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- PDB-5dxi: Structure of C. albicans Trehalose-6-phosphate phosphatase C-term... -

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Basic information

Entry
Database: PDB / ID: 5dxi
TitleStructure of C. albicans Trehalose-6-phosphate phosphatase C-terminal domain
Componentstrehalose-6-phosphate phosphatase
KeywordsHYDROLASE / trehalose-6-phosphate phosphatase
Function / homology
Function and homology information


alpha,alpha-trehalose-phosphate synthase complex (UDP-forming) / trehalose metabolism in response to stress / negative regulation of flocculation / trehalose-phosphatase activity / filamentous growth of a population of unicellular organisms in response to starvation / alpha,alpha-trehalose-phosphate synthase (UDP-forming) activity / trehalose biosynthetic process / fungal-type cell wall organization / filamentous growth / cellular response to osmotic stress ...alpha,alpha-trehalose-phosphate synthase complex (UDP-forming) / trehalose metabolism in response to stress / negative regulation of flocculation / trehalose-phosphatase activity / filamentous growth of a population of unicellular organisms in response to starvation / alpha,alpha-trehalose-phosphate synthase (UDP-forming) activity / trehalose biosynthetic process / fungal-type cell wall organization / filamentous growth / cellular response to osmotic stress / cellular response to starvation / cellular response to heat / cellular response to oxidative stress / 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 / BERYLLIUM TRIFLUORIDE ION / Trehalose-phosphatase
Similarity search - Component
Biological speciesCandida albicans (yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2 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 6, 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 / diffrn_radiation_wavelength / 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_assembly_gen / pdbx_struct_conn_angle / struct_asym / 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_assembly_gen.asym_id_list / _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.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_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.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_asym.entity_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Mar 6, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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)69,1778
Polymers68,3122
Non-polymers8656
Water7,116395
1
A: trehalose-6-phosphate phosphatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,5894
Polymers34,1561
Non-polymers4333
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: trehalose-6-phosphate phosphatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,5894
Polymers34,1561
Non-polymers4333
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)58.757, 87.200, 139.271
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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


Mass: 34155.891 Da / Num. of mol.: 2 / Fragment: phosphatase domain (UNP residues 535-833)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Candida albicans (yeast) / Strain: SC5314 / ATCC MYA-2876 / Gene: TPS2, CaO19.10556, CaO19.3038, I503_00327, W5Q_00328 / Production host: Escherichia coli (E. coli)
References: UniProt: Q5AI14, alpha,alpha-trehalose-phosphate synthase (UDP-forming)
#2: Polysaccharide alpha-D-glucopyranose-(1-1)-alpha-D-glucopyranose / trehalose


Type: oligosaccharide, Oligosaccharide / Class: Nutrient / Mass: 342.297 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: oligosaccharide with reducing-end-to-reducing-end glycosidic bond
References: trehalose
DescriptorTypeProgram
DGlcpa1-1DGlcpaGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1a_1-5]/1-1/a1-b1WURCSPDB2Glycan 1.1.0
[][a-D-Glcp]{[(1+1)][a-D-Glcp]{}}LINUCSPDB-CARE
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: Mg
#4: Chemical ChemComp-BEF / BERYLLIUM TRIFLUORIDE ION


Mass: 66.007 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: BeF3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 395 / 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: 2.62 Å3/Da / Density % sol: 53.03 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop
Details: 0.1 M Tris, 0.2 M lithium sulfate, 2 M ammonium sulfate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.1 / Wavelength: 0.97741 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Feb 28, 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→50 Å / Num. obs: 49245 / % possible obs: 99.9 % / Redundancy: 4.8 % / Biso Wilson estimate: 34.43 Å2 / Rmerge(I) obs: 0.053 / Rpim(I) all: 0.027 / Rrim(I) all: 0.06 / Χ2: 1.173 / Net I/av σ(I): 31.516 / Net I/σ(I): 11 / Num. measured all: 236274
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2-2.034.70.52724620.9190.2720.5940.783100
2.03-2.074.70.46624090.9240.240.5251.062100
2.07-2.114.90.43524260.9530.2190.4880.881100
2.11-2.154.90.36524220.9540.1830.4090.843100
2.15-2.24.90.30424080.970.1520.3410.85100
2.2-2.254.80.27124600.9740.1370.3041.29199.9
2.25-2.314.90.24323990.9810.1220.2720.918100
2.31-2.374.90.17824590.9880.0890.20.858100
2.37-2.444.90.1524510.9910.0750.1680.866100
2.44-2.524.90.13424160.9930.0670.150.888100
2.52-2.614.90.11424590.9950.0570.1280.933100
2.61-2.714.90.10324470.9950.0520.1161.033100
2.71-2.844.90.07924540.9970.040.0890.986100
2.84-2.994.90.06524480.9980.0330.0731.04499.9
2.99-3.174.90.0624720.9970.0310.0681.499.9
3.17-3.424.80.05824850.9970.030.0652.111100
3.42-3.764.60.04824690.9980.0250.0552.54599.8
3.76-4.314.60.04425040.9980.0230.052.53999.8
4.31-5.434.60.02425430.9990.0130.0270.98999.9
5.43-504.60.02265210.010.0220.78298.9

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Processing

Software
NameVersionClassification
PHENIXrefinement
HKL-2000data scaling
PDB_EXTRACT3.15data extraction
HKL-2000data reduction
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 2→36.426 Å / FOM work R set: 0.8024 / SU ML: 0.23 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 26.56 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2416 1998 4.07 %
Rwork0.1995 47139 -
obs0.2011 49137 99.7 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 84.17 Å2 / Biso mean: 38.94 Å2 / Biso min: 18.31 Å2
Refinement stepCycle: final / Resolution: 2→36.426 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4602 0 56 395 5053
Biso mean--29.27 42.83 -
Num. residues----579
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0084757
X-RAY DIFFRACTIONf_angle_d1.0996439
X-RAY DIFFRACTIONf_chiral_restr0.047710
X-RAY DIFFRACTIONf_plane_restr0.006828
X-RAY DIFFRACTIONf_dihedral_angle_d13.7161804
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 (%)
1.9985-2.04850.29971390.25653276341598
2.0485-2.10390.2871410.252433423483100
2.1039-2.16580.28391390.237932893428100
2.1658-2.23570.28251420.22333463488100
2.2357-2.31560.2921420.246933263468100
2.3156-2.40830.28651410.21333323473100
2.4083-2.51790.24511420.216533403482100
2.5179-2.65060.27791420.211133633505100
2.6506-2.81660.28441430.22233673510100
2.8166-3.0340.27141430.214633573500100
3.034-3.33910.27021430.213333833526100
3.3391-3.82180.2341440.189733973541100
3.8218-4.81330.20241460.164834483594100
4.8133-36.43210.19511510.18193573372499

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