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- PDB-5l3k: Structure of Mycobacterium thermoresistibile trehalose-6-phosphat... -

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Basic information

Entry
Database: PDB / ID: 5l3k
TitleStructure of Mycobacterium thermoresistibile trehalose-6-phosphate synthase in a ternary complex with ADP and fructose-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) / 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 / 6-O-phosphono-beta-D-fructofuranose / PHOSPHATE ION / alpha,alpha-trehalose-phosphate synthase (ADP-forming)
Similarity search - Component
Biological speciesMycobacterium thermoresistibile (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.305 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: PDBE / 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 1.3Jul 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 1.4Jan 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
B: Alpha,alpha-trehalose-phosphate synthase
C: Alpha,alpha-trehalose-phosphate synthase
D: Alpha,alpha-trehalose-phosphate synthase
E: Alpha,alpha-trehalose-phosphate synthase
F: Alpha,alpha-trehalose-phosphate synthase
G: Alpha,alpha-trehalose-phosphate synthase
H: Alpha,alpha-trehalose-phosphate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)442,92330
Polymers437,4488
Non-polymers5,47422
Water28,4281578
1
A: Alpha,alpha-trehalose-phosphate synthase
B: Alpha,alpha-trehalose-phosphate synthase
C: Alpha,alpha-trehalose-phosphate synthase
D: Alpha,alpha-trehalose-phosphate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)221,62216
Polymers218,7244
Non-polymers2,89812
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
E: Alpha,alpha-trehalose-phosphate synthase
F: Alpha,alpha-trehalose-phosphate synthase
G: Alpha,alpha-trehalose-phosphate synthase
H: Alpha,alpha-trehalose-phosphate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)221,30014
Polymers218,7244
Non-polymers2,57610
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)216.960, 216.960, 159.835
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number171
Space group name H-MP62

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Components

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Protein / Sugars , 2 types, 13 molecules ABCDEFGH

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


Mass: 54681.047 Da / Num. of mol.: 8
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
#4: Sugar
ChemComp-F6P / 6-O-phosphono-beta-D-fructofuranose / FRUCTOSE-6-PHOSPHATE / 6-O-phosphono-beta-D-fructose / 6-O-phosphono-D-fructose / 6-O-phosphono-fructose


Type: D-saccharide, beta linking / Mass: 260.136 Da / Num. of mol.: 5
Source method: isolated from a genetically manipulated source
Formula: C6H13O9P
IdentifierTypeProgram
b-D-Fruf6PO3IUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0

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Non-polymers , 4 types, 1595 molecules

#2: Chemical
ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: PO4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1578 / 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: 2.48 Å3/Da / Density % sol: 50.45 %
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: 0.92818 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Jan 16, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92818 Å / Relative weight: 1
Reflection twinOperator: h,-h-k,-l / Fraction: 0.3
ReflectionResolution: 2.305→159.84 Å / Num. obs: 187701 / % possible obs: 100 % / Redundancy: 10.3 % / CC1/2: 0.987 / Rmerge(I) obs: 0.288 / Net I/σ(I): 7
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsDiffraction-ID% possible all
2.31-2.439.81.2311100
7.29-159.849.80.12199.7

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation7.66 Å121.74 Å
Translation7.66 Å121.74 Å

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Processing

Software
NameVersionClassification
PHENIX(1.10_2155: ???)refinement
Aimless0.5.15data scaling
PHASER2.6.0phasing
PDB_EXTRACT3.2data extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5JIJ

