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

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Basic information

Entry
Database: PDB / ID: 6upe
TitleStructure of trehalose-6-phosphate phosphatase from Salmonella typhimurium inhibited by 4-n-octylphenyl alpha-D-glucopyranoside-6-sulfate
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
4-octylphenyl 6-O-sulfo-alpha-D-glucopyranoside / Trehalose-phosphate phosphatase
Similarity search - Component
Biological speciesSalmonella typhimurium (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.244 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)59,5396
Polymers58,5932
Non-polymers9464
Water3,099172
1
A: Trehalose-phosphate phosphatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,7693
Polymers29,2961
Non-polymers4732
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Trehalose-phosphate phosphatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,7693
Polymers29,2961
Non-polymers4732
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)46.159, 52.419, 108.615
Angle α, β, γ (deg.)90.000, 100.580, 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: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-OGS / 4-octylphenyl 6-O-sulfo-alpha-D-glucopyranoside


Mass: 448.528 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C20H32O9S / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 172 / 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: 2.42 Å3/Da / Density % sol: 49.08 % / 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, 400 mM lithium citrate, 30 mM magnesium chloride, 40 mM mixture of MES, MOPS, and TAPS at pH 7.5), and 0.5 uL ...Details: Drop contained: 1.5 uL 40 mg/mL protein, 2 uL reservoir solution (15% PEG 3350, 400 mM lithium citrate, 30 mM magnesium chloride, 40 mM mixture of MES, MOPS, and TAPS at pH 7.5), and 0.5 uL 1:10^3 dilution of seed stock prepared according to Seed Bead protocol. Crystals were transferred to drop containing 18% PEG 3350, 400mM lithium citrate, 40 mM magnesium chloride, 10% ethylene glycol, and 1mM OGS for 24 prior to cryocooling

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Data collection

DiffractionMean temperature: 290 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL14-1 / Wavelength: 1.378 Å
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: May 23, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.378 Å / Relative weight: 1
ReflectionResolution: 2.24→50 Å / Num. obs: 24547 / % possible obs: 99.3 % / Redundancy: 4 % / Biso Wilson estimate: 37.51 Å2 / CC1/2: 0.978 / Rmerge(I) obs: 0.107 / Rpim(I) all: 0.06 / Rrim(I) all: 0.123 / Χ2: 2.645 / Net I/σ(I): 9.3
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.24-2.283.10.42211240.840.2730.5051.49390.6
2.28-2.323.30.41511720.8390.2620.4931.49297.7
2.32-2.363.50.42912140.7890.2650.5061.49298.9
2.36-2.413.70.39212380.8380.2330.4571.76899.7
2.41-2.473.90.41112010.8810.2370.4761.539100
2.47-2.5240.35712260.9090.2020.4111.563100
2.52-2.594.10.32912370.9330.1820.3761.652100
2.59-2.664.10.31412160.940.1720.3591.825100
2.66-2.734.10.28512370.950.1560.3262.281100
2.73-2.824.20.23512100.9560.1280.2682.254100
2.82-2.924.10.20812530.9540.1150.2382.164100
2.92-3.044.20.17512290.9690.0960.22.5100
3.04-3.184.20.15112200.9770.0830.1732.632100
3.18-3.354.20.1212450.9840.0670.1382.817100
3.35-3.564.10.10612420.9860.0580.1213.218100
3.56-3.834.20.08712380.990.0480.0993.272100
3.83-4.224.20.07412470.9920.0410.0853.739100
4.22-4.824.20.0612410.9950.0330.0694.028100
4.82-6.084.20.06212540.9940.0330.072.669100
6.08-5040.08713030.9870.0480.17.01399.6

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation6.94 Å37.4 Å
Translation6.94 Å37.4 Å

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Processing

Software
NameVersionClassification
HKL-2000data scaling
PHASER2.6.0phasing
PHENIX1.13_2998refinement
PDB_EXTRACT3.25data extraction
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6UPB

6upb


Resolution: 2.244→37.402 Å / SU ML: 0.27 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 24.29 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.232 2009 8.19 %
Rwork0.1862 22519 -
obs0.19 24528 99.28 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 101.68 Å2 / Biso mean: 43.978 Å2 / Biso min: 20.13 Å2
Refinement stepCycle: final / Resolution: 2.244→37.402 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3772 0 62 172 4006
Biso mean--49.95 44.98 -
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 (%)
2.244-2.30.29581300.2421148492
2.3-2.36220.26871430.2468156398
2.3622-2.43170.30011470.22611610100
2.4317-2.51010.26541380.22861607100
2.5101-2.59980.25521500.21271610100
2.5998-2.70390.29711410.21391602100
2.7039-2.82690.26661430.2081592100
2.8269-2.97590.24761440.20961613100
2.9759-3.16220.24571460.19971623100
3.1622-3.40630.22711430.18991620100
3.4063-3.74880.24071480.18091624100
3.7488-4.29050.21371420.15791635100
4.2905-5.4030.19871410.15661644100
5.403-37.40.19931530.17311692100

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