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- PDB-4ofz: Structure of unliganded trehalose-6-phosphate phosphatase from Br... -

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Basic information

Entry
Database: PDB / ID: 4ofz
TitleStructure of unliganded trehalose-6-phosphate phosphatase from Brugia malayi
ComponentsTrehalose-phosphatase
KeywordsHYDROLASE / HAD superfamily/Rossmann fold / trehalose-6-phosphate phosphohydrolase
Function / homology
Function and homology information


trehalose-phosphatase / carbohydrate derivative catabolic process / trehalose-phosphatase activity / trehalose biosynthetic process / dephosphorylation / magnesium ion binding
Similarity search - Function
Methane Monooxygenase Hydroxylase; Chain G, domain 1 - #1800 / Alpha-Beta Plaits - #3080 / Trehalose-6-phosphate phosphatase, helical bundle domain / : / Trehalose-6-phosphate phosphatase N-terminal helical bundle domain / Trehalose-6-phosphate phosphatase, C-terminal / HAD superfamily/HAD-like / Methane Monooxygenase Hydroxylase; Chain G, domain 1 / HAD superfamily / HAD-like superfamily ...Methane Monooxygenase Hydroxylase; Chain G, domain 1 - #1800 / Alpha-Beta Plaits - #3080 / Trehalose-6-phosphate phosphatase, helical bundle domain / : / Trehalose-6-phosphate phosphatase N-terminal helical bundle domain / Trehalose-6-phosphate phosphatase, C-terminal / HAD superfamily/HAD-like / Methane Monooxygenase Hydroxylase; Chain G, domain 1 / HAD superfamily / HAD-like superfamily / Alpha-Beta Plaits / Up-down Bundle / Rossmann fold / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Trehalose-phosphatase
Similarity search - Component
Biological speciesBrugia malayi (agent of lymphatic filariasis)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 3 Å
AuthorsFarelli, J.D. / Allen, K.N. / Carlow, C.K.S. / Dunaway-Mariano, D.
CitationJournal: Plos Pathog. / Year: 2014
Title: Structure of the Trehalose-6-phosphate Phosphatase from Brugia malayi Reveals Key Design Principles for Anthelmintic Drugs.
Authors: Farelli, J.D. / Galvin, B.D. / Li, Z. / Liu, C. / Aono, M. / Garland, M. / Hallett, O.E. / Causey, T.B. / Ali-Reynolds, A. / Saltzberg, D.J. / Carlow, C.K. / Dunaway-Mariano, D. / Allen, K.N.
History
DepositionJan 15, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 16, 2014Provider: repository / Type: Initial release
Revision 1.1Jan 24, 2018Group: Structure summary / Category: audit_author / Item: _audit_author.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Trehalose-phosphatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,6822
Polymers57,6571
Non-polymers241
Water1,56787
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Trehalose-phosphatase
hetero molecules

A: Trehalose-phosphatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)115,3634
Polymers115,3152
Non-polymers492
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_555-y,-x,-z+1/31
Buried area2340 Å2
ΔGint-25 kcal/mol
Surface area35800 Å2
MethodPISA
Unit cell
Length a, b, c (Å)166.940, 166.940, 99.562
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number181
Space group name H-MP6422

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Components

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


Mass: 57657.297 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Brugia malayi (agent of lymphatic filariasis)
Gene: Bm1_08695 / Plasmid: pET-15(TEV) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: A8NS89, trehalose-phosphatase
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 87 / 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: 3.47 Å3/Da / Density % sol: 64.58 %
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop / pH: 5
Details: 15 mg/ml, crystallization buffer: 33% PEG 300, 0.1 M sodium citrate pH 5.0, 13% ethylene glycol (EG) and 10 mM CoCl2. For cryoprotection, the concentration of EG was slowly increased to 25% ...Details: 15 mg/ml, crystallization buffer: 33% PEG 300, 0.1 M sodium citrate pH 5.0, 13% ethylene glycol (EG) and 10 mM CoCl2. For cryoprotection, the concentration of EG was slowly increased to 25% by adding a concentrated solution directly to the crystal drop. Crystals were harvested using CryoLoops (Hampton Research), looped through LV CryoOil (MiTeGen), frozen in liquid nitrogen, VAPOR DIFFUSION, HANGING DROP, temperature 290K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 0.9795 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.9→20 Å / Num. obs: 16791

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Processing

Software
NameVersionClassification
HKL-3000data collection
MLPHAREphasing
PHENIX(phenix.refine: 1.8.2_1309)refinement
HKL-3000data reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: SAD / Resolution: 3→19.908 Å / SU ML: 0.37 / σ(F): 1.35 / Phase error: 30.76 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2732 1679 10 %
Rwork0.2157 --
obs0.2213 16791 99.96 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3→19.908 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3296 0 1 87 3384
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0133354
X-RAY DIFFRACTIONf_angle_d1.7224525
X-RAY DIFFRACTIONf_dihedral_angle_d16.7581258
X-RAY DIFFRACTIONf_chiral_restr0.065517
X-RAY DIFFRACTIONf_plane_restr0.008577
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3-3.0880.32121360.28451228X-RAY DIFFRACTION100
3.088-3.18730.36751360.24971224X-RAY DIFFRACTION100
3.1873-3.30070.34441370.25141230X-RAY DIFFRACTION100
3.3007-3.43220.33661370.25651243X-RAY DIFFRACTION100
3.4322-3.58750.33441370.23171233X-RAY DIFFRACTION100
3.5875-3.77550.25821390.23051244X-RAY DIFFRACTION100
3.7755-4.01020.25791390.21181254X-RAY DIFFRACTION100
4.0102-4.31690.24721400.21261X-RAY DIFFRACTION100
4.3169-4.7460.23461390.18051258X-RAY DIFFRACTION100
4.746-5.42070.26751420.20541269X-RAY DIFFRACTION100
5.4207-6.78430.34011440.25411294X-RAY DIFFRACTION100
6.7843-19.90860.2191530.19121374X-RAY DIFFRACTION100

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