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Entry
Database: PDB / ID: 5hut
TitleStructure of Candida albicans trehalose-6-phosphate synthase in complex with UDP-glucose
ComponentsAlpha,alpha-trehalose-phosphate synthase [UDP-forming]
KeywordsTRANSFERASE / trehalose-6-phosphate synthase
Function / homology
Function and homology information


filamentous growth of a population of unicellular organisms in response to heat / cellular response to desiccation / filamentous growth of a population of unicellular organisms in response to biotic stimulus / alpha,alpha-trehalose-phosphate synthase (UDP-forming) / alpha,alpha-trehalose-phosphate synthase (UDP-forming) activity / alpha,alpha-trehalose-phosphate synthase complex (UDP-forming) / trehalose-phosphatase activity / trehalose biosynthetic process / trehalose metabolism in response to stress / filamentous growth ...filamentous growth of a population of unicellular organisms in response to heat / cellular response to desiccation / filamentous growth of a population of unicellular organisms in response to biotic stimulus / alpha,alpha-trehalose-phosphate synthase (UDP-forming) / alpha,alpha-trehalose-phosphate synthase (UDP-forming) activity / alpha,alpha-trehalose-phosphate synthase complex (UDP-forming) / trehalose-phosphatase activity / trehalose biosynthetic process / trehalose metabolism in response to stress / filamentous growth / cellular response to heat / cytosol
Similarity search - Function
Alpha,alpha-trehalose-phosphate synthase / Glycosyl transferase, family 20 / Glycosyltransferase family 20 / Glycogen Phosphorylase B; / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
URIDINE-5'-DIPHOSPHATE-GLUCOSE / Alpha,alpha-trehalose-phosphate synthase [UDP-forming]
Similarity search - Component
Biological speciesCandida albicans (yeast)
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)1P01AI104533-01A1 United States
CitationJournal: MBio / Year: 2017
Title: Structural and In Vivo Studies on Trehalose-6-Phosphate Synthase from Pathogenic Fungi Provide Insights into Its Catalytic Mechanism, Biological Necessity, and Potential for Novel Antifungal Drug Design.
Authors: Miao, Y. / Tenor, J.L. / Toffaletti, D.L. / Maskarinec, S.A. / Liu, J. / Lee, R.E. / Perfect, J.R. / Brennan, R.G.
History
DepositionJan 27, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 3, 2017Provider: repository / Type: Initial release
Revision 1.1Sep 20, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Sep 27, 2017Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 2.0Sep 25, 2019Group: Advisory / Atomic model ...Advisory / Atomic model / Author supporting evidence / Data collection / Derived calculations / Non-polymer description / Other / Refinement description / Structure summary
Category: atom_site / atom_type ...atom_site / atom_type / cell / chem_comp / diffrn / entity / pdbx_entity_instance_feature / pdbx_entity_nonpoly / pdbx_entry_details / pdbx_nonpoly_scheme / pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / pdbx_struct_conn_angle / pdbx_struct_sheet_hbond / pdbx_validate_close_contact / pdbx_validate_symm_contact / pdbx_validate_torsion / pdbx_version / refine / refine_hist / refine_ls_restr / refine_ls_shell / reflns / software / struct / struct_asym / struct_conf / struct_conn / struct_mon_prot_cis / struct_sheet_range / struct_site / struct_site_gen / symmetry
Item: _cell.volume / _chem_comp.formula ..._cell.volume / _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 / _diffrn.pdbx_serial_crystal_experiment / _pdbx_struct_assembly.details / _pdbx_struct_assembly.method_details / _pdbx_struct_assembly_prop.value / _pdbx_struct_sheet_hbond.range_1_auth_comp_id / _pdbx_struct_sheet_hbond.range_1_auth_seq_id / _pdbx_struct_sheet_hbond.range_1_label_comp_id / _pdbx_struct_sheet_hbond.range_1_label_seq_id / _pdbx_struct_sheet_hbond.range_2_auth_comp_id / _pdbx_struct_sheet_hbond.range_2_auth_seq_id / _pdbx_struct_sheet_hbond.range_2_label_comp_id / _pdbx_struct_sheet_hbond.range_2_label_seq_id / _refine.B_iso_max / _refine.B_iso_mean / _refine.B_iso_min / _refine.details / _refine.ls_R_factor_R_free / _refine.ls_R_factor_R_work / _refine.ls_R_factor_obs / _refine.ls_d_res_low / _refine.ls_number_reflns_R_free / _refine.ls_number_reflns_R_work / _refine.ls_number_reflns_obs / _refine.ls_percent_reflns_obs / _refine.overall_FOM_work_R_set / _refine.overall_SU_ML / _refine.pdbx_ls_sigma_F / _refine.pdbx_overall_phase_error / _refine.pdbx_stereochemistry_target_values / _refine_hist.cycle_id / _refine_hist.d_res_low / _refine_hist.number_atoms_solvent / _refine_hist.number_atoms_total / _refine_hist.pdbx_B_iso_mean_ligand / _refine_hist.pdbx_B_iso_mean_solvent / _refine_hist.pdbx_number_atoms_ligand / _refine_hist.pdbx_number_residues_total / _refine_ls_restr.dev_ideal / _refine_ls_restr.number / _refine_ls_shell.R_factor_R_free / _refine_ls_shell.R_factor_R_work / _refine_ls_shell.d_res_high / _refine_ls_shell.d_res_low / _refine_ls_shell.number_reflns_R_free / _refine_ls_shell.number_reflns_R_work / _refine_ls_shell.number_reflns_all / _refine_ls_shell.pdbx_total_number_of_bins_used / _refine_ls_shell.percent_reflns_obs / _reflns.B_iso_Wilson_estimate / _software.classification / _software.name / _software.version / _struct.pdbx_CASP_flag / _struct_sheet_range.beg_auth_comp_id / _struct_sheet_range.beg_auth_seq_id / _struct_sheet_range.beg_label_comp_id / _struct_sheet_range.beg_label_seq_id / _struct_sheet_range.end_auth_comp_id / _struct_sheet_range.end_auth_seq_id / _struct_sheet_range.end_label_comp_id / _struct_sheet_range.end_label_seq_id / _symmetry.space_group_name_Hall
Description: Polymer geometry / Provider: author / Type: Coordinate replacement
Revision 2.1Dec 11, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 2.2Mar 6, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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
Revision 2.3Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Alpha,alpha-trehalose-phosphate synthase [UDP-forming]
B: Alpha,alpha-trehalose-phosphate synthase [UDP-forming]
hetero molecules


