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

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Basic information

Entry
Database: PDB / ID: 5jij
TitleStructure of Mycobacterium thermoresistibile trehalose-6-phosphate synthase (APO form).
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 metabolism in response to stress / alpha,alpha-trehalose-phosphate synthase complex (UDP-forming) / trehalose-phosphatase activity / trehalose biosynthetic process / hexosyltransferase activity / cellular response to heat / nucleotide binding / cytosol
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
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: 1.82 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 2.1Jan 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)55,44711
Polymers54,6811
Non-polymers76610
Water5,368298
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)221,78844
Polymers218,7244
Non-polymers3,06440
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_545y+1/2,x-1/2,-z+1/21
crystal symmetry operation10_655-x+1,-y,z1
crystal symmetry operation16_555-y+1/2,-x+1/2,-z+1/21
MethodPISA
Unit cell
Length a, b, c (Å)126.860, 126.860, 207.190
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-845-

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-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
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 298 / 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: 3.81 Å3/Da / Density % sol: 67.73 %
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: I04 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Dec 11, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.82→60.66 Å / Num. obs: 75576 / % possible obs: 100 % / Redundancy: 11 % / Biso Wilson estimate: 26.47 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.119 / Rpim(I) all: 0.037 / Rrim(I) all: 0.125 / Net I/σ(I): 9.5 / Num. measured all: 833006 / Scaling rejects: 1397
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsDiffraction-ID% possible all
1.82-1.8611.30.7451100
9.1-60.669.80.055199.7

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation7.5 Å60.66 Å
Translation7.5 Å60.66 Å

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
Aimless0.1.26data scaling
PHASER2.5.3phasing
PDB_EXTRACT3.2data extraction
iMOSFLMdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1UQU

1uqu


Resolution: 1.82→60.657 Å / SU ML: 0.14 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 20.59
RfactorNum. reflection% reflection
Rfree0.1855 3751 5.06 %
Rwork0.1646 --
obs0.1657 74139 98.13 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.82→60.657 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3612 0 49 298 3959
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0073764
X-RAY DIFFRACTIONf_angle_d1.0095111
X-RAY DIFFRACTIONf_dihedral_angle_d13.7361395
X-RAY DIFFRACTIONf_chiral_restr0.043569
X-RAY DIFFRACTIONf_plane_restr0.005669
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.82-1.8430.22791350.22012506X-RAY DIFFRACTION97
1.843-1.86730.23061230.21392569X-RAY DIFFRACTION96
1.8673-1.89290.27391450.21672499X-RAY DIFFRACTION97
1.8929-1.91990.26621290.28062477X-RAY DIFFRACTION94
1.9199-1.94860.27211420.22622464X-RAY DIFFRACTION94
1.9486-1.9790.21641570.20152514X-RAY DIFFRACTION98
1.979-2.01150.22851270.18762608X-RAY DIFFRACTION98
2.0115-2.04620.19251510.17562592X-RAY DIFFRACTION98
2.0462-2.08340.21211250.19552575X-RAY DIFFRACTION98
2.0834-2.12350.18951310.1742552X-RAY DIFFRACTION98
2.1235-2.16680.18891290.16122643X-RAY DIFFRACTION99
2.1668-2.21390.20281490.16642592X-RAY DIFFRACTION99
2.2139-2.26540.19431280.22503X-RAY DIFFRACTION95
2.2654-2.32210.18091620.16532554X-RAY DIFFRACTION97
2.3221-2.38490.18751540.16692585X-RAY DIFFRACTION99
2.3849-2.4550.20231240.1712594X-RAY DIFFRACTION98
2.455-2.53430.20841310.17162645X-RAY DIFFRACTION99
2.5343-2.62490.18841280.16962620X-RAY DIFFRACTION99
2.6249-2.730.20631440.17472623X-RAY DIFFRACTION99
2.73-2.85420.19511410.18192669X-RAY DIFFRACTION99
2.8542-3.00470.1891490.17872638X-RAY DIFFRACTION100
3.0047-3.19290.21451320.17892665X-RAY DIFFRACTION100
3.1929-3.43940.19741460.16442664X-RAY DIFFRACTION100
3.4394-3.78550.17981430.15262696X-RAY DIFFRACTION100
3.7855-4.33310.15631250.13252730X-RAY DIFFRACTION100
4.3331-5.45870.13421360.13132750X-RAY DIFFRACTION100
5.4587-60.69080.16721650.1552861X-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)
12.05170.11330.48171.26010.05033.2326-0.1782-0.05470.2596-0.0998-0.01310.3041-0.4244-1.2030.08110.23420.1761-0.0390.622-0.05210.275527.5829-6.474245.2528
21.29070.3021-0.30360.8692-0.18622.206-0.03470.05380.0697-0.1316-0.0170.05460.033-0.33460.03580.21430.0092-0.00260.1574-0.02060.175647.7637-12.776527.2523
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 8 through 237 )
2X-RAY DIFFRACTION2chain 'A' and (resid 238 through 477 )

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