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- PDB-6upd: Structure of trehalose-6-phosphate phosphatase from Salmonella ty... -

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Basic information

Entry
Database: PDB / ID: 6upd
TitleStructure of trehalose-6-phosphate phosphatase from Salmonella typhimurium in complex with trehalose
ComponentsTrehalose-phosphate phosphatase
KeywordsHYDROLASE / HAD Superfamily / Rossmann fold / sugar binding
Function / homology
Function and homology information


trehalose-phosphatase / trehalose-phosphatase activity / trehalose biosynthetic process / magnesium ion binding
Similarity search - Function
Trehalose 6-phosphate OTSB-like / Trehalose-phosphatase / Trehalose-phosphatase / HAD-superfamily hydrolase, subfamily IIB / HAD superfamily / HAD-like superfamily
Similarity search - Domain/homology
trehalose / Trehalose-phosphate phosphatase
Similarity search - Component
Biological speciesSalmonella typhimurium (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.052 Å
AuthorsHarvey, C.M. / O'Toole, K.H. / Allen, K.N.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R21 AI127623 United States
CitationJournal: Biochemistry / Year: 2020
Title: Structural Analysis of Binding Determinants ofSalmonella typhimuriumTrehalose-6-phosphate Phosphatase Using Ground-State Complexes.
Authors: Harvey, C.M. / O'Toole, K.H. / Liu, C. / Mariano, P. / Dunaway-Mariano, D. / Allen, K.N.
History
DepositionOct 17, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 26, 2020Provider: repository / Type: Initial release
Revision 1.1Sep 23, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation_author.name
Revision 1.2Oct 11, 2023Group: 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

Downloads & links

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Assembly

Deposited unit
A: Trehalose-phosphate phosphatase
B: Trehalose-phosphate phosphatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,3978
Polymers58,5932
Non-polymers8046
Water2,504139
1
A: Trehalose-phosphate phosphatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,6984
Polymers29,2961
Non-polymers4023
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Trehalose-phosphate phosphatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,6984
Polymers29,2961
Non-polymers4023
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)46.767, 52.955, 108.762
Angle α, β, γ (deg.)90.000, 100.610, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Trehalose-phosphate phosphatase / TPP / Trehalose 6-phosphate phosphatase / Trehalose-phosphatase


Mass: 29296.418 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Salmonella typhimurium (strain SL1344) (bacteria)
Strain: SL1344 / Gene: otsB, SL1344_1863 / Plasmid: pET15bTEV / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: E1WGG9, trehalose-phosphatase
#2: Polysaccharide alpha-D-glucopyranose-(1-1)-alpha-D-glucopyranose / trehalose


Type: oligosaccharide, Oligosaccharide / Class: Nutrient / Mass: 342.297 Da / Num. of mol.: 2
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-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 139 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 50.31 % / Description: rod
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop
Details: Drop Contained: 2 uL 40 mg/mL protein, 2 uL reservoir solution (16% PEG 3350, 450 mM lithium citrate and 10 mM magnesium chloride) and 0.5 uL 1:10^3 dilution of seed stock prepared according ...Details: Drop Contained: 2 uL 40 mg/mL protein, 2 uL reservoir solution (16% PEG 3350, 450 mM lithium citrate and 10 mM magnesium chloride) and 0.5 uL 1:10^3 dilution of seed stock prepared according to the Seed Bead protocol. Crystals were transferred to a drop containing 35% PEG 3350, 166 mM lithium citrate, 166 mM magnesium chloride, 10% ethylene glycol and 50 mM trehalose for 30 minutes prior to cryocooling.

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Data collection

DiffractionMean temperature: 290 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.97919 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 14, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97919 Å / Relative weight: 1
ReflectionResolution: 2.05→106.9 Å / Num. obs: 32534 / % possible obs: 98.6 % / Redundancy: 3.6 % / Biso Wilson estimate: 40.4 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.084 / Rpim(I) all: 0.051 / Rrim(I) all: 0.098 / Net I/σ(I): 9.4 / Num. measured all: 117234 / Scaling rejects: 76
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
2.05-2.113.60.859809822700.5770.5191.0071.288.8
8.95-106.93.40.03914524330.9970.0250.04628.899.6

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation6.15 Å106.9 Å
Translation6.15 Å106.9 Å

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Processing

Software
NameVersionClassification
Aimless0.5.23data scaling
PHASER2.8.1phasing
PHENIX1.13_2998refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6upb

6upb


Resolution: 2.052→53.451 Å / SU ML: 0.32 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 30.93 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2615 2016 6.21 %
Rwork0.2182 30467 -
obs0.221 32483 98.4 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 98.09 Å2 / Biso mean: 48.6048 Å2 / Biso min: 20.54 Å2
Refinement stepCycle: final / Resolution: 2.052→53.451 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3772 0 50 139 3961
Biso mean--52.97 45.96 -
Num. residues----492
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.0523-2.10360.36671290.3594190687
2.1036-2.16050.39431450.33652182100
2.1605-2.22410.33981520.29922219100
2.2241-2.29590.3721360.27812179100
2.2959-2.37790.271480.26032175100
2.3779-2.47320.30171400.2484219399
2.4732-2.58570.26671440.24572198100
2.5857-2.7220.27821440.25192181100
2.722-2.89260.30691440.22712210100
2.8926-3.11590.30121450.239221099
3.1159-3.42940.25741440.2201216599
3.4294-3.92550.26571470.1987220798
3.9255-4.94520.21211480.1741217498
4.9452-53.450.21791500.1908226898

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