Theoretical massNumber of molelcules
Total (without water)111,94318
Polymers109,0422
Non-polymers2,90016
Water7,963442
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7570 Å2
ΔGint-153 kcal/mol
Surface area36920 Å2
MethodPISA
2
A: Alpha,alpha-trehalose-phosphate synthase [UDP-forming]
B: Alpha,alpha-trehalose-phosphate synthase [UDP-forming]
hetero molecules

A: Alpha,alpha-trehalose-phosphate synthase [UDP-forming]
B: Alpha,alpha-trehalose-phosphate synthase [UDP-forming]
hetero molecules


Theoretical massNumber of molelcules
Total (without water)223,88536
Polymers218,0854
Non-polymers5,80032
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_745-x+2,-y-1,z1
Buried area20340 Å2
ΔGint-322 kcal/mol
Surface area68640 Å2
MethodPISA
Unit cell
Length a, b, c (Å)98.714, 98.714, 187.653
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number172
Space group name H-MP64
Space group name HallP64

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Alpha,alpha-trehalose-phosphate synthase [UDP-forming] / Trehalose-6-phosphate synthase / UDP-glucose-glucosephosphate glucosyltransferase


Mass: 54521.172 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Candida albicans (strain SC5314 / ATCC MYA-2876) (yeast)
Strain: SC5314 / ATCC MYA-2876 / Gene: TPS1, CaO19.13961, CaO19.6640 / Production host: Escherichia coli (E. coli)
References: UniProt: Q92410, alpha,alpha-trehalose-phosphate synthase (UDP-forming)

