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- PDB-5dx9: Structure of trehalose-6-phosphate phosphatase from Cryptococcus ... -

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Basic information

Entry
Database: PDB / ID: 5dx9
TitleStructure of trehalose-6-phosphate phosphatase from Cryptococcus neoformans
Componentstrehalose-6-phosphate phosphatase
KeywordsHYDROLASE / trehalose-6-phosphate / phosphatase
Function / homology
Function and homology information


trehalose-phosphatase activity / trehalose biosynthetic process / 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
trehalose-6-phosphate / BETA-MERCAPTOETHANOL / Trehalose-6-phosphate phosphatase
Similarity search - Component
Biological speciesCryptococcus neoformans (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.15 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 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Non-polymer description / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / entity_name_com / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_molecule_features / pdbx_nonpoly_scheme / pdbx_struct_conn_angle / struct_conn / struct_conn_type / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.pdbx_synonyms / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.src_method / _entity.type / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.value / _struct_conn_type.id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)36,3714
Polymers35,8471
Non-polymers5253
Water1,72996
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1150 Å2
ΔGint-8 kcal/mol
Surface area14430 Å2
MethodPISA
Unit cell
Length a, b, c (Å)63.074, 63.074, 284.315
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number178
Space group name H-MP6122
Components on special symmetry positions
IDModelComponents
11A-579-

HOH

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Components

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


Mass: 35846.508 Da / Num. of mol.: 1 / Fragment: UNP residues 682-987
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Cryptococcus neoformans (fungus) / Gene: TPS2, CNAG_03765 / Production host: Escherichia coli (E. coli)
References: UniProt: Q059G6, alpha,alpha-trehalose-phosphate synthase (UDP-forming)
#2: Polysaccharide 6-O-phosphono-alpha-D-glucopyranose-(1-1)-alpha-D-glucopyranose / trehalose-6-phosphate


Type: oligosaccharide, Oligosaccharide / Class: Substrate analog / Mass: 422.277 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: oligosaccharide with reducing-end-to-reducing-end glycosidic bond
References: trehalose-6-phosphate
DescriptorTypeProgram
WURCS=2.0/2,2,1/[a2122h-1a_1-5][a2122h-1a_1-5_6*OPO/3O/3=O]/1-2/a1-b1WURCSPDB2Glycan 1.1.0
[][a-D-Glcp]{[(1+1)][a-D-Glcp]{[(6+0)][P]{}}}LINUCSPDB-CARE
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-BME / BETA-MERCAPTOETHANOL


Mass: 78.133 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6OS
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 96 / 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: 2.36 Å3/Da / Density % sol: 47.87 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.5 / Details: 0.1 M magnesium chloride, 20% PEG400, 10% PEG8000

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Data collection

DiffractionMean temperature: 200 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.1 / Wavelength: 0.97741 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 26, 2015
RadiationMonochromator: Si(220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97741 Å / Relative weight: 1
ReflectionResolution: 2.15→50 Å / Num. obs: 19314 / % possible obs: 99.3 % / Redundancy: 9.9 % / Biso Wilson estimate: 50.03 Å2 / Rmerge(I) obs: 0.088 / Rpim(I) all: 0.03 / Rrim(I) all: 0.093 / Χ2: 1.182 / Net I/av σ(I): 25.466 / Net I/σ(I): 10.3 / Num. measured all: 192164
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.15-2.199.60.8839580.7940.2980.9330.719100
2.19-2.2310.40.759310.8610.2410.7880.713100
2.23-2.2710.40.69360.9220.1930.6310.721100
2.27-2.3210.50.5129250.9240.1630.5380.733100
2.32-2.3710.50.4549370.9430.1450.4770.764100
2.37-2.4210.40.4019670.9550.1280.4210.793100
2.42-2.4810.30.3299230.9650.1060.3470.825100
2.48-2.5510.50.289530.9790.0890.2940.838100
2.55-2.6210.30.2399560.9810.0770.2520.898100
2.62-2.7110.40.1979380.9860.0630.2071.018100
2.71-2.8110.30.1579520.9920.050.1651.035100
2.81-2.9210.30.1389710.9950.0440.1451.14100
2.92-3.0510.20.129610.9950.0380.1261.324100
3.05-3.2110.10.0979640.9970.0310.1021.44599.8
3.21-3.41100.0849720.9980.0270.0891.58499.9
3.41-3.689.70.0749820.9970.0240.0781.72299.5
3.68-4.059.50.0849840.9930.0280.0881.96299.1
4.05-4.638.70.0899850.9920.0320.0952.43697.8
4.63-5.838.70.07110120.9960.0250.0761.86197.2
5.83-508.50.05211070.9980.0180.0561.41894.2

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Processing

Software
NameVersionClassification
PHENIXrefinement
HKL-2000data collection
PDB_EXTRACT3.15data extraction
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.15→43.311 Å / FOM work R set: 0.7338 / SU ML: 0.3 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 29.6 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.267 1924 10 %
Rwork0.23 17317 -
obs0.2336 19241 99.45 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 136.87 Å2 / Biso mean: 52.84 Å2 / Biso min: 34.09 Å2
Refinement stepCycle: final / Resolution: 2.15→43.311 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2412 0 61 96 2569
Biso mean--51.87 49.56 -
Num. residues----307
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0032497
X-RAY DIFFRACTIONf_angle_d0.7233398
X-RAY DIFFRACTIONf_chiral_restr0.027390
X-RAY DIFFRACTIONf_plane_restr0.003439
X-RAY DIFFRACTIONf_dihedral_angle_d12.875942
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 (%)
2.15-2.20370.37141330.311112021335100
2.2037-2.26330.37651360.291612161352100
2.2633-2.32990.37011330.296512011334100
2.3299-2.40510.33571330.289311991332100
2.4051-2.49110.32941370.301512221359100
2.4911-2.59080.34961320.274211971329100
2.5908-2.70870.29691360.272412231359100
2.7087-2.85150.32141350.29412321367100
2.8515-3.03010.30951380.300212301368100
3.0301-3.2640.32691370.27912321369100
3.264-3.59230.28191390.23921245138499
3.5923-4.11170.24811380.20671257139599
4.1117-5.1790.20631420.17691274141697
5.179-43.32020.2141550.18961387154298

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