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

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Basic information

Entry
Database: PDB / ID: 5dxo
TitleStructure of Aspergillus fumigatus trehalose-6-phosphate phosphatase crystal form 3
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) / : / alpha,alpha-trehalose-phosphate synthase (UDP-forming) / hyphal growth / trehalose-phosphatase activity / alpha,alpha-trehalose-phosphate synthase (UDP-forming) activity / trehalose biosynthetic process / fungal-type cell wall organization / cellular response to nitrogen starvation ...asexual sporulation resulting in formation of a cellular spore / alpha,alpha-trehalose-phosphate synthase complex (UDP-forming) / : / alpha,alpha-trehalose-phosphate synthase (UDP-forming) / hyphal growth / 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: 1.9 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 ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)65,4014
Polymers65,3522
Non-polymers492
Water3,351186
1
A: trehalose-6-phosphate phosphatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,7002
Polymers32,6761
Non-polymers241
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: trehalose-6-phosphate phosphatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,7002
Polymers32,6761
Non-polymers241
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)44.963, 76.787, 83.686
Angle α, β, γ (deg.)90.000, 94.350, 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.: 2 / 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.: 2 / Source method: obtained synthetically / Formula: Mg
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 186 / 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: 2.2 Å3/Da / Density % sol: 44.2 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 0.1 M HEPES, 12% PEG3350

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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: 1.9→50 Å / Num. obs: 44707 / % possible obs: 99.2 % / Redundancy: 3.7 % / Biso Wilson estimate: 39.33 Å2 / Rmerge(I) obs: 0.07 / Rpim(I) all: 0.042 / Rrim(I) all: 0.082 / Χ2: 1.83 / Net I/av σ(I): 27.877 / Net I/σ(I): 12.7 / Num. measured all: 166375
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.9-1.933.50.56822290.7250.3570.6730.816100
1.93-1.973.60.47222660.8050.2920.5560.82599.9
1.97-2.013.70.37522180.8680.2290.4410.887100
2.01-2.053.70.33222710.8840.2010.3890.963100
2.05-2.093.70.27922070.9120.1680.3261.105100
2.09-2.143.80.23622700.9280.1420.2761.219100
2.14-2.193.70.19622230.9480.1180.2291.428100
2.19-2.253.80.17522540.960.1050.2041.544100
2.25-2.323.80.14822180.9670.0880.1731.593100
2.32-2.393.80.13422780.9740.080.1561.791100
2.39-2.483.80.11922230.9760.0710.1391.923100
2.48-2.583.80.10622390.9820.0630.1231.962100
2.58-2.73.80.09722650.9830.0580.1132.086100
2.7-2.843.80.08722640.9860.0520.1022.218100
2.84-3.023.80.07922420.9890.0470.0912.38199.9
3.02-3.253.80.07222500.990.0430.0842.515100
3.25-3.583.80.06622520.9920.040.0772.826100
3.58-4.093.80.0622800.9940.0350.0692.792100
4.09-5.163.70.05822680.9910.0360.0682.73199.5
5.16-503.50.06119900.9890.0380.0732.94885.6

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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: 1.9→31.768 Å / FOM work R set: 0.7662 / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 25.84 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2499 2000 4.48 %
Rwork0.207 42681 -
obs0.2089 44681 98.71 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 108.05 Å2 / Biso mean: 45.7 Å2 / Biso min: 20 Å2
Refinement stepCycle: final / Resolution: 1.9→31.768 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4344 0 2 186 4532
Biso mean--37.36 48.04 -
Num. residues----544
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0084446
X-RAY DIFFRACTIONf_angle_d1.0566012
X-RAY DIFFRACTIONf_chiral_restr0.045640
X-RAY DIFFRACTIONf_plane_restr0.005786
X-RAY DIFFRACTIONf_dihedral_angle_d14.0331656
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 (%)
1.8934-1.94070.29021360.25092848298493
1.9407-1.99320.30571520.250230603212100
1.9932-2.05180.30231300.243330783208100
2.0518-2.1180.27351430.234830843227100
2.118-2.19370.25451550.225530713226100
2.1937-2.28150.31231370.220930803217100
2.2815-2.38530.28781420.224330873229100
2.3853-2.51110.26651510.224630573208100
2.5111-2.66830.25321440.229530823226100
2.6683-2.87420.2911420.233230993241100
2.8742-3.16320.2521460.230130903236100
3.1632-3.62040.27221430.2130883231100
3.6204-4.55920.23061470.180131163263100
4.5592-31.77290.20471320.18452841297390

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