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- PDB-5k41: Structure of Mycobacterium thermoresistibile trehalose-6-phosphat... -

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Basic information

Entry
Database: PDB / ID: 5k41
TitleStructure of Mycobacterium thermoresistibile trehalose-6-phosphate synthase in a complex with ADP-glucose.
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
ADENOSINE-5'-DIPHOSPHATE-GLUCOSE / 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: 1.971 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 20, 2016Deposition site: RCSB / Processing site: PDBE
Revision 1.0Jun 21, 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 1.3Jan 10, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)55,7888
Polymers54,6811
Non-polymers1,1077
Water6,431357
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)223,15232
Polymers218,7244
Non-polymers4,42828
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_457y-1/2,x+1/2,-z+5/21
crystal symmetry operation10_675-x+1,-y+2,z1
crystal symmetry operation16_667-y+3/2,-x+3/2,-z+5/21
Unit cell
Length a, b, c (Å)127.412, 127.412, 205.620
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number98
Space group name H-MI4122
Components on special symmetry positions
IDModelComponents
11A-878-

HOH

21A-926-

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-ADQ / ADENOSINE-5'-DIPHOSPHATE-GLUCOSE / ADENOSINE-5'-MONOPHOSPHATE GLUCOPYRANOSYL-MONOPHOSPHATE ESTER


Mass: 589.342 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H25N5O15P2
#3: Chemical ChemComp-NHE / 2-[N-CYCLOHEXYLAMINO]ETHANE SULFONIC ACID / N-CYCLOHEXYLTAURINE / CHES


Mass: 207.290 Da / Num. of mol.: 1 / 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.: 5 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 357 / 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: 3.82 Å3/Da / Density % sol: 67.76 %
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: 1.97→102.81 Å / Num. obs: 59763 / % possible obs: 100 % / Redundancy: 12.6 % / Biso Wilson estimate: 28.19 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.163 / Rpim(I) all: 0.048 / Rrim(I) all: 0.17 / Net I/σ(I): 9.5 / Num. measured all: 753000
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsDiffraction-ID% possible all
1.97-2.212.90.689199.9
4.41-102.8111.30.0951100

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation7.44 Å90.09 Å
Translation7.44 Å90.09 Å

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Processing

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

5jij


Resolution: 1.971→90.094 Å / SU ML: 0.18 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 21.36
RfactorNum. reflection% reflection
Rfree0.1911 2850 4.78 %
Rwork0.1652 --
obs0.1664 59634 99.78 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 114.18 Å2 / Biso mean: 45.275 Å2 / Biso min: 22.09 Å2
Refinement stepCycle: final / Resolution: 1.971→90.094 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3641 0 71 357 4069
Biso mean--43.01 49.23 -
Num. residues----463
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0073829
X-RAY DIFFRACTIONf_angle_d1.0425215
X-RAY DIFFRACTIONf_chiral_restr0.042581
X-RAY DIFFRACTIONf_plane_restr0.004676
X-RAY DIFFRACTIONf_dihedral_angle_d14.1091408
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.9709-2.00490.31251460.28227932939100
2.0049-2.04140.28941360.249628032939100
2.0414-2.08060.25331380.238127902928100
2.0806-2.12310.27021590.21712778293799
2.1231-2.16930.23611300.19942816294699
2.1693-2.21970.24451440.190127762920100
2.2197-2.27520.2031360.187728222958100
2.2752-2.33680.22551550.171227772932100
2.3368-2.40550.2511370.176928472984100
2.4055-2.48320.21441350.171628072942100
2.4832-2.57190.2051490.172828212970100
2.5719-2.67490.22011400.172928332973100
2.6749-2.79670.23031430.176328252968100
2.7967-2.94410.1751600.168628232983100
2.9441-3.12860.21771420.173828422984100
3.1286-3.37020.20371550.16528583013100
3.3702-3.70930.17721210.150128923013100
3.7093-4.24610.14551340.135828933027100
4.2461-5.34950.1261300.129929363066100
5.3495-90.18810.16661600.157630523212100
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)
12.12960.01680.23551.37360.3811.5943-0.07530.14750.2445-0.1538-0.06430.3155-0.4884-0.92650.10430.38260.1929-0.01380.686-0.03450.302428.4782123.3539249.6232
21.18670.2373-0.40410.859-0.06172.366-0.0660.1160.0071-0.08370.01910.0940.0727-0.42030.0440.2796-0.0089-0.00140.2446-0.0240.187846.4125113.6188234.1945
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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