
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8484-1.87270.31871380.29092635X-RAY DIFFRACTION100
1.8727-1.89840.28671310.25162626X-RAY DIFFRACTION100
1.8984-1.92550.26521350.23222599X-RAY DIFFRACTION100
1.9255-1.95420.23811480.2162608X-RAY DIFFRACTION100
1.9542-1.98480.25321120.20392626X-RAY DIFFRACTION100
1.9848-2.01730.20321500.18792637X-RAY DIFFRACTION100
2.0173-2.05210.2011440.18142620X-RAY DIFFRACTION100
2.0521-2.08940.19071480.17642605X-RAY DIFFRACTION100
2.0894-2.12960.18551530.16322610X-RAY DIFFRACTION100
2.1296-2.17310.18411190.15312665X-RAY DIFFRACTION100
2.1731-2.22030.16641540.15252599X-RAY DIFFRACTION100
2.2203-2.2720.18941340.14722639X-RAY DIFFRACTION100
2.272-2.32880.18221340.14322645X-RAY DIFFRACTION100
2.3288-2.39170.1721350.15442637X-RAY DIFFRACTION100
2.3917-2.46210.18391420.15562641X-RAY DIFFRACTION100
2.4621-2.54160.18441400.15932663X-RAY DIFFRACTION100
2.5416-2.63240.19231340.15992637X-RAY DIFFRACTION100
2.6324-2.73780.19141540.16332638X-RAY DIFFRACTION100
2.7378-2.86230.24051370.16922685X-RAY DIFFRACTION100
2.8623-3.01320.18531350.16412657X-RAY DIFFRACTION100
3.0132-3.20190.19971220.16412685X-RAY DIFFRACTION100
3.2019-3.4490.17441310.15642687X-RAY DIFFRACTION100
3.449-3.79590.16231400.13372689X-RAY DIFFRACTION100
3.7959-4.34470.13171240.11492731X-RAY DIFFRACTION100
4.3447-5.47190.13141470.11472740X-RAY DIFFRACTION100
5.4719-41.58820.1511540.14422869X-RAY DIFFRACTION100
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)
11.9774-0.07260.39831.34770.28231.9605-0.13580.06040.2777-0.1115-0.00860.2667-0.3796-0.79310.10270.25710.1364-0.02270.4993-0.01860.295155.3639122.939944.6332
21.15060.2703-0.38460.8513-0.19981.8696-0.02720.04680.0593-0.08280.00460.06060.0274-0.33180.01580.20840.0073-0.00790.1772-0.02330.199173.2448113.566629.0699
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 8 through 213 )
2X-RAY DIFFRACTION2chain 'A' and (resid 214 through 477 )

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