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- PDB-5e0o: Brugia malayi Trehalose-6 Phosphate Phosphatase in complex with P... -

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Basic information

Entry
Database: PDB / ID: 5e0o
TitleBrugia malayi Trehalose-6 Phosphate Phosphatase in complex with PEG at the active site.
ComponentsTrehalose-phosphatase
KeywordsHYDROLASE / HAD / Complex / Phosphatase
Function / homology
Function and homology information


trehalose-phosphatase / trehalose-phosphatase activity / carbohydrate derivative catabolic process / 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
DI(HYDROXYETHYL)ETHER / Trehalose-phosphatase
Similarity search - Component
Biological speciesBrugia malayi (agent of lymphatic filariasis)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsAgarwal, A. / Misra-Bhattacharya, S. / Ravishankar, R.
Funding support India, 1items
OrganizationGrant numberCountry
Council of Scientific and Industrial ResearchBSC0104 India
Citation
Journal: To Be Published / Year: 2015
Title: Brugia malayi Trehalose Phosphate Phosphatase in complex with PEG at the active site
Authors: Agarwal, A. / Misra-Bhattacharya, S. / Ravishankar, R.
#1: Journal: 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
DepositionSep 29, 2015Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Oct 28, 2015Provider: repository / Type: Initial release
Revision 1.1Nov 8, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2 / pdbx_initial_refinement_model / pdbx_prerelease_seq / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _database_2.pdbx_DOI ..._citation.journal_id_CSD / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Trehalose-phosphatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,9674
Polymers58,7411
Non-polymers2263
Water84747
1
A: Trehalose-phosphatase
hetero molecules

A: Trehalose-phosphatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)117,9348
Polymers117,4812
Non-polymers4536
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_555-y,-x,-z+1/31
Buried area3330 Å2
ΔGint-68 kcal/mol
Surface area34980 Å2
MethodPISA
Unit cell
Length a, b, c (Å)167.931, 167.931, 102.956
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number181
Space group name H-MP6422
Components on special symmetry positions
IDModelComponents
11A-619-

HOH

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Components

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


Mass: 58740.660 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 / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / 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: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 47 / 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: 3.57 Å3/Da / Density % sol: 65.52 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: Large good diffractable crystal grow with in 7-8 days.
PH range: 6.0-7.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.987 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Dec 8, 2013
RadiationMonochromator: Si (III) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.987 Å / Relative weight: 1
ReflectionResolution: 3→43.859 Å / Num. obs: 18275 / % possible obs: 99.5 % / Redundancy: 25.6 % / Rmerge(I) obs: 0.144 / Net I/σ(I): 16.25
Reflection shellResolution: 3→3.2 Å / Redundancy: 20.4 % / Rmerge(I) obs: 0.8 / Mean I/σ(I) obs: 2 / % possible all: 98.6

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Processing

Software
NameVersionClassification
PHENIX1.9-1692refinement
HKL-2000data scaling
PDB_EXTRACT3.15data extraction
HKL-2000data reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4OFZ

4ofz


Resolution: 3→43.859 Å / SU ML: 0.33 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 25.53 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2574 788 5.17 %
Rwork0.2182 --
obs0.2202 15235 86.37 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 244.89 Å2 / Biso mean: 53.0636 Å2 / Biso min: 3.66 Å2
Refinement stepCycle: final / Resolution: 3→43.859 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3291 0 13 47 3351
Biso mean--54.08 26.01 -
Num. residues----418
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)
10.77670.4360.09240.49330.06260.11730.1018-0.10420.42840.3766-0.05070.4483-0.1276-0.1385-0.10840.3837-0.03080.17810.18230.0110.446363.3019-6.152321.7835
20.28570.1775-0.14520.3577-0.35150.55890.08410.10490.1995-0.10870.06670.3050.1341-0.32050.17430.2848-0.0845-0.03870.27340.07690.369762.4737-20.54583.8292
30.27270.1550.03120.1924-0.0350.2122-0.0106-0.0642-0.15020.1112-0.0051-0.0619-0.06290.107-0.00290.39-0.11060.01080.24550.04980.356275.4149-27.951218.3223
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 63 through 204 )A0
2X-RAY DIFFRACTION2chain 'A' and (resid 205 through 388 )A0
3X-RAY DIFFRACTION3chain 'A' and (resid 389 through 491 )A0

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