5jij


Resolution: 2.305→121.744 Å / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 30.32 / Stereochemistry target values: TWIN_LSQ_F
RfactorNum. reflection% reflection
Rfree0.2132 9365 4.99 %
Rwork0.1535 --
obs0.1573 187654 99.99 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.305→121.744 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms28062 0 338 1578 29978
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00929033
X-RAY DIFFRACTIONf_angle_d1.04839591
X-RAY DIFFRACTIONf_dihedral_angle_d22.92317135
X-RAY DIFFRACTIONf_chiral_restr0.0574434
X-RAY DIFFRACTIONf_plane_restr0.0075135
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)
14.07832.95463.0322.6381.73432.7051-0.80540.97380.7637-1.06440.34120.6416-1.18120.00920.22670.57330.0719-0.10780.73150.16260.3739155.1334139.3296167.224
20.8810.1871-0.75160.6254-0.08522.2787-0.10050.2072-0.0054-0.10890.0310.090.1378-0.48820.06150.2008-0.0249-0.02970.2417-0.00290.1261169.2118125.8189164.8187
32.29220.516-0.21891.7179-0.85441.9687-0.05830.1125-0.2506-0.1196-0.0288-0.22570.18710.43620.05750.17830.03970.01130.2980.01820.1493222.7334151.1534172.8022
41.13040.28680.14040.94-0.07051.103-0.01050.0751-0.0039-0.1068-0.0309-0.0328-0.01360.08120.0320.15910.0020.00240.14140.03010.1039203.7531157.2754156.0996
50.4637-0.23160.771.4027-0.1271.3721-0.2384-0.15020.16860.67390.20070.2248-1.01-0.4531-0.01220.75330.24910.05130.31890.02410.2546187.8301174.7241187.3956
61.40230.27890.7351.19880.22892.2709-0.1848-0.15450.1965-0.00940.02950.0257-0.5223-0.09120.04670.25460.0394-0.03470.1597-0.03240.1264201.0644159.6537204.1973
71.4548-0.0280.07492.63030.00922.12690.0134-0.0893-0.05050.089-0.0486-0.25530.34490.29560.03640.22660.05130.0540.19330.02130.1501193.5743107.1693187.7906
80.79410.1992-0.16951.3675-0.21270.9987-0.0723-0.1261-0.0980.02220.0494-0.00820.1113-0.04280.01680.14570.01340.02080.19310.03840.108180.8711121.2294204.0236
91.7128-0.4589-0.32631.6715-0.05271.7665-0.00740.1053-0.2944-0.1138-0.00140.00340.35910.17220.00380.20660.035-0.00340.1427-0.00620.1576190.5067165.6598119.9083
101.2454-0.17770.14150.7515-0.06551.096-0.0090.09040.0048-0.11760.0081-0.05560.00460.08570.00130.1426-0.01910.02420.1245-0.01750.1107183.718184.0308104.3451
112.3545-0.2806-0.14541.970.75352.22140.04330.18890.2915-0.2224-0.21530.0532-0.5037-0.34730.12910.27730.0776-0.01450.2451-0.0730.2129134.7165204.5445122.3077
121.18380.1840.22630.68730.41651.3459-0.03140.03080.0152-0.1117-0.09090.1744-0.0762-0.2430.09230.1373-0.0019-0.03450.2159-0.04130.1732139.8153186.0627105.7782
134.14892.0625-4.76641.2745-2.48065.8198-0.1428-1.2863-0.40290.6932-0.2770.22890.65830.62640.16461.0275-0.22050.02050.63610.01250.4527140.8631155.7544144.9551
141.18220.20810.29350.58230.2552.2892-0.0114-0.2021-0.14140.1296-0.04260.12090.3597-0.3770.03750.2432-0.02160.08120.25460.00880.2006140.1347175.8673145.5949
155.2008-0.44290.85464.189-1.17122.8950.2491-1.4931-0.21080.8225-0.3345-0.0522-0.171-0.70450.01410.6104-0.07170.03930.4520.00180.1844184.6767213.2751145.321
160.86880.1994-0.14210.8109-0.20841.2724-0.0112-0.06240.08040.0637-0.0069-0.0024-0.1570.0920.01630.1862-0.0084-0.01480.1248-0.02690.1103185.9627196.9179143.4369
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 10 through 89 )
2X-RAY DIFFRACTION2chain 'A' and (resid 90 through 477 )
3X-RAY DIFFRACTION3chain 'B' and (resid 10 through 222 )
4X-RAY DIFFRACTION4chain 'B' and (resid 223 through 477 )
5X-RAY DIFFRACTION5chain 'C' and (resid 10 through 213 )
6X-RAY DIFFRACTION6chain 'C' and (resid 214 through 475 )
7X-RAY DIFFRACTION7chain 'D' and (resid 9 through 213 )
8X-RAY DIFFRACTION8chain 'D' and (resid 214 through 477 )
9X-RAY DIFFRACTION9chain 'E' and (resid 9 through 213 )
10X-RAY DIFFRACTION10chain 'E' and (resid 214 through 477 )
11X-RAY DIFFRACTION11chain 'F' and (resid 9 through 213 )
12X-RAY DIFFRACTION12chain 'F' and (resid 214 through 477 )
13X-RAY DIFFRACTION13chain 'G' and (resid 10 through 82 )
14X-RAY DIFFRACTION14chain 'G' and (resid 83 through 475 )
15X-RAY DIFFRACTION15chain 'H' and (resid 9 through 58 )
16X-RAY DIFFRACTION16chain 'H' and (resid 59 through 477 )

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