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- PDB-6upb: Structure of apo trehalose-6-phosphate phosphatase from Salmonell... -

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Basic information

Entry
Database: PDB / ID: 6upb
TitleStructure of apo trehalose-6-phosphate phosphatase from Salmonella typhimurium
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-phosphate phosphatase
Similarity search - Component
Biological speciesSalmonella typhimurium (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.89 Å
AuthorsHarvey, C.M. / 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 1.2Mar 13, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
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: Trehalose-phosphate phosphatase
B: Trehalose-phosphate phosphatase


Theoretical massNumber of molelcules
Total (without water)58,5932
Polymers58,5932
Non-polymers00
Water7,927440
1
A: Trehalose-phosphate phosphatase


Theoretical massNumber of molelcules
Total (without water)29,2961
Polymers29,2961
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Trehalose-phosphate phosphatase


Theoretical massNumber of molelcules
Total (without water)29,2961
Polymers29,2961
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)45.988, 52.447, 105.555
Angle α, β, γ (deg.)90.000, 98.450, 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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 440 / 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: 2.35 Å3/Da / Density % sol: 47.76 % / Description: rod
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop
Details: Drop contained: 1.5 uL 40 mg/mL protein, 2 uL reservoir solution (15% PEG 3350, 350 mM lithium citrate), 2 uL water, and 0.5 uL 1:10^5 dilution of seed stock prepared according to Seed Bead ...Details: Drop contained: 1.5 uL 40 mg/mL protein, 2 uL reservoir solution (15% PEG 3350, 350 mM lithium citrate), 2 uL water, and 0.5 uL 1:10^5 dilution of seed stock prepared according to Seed Bead protocol. Crystals were cryoprotected in a solution containing 15% PEG 3350, 350mM lithium citrate, and 10% ethylene glycol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.9791 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Feb 17, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 1.89→104.4 Å / Num. obs: 39938 / % possible obs: 99.6 % / Redundancy: 8.4 % / Biso Wilson estimate: 24.52 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.109 / Net I/σ(I): 14.9
Reflection shellResolution: 1.89→1.958 Å / Redundancy: 8.1 % / Rmerge(I) obs: 0.6532 / Mean I/σ(I) obs: 3.36 / Num. unique obs: 3940 / CC1/2: 0.846 / % possible all: 99.6

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Processing

Software
NameVersionClassification
XDSdata reduction
Aimlessdata scaling
PHENIX1.13_2998refinement
PDB_EXTRACT3.25data extraction
PHENIXphasing
RefinementMethod to determine structure: MAD / Resolution: 1.89→104.4 Å / SU ML: 0.19 / Cross valid method: THROUGHOUT / σ(F): 1.37 / Phase error: 21.95
RfactorNum. reflection% reflection
Rfree0.2152 1707 4.28 %
Rwork0.1868 --
obs0.188 39919 99.56 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 90.51 Å2 / Biso mean: 34.3761 Å2 / Biso min: 11.62 Å2
Refinement stepCycle: final / Resolution: 1.89→104.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3772 0 0 440 4212
Biso mean---35.21 -
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 (%)
1.89-1.94560.2761400.25873146100
1.9456-2.00840.24811410.2213164100
2.0084-2.08020.2341380.20873168100
2.0802-2.16350.23621400.2035316999
2.1635-2.2620.21761470.1958314299
2.262-2.38120.21461440.19793190100
2.3812-2.53040.2361400.20753180100
2.5304-2.72580.24761470.2101317799
2.7258-3.00020.24131450.19893171100
3.0002-3.43430.21451390.1855320199
3.4343-4.32690.17811400.15683225100
4.3269-104.40.19831460.1663327999

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