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- PDB-5dxn: Structure of Aspergillus fumigatus trehalose-6-phosphate phosphat... -

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Basic information

Entry
Database: PDB / ID: 5dxn
TitleStructure of Aspergillus fumigatus trehalose-6-phosphate phosphatase crystal form 2
Componentstrehalose-6-phosphate phosphatase
KeywordsHYDROLASE / trehalose-6-phosphate / phosphatase
Function / homology
Function and homology information


asexual sporulation resulting in formation of a cellular spore / alpha,alpha-trehalose-phosphate synthase complex (UDP-forming) / hyphal growth / alpha,alpha-trehalose-phosphate synthase (UDP-forming) / trehalose-phosphatase activity / alpha,alpha-trehalose-phosphate synthase (UDP-forming) activity / trehalose biosynthetic process / fungal-type cell wall organization / cellular response to nitrogen starvation / positive regulation of autophagy ...asexual sporulation resulting in formation of a cellular spore / alpha,alpha-trehalose-phosphate synthase complex (UDP-forming) / hyphal growth / alpha,alpha-trehalose-phosphate synthase (UDP-forming) / trehalose-phosphatase activity / alpha,alpha-trehalose-phosphate synthase (UDP-forming) activity / trehalose biosynthetic process / fungal-type cell wall organization / cellular response to nitrogen starvation / positive regulation of autophagy / cellular response to heat / metal ion binding
Similarity search - Function
Trehalose-phosphatase / Trehalose-phosphatase / Glycosyl transferase, family 20 / Glycosyltransferase family 20 / HAD-superfamily hydrolase, subfamily IIB / HAD superfamily / HAD-like superfamily
Similarity search - Domain/homology
Alpha,alpha-trehalose-phosphate synthase subunit Tps2, putative
Similarity search - Component
Biological speciesNeosartorya fumigata (mold)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.65 Å
AuthorsMiao, Y. / Brennan, R.G.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)1P01 AI104533-01A1 United States
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2016
Title: Structures of trehalose-6-phosphate phosphatase from pathogenic fungi reveal the mechanisms of substrate recognition and catalysis.
Authors: Miao, Y. / Tenor, J.L. / Toffaletti, D.L. / Washington, E.J. / Liu, J. / Shadrick, W.R. / Schumacher, M.A. / Lee, R.E. / Perfect, J.R. / Brennan, R.G.
History
DepositionSep 23, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 15, 2016Provider: repository / Type: Initial release
Revision 1.1Jun 29, 2016Group: Database references
Revision 1.2Jul 13, 2016Group: Database references
Revision 1.3Sep 13, 2017Group: Author supporting evidence / Database references / Derived calculations
Category: citation / pdbx_audit_support / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.4Dec 11, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5Sep 27, 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

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Assembly

Deposited unit
A: trehalose-6-phosphate phosphatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,7002
Polymers32,6761
Non-polymers241
Water4,324240
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area110 Å2
ΔGint-9 kcal/mol
Surface area13430 Å2
MethodPISA
Unit cell
Length a, b, c (Å)39.843, 42.672, 80.221
Angle α, β, γ (deg.)90.000, 99.460, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein trehalose-6-phosphate phosphatase / Alpha / alpha-trehalose-phosphate synthase subunit Tps2


Mass: 32675.988 Da / Num. of mol.: 1 / Fragment: UNP residues 674-949
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Neosartorya fumigata (mold) / Strain: ATCC MYA-4609 / Af293 / CBS 101355 / FGSC A1100 / Gene: AFUA_3G05650 / Production host: Escherichia coli (E. coli)
References: UniProt: Q4WWF5, alpha,alpha-trehalose-phosphate synthase (UDP-forming)
#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.: 240 / 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: 2.06 Å3/Da / Density % sol: 40.25 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: 0.1 M HEPES, 15% PEG20000

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Data collection

DiffractionMean temperature: 200 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: Jul 31, 2015
RadiationMonochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.65→50 Å / Num. obs: 31571 / % possible obs: 97.1 % / Redundancy: 3.5 % / Rmerge(I) obs: 0.077 / Rpim(I) all: 0.048 / Rrim(I) all: 0.091 / Χ2: 1.631 / Net I/av σ(I): 19.4 / Net I/σ(I): 14 / Num. measured all: 110336
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.65-1.682.20.52113070.6920.3970.6580.7580.3
1.68-1.712.80.47815360.730.3360.5880.75196.1
1.71-1.743.30.45816100.8180.2980.5480.84699
1.74-1.783.50.37616060.8830.2350.4440.84399.2
1.78-1.823.50.31416060.930.1950.370.98799.2
1.82-1.863.60.26415630.9450.1620.3111.03199.2
1.86-1.93.60.22816180.9520.1410.2691.21799.6
1.9-1.963.70.18716000.9540.1150.221.42499.6
1.96-2.013.70.15716210.970.0950.1841.64399.6
2.01-2.083.70.12615960.9820.0770.1481.76599.3
2.08-2.153.70.10516050.9850.0650.1231.96799.1
2.15-2.243.70.0916170.9870.0560.1072.18599.1
2.24-2.343.70.08116120.9890.050.0952.08599.3
2.34-2.463.70.07716020.9880.0480.0912.32699.4
2.46-2.623.70.06916060.9910.0430.0812.12299.1
2.62-2.823.70.0716340.9890.0430.0832.05299.5
2.82-3.113.70.07416260.9860.0450.0872.04699.3
3.11-3.553.70.06516240.990.040.0761.94799.5
3.55-4.483.50.05716170.9930.0360.0681.7397.1
4.48-503.10.05813650.9910.0380.071.83480.5

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Processing

Software
NameVersionClassification
HKL-2000data scaling
PHENIXrefinement
PDB_EXTRACT3.15data extraction
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 5DXL

5dxl


Resolution: 1.65→20.6 Å / FOM work R set: 0.7933 / SU ML: 0.18 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 27.27 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2533 1985 6.29 %
Rwork0.2187 29559 -
obs0.2209 31544 97.2 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 64.58 Å2 / Biso mean: 29.63 Å2 / Biso min: 10.79 Å2
Refinement stepCycle: final / Resolution: 1.65→20.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2122 0 1 240 2363
Biso mean--19.21 38.44 -
Num. residues----265
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072169
X-RAY DIFFRACTIONf_angle_d1.0482927
X-RAY DIFFRACTIONf_chiral_restr0.044313
X-RAY DIFFRACTIONf_plane_restr0.004379
X-RAY DIFFRACTIONf_dihedral_angle_d13.267805
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.6467-1.68790.30471180.25021814193285
1.6879-1.73350.29511470.2532156230398
1.7335-1.78450.27771480.23342115226399
1.7845-1.84210.25971360.22712158229499
1.8421-1.90790.25611550.23112142229799
1.9079-1.98420.2851450.221221392284100
1.9842-2.07440.24221530.22522126227999
2.0744-2.18370.28731370.21942149228699
2.1837-2.32030.27651420.22482161230399
2.3203-2.49920.25641420.22642159230199
2.4992-2.75020.25221420.22932166230899
2.7502-3.14690.24441470.22762157230499
3.1469-3.96010.23381470.20032190233799
3.9601-20.60190.24281260.20791927205386

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