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Non-polymers , 5 types, 458 molecules

#2: Chemical ChemComp-UPG / URIDINE-5'-DIPHOSPHATE-GLUCOSE / URIDINE-5'-MONOPHOSPHATE GLUCOPYRANOSYL-MONOPHOSPHATE ESTER


Mass: 566.302 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C15H24N2O17P2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: SO4
#4: Chemical
ChemComp-1PE / PENTAETHYLENE GLYCOL / PEG400


Mass: 238.278 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Formula: C10H22O6 / Comment: precipitant*YM
#5: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: Na
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 442 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 2.42 Å3/Da / Density % sol: 49.18 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.5 / Details: 0.2 M lithium sulfate, 0.1 M Tris, 40% PEG 400

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: RAYONIX MX300-HS / Detector: CCD / Date: Jun 12, 2014
RadiationProtocol: 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: 81397 / % possible obs: 99.9 % / Redundancy: 5.8 % / Biso Wilson estimate: 30.86 Å2 / Rmerge(I) obs: 0.066 / Rpim(I) all: 0.03 / Rrim(I) all: 0.072 / Χ2: 0.7 / Net I/av σ(I): 21.507 / Net I/σ(I): 8.1 / Num. measured all: 469403
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.9-1.935.60.67240310.9020.3120.7420.54299.9
1.93-1.975.70.57940770.9210.2650.6370.5599.8
1.97-2.015.70.47540350.950.2170.5230.56299.9
2.01-2.055.70.41840410.9490.190.4590.57599.9
2.05-2.095.80.34440900.9670.1570.3780.59299.9
2.09-2.145.80.28140690.9750.1280.3090.588100
2.14-2.195.80.23140710.9830.1050.2530.591100
2.19-2.255.80.19940710.9880.0910.2190.604100
2.25-2.325.80.17440030.990.0790.1910.62699.9
2.32-2.395.80.14540900.9910.0660.160.647100
2.39-2.485.80.12940800.9930.0590.1420.677100
2.48-2.585.80.10740600.9940.0490.1170.676100
2.58-2.75.80.0940930.9950.0410.0990.678100
2.7-2.845.80.07840490.9960.0350.0860.689100
2.84-3.025.80.06640750.9970.030.0720.712100
3.02-3.255.80.06240860.9970.0280.0680.881100
3.25-3.585.80.05740820.9970.0260.0631.017100
3.58-4.095.80.04540920.9980.020.0490.966100
4.09-5.165.80.0440900.9980.0180.0440.90299.8
5.16-505.60.03941120.9980.0180.0430.89699.2

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Processing

Software
NameVersionClassification
PHENIX1.16refinement
HKL-2000data scaling
PDB_EXTRACT3.15data extraction
PHASERphasing
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: E. coli OtsA

Resolution: 1.9→35.29 Å / SU ML: 0.1647 / Cross valid method: FREE R-VALUE / σ(F): 0.14 / Phase error: 21.2879
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Details: The following adjustments were made to the previously released model. Polymer geometry: Six unjustified cis-nonPro peptides in poor density were rebuilt as trans (chain A: G23, G40, T44, ...Details: The following adjustments were made to the previously released model. Polymer geometry: Six unjustified cis-nonPro peptides in poor density were rebuilt as trans (chain A: G23, G40, T44, chain B: G32, G40, T44). A few incorrectly modeled peptide rotations were corrected. Ligand geometry: Alternate conformations added for UPG in both chain A and B. Ligand identity: New ligands were added, replacing waters: SO4 (added as residue numbers 503, 504, 505 in both chain A and B), 1PE (added as residue numbers 510, 511 in both chain A and B), and NA (added as residue number 520 in both chain A and B). Some waters were moved/deleted. Other: Some backbone atoms outside of density were adjusted. Alternate conformation added for sidechain of chain B TRP 49.
RfactorNum. reflection% reflection
Rfree0.1962 1913 2.47 %
Rwork0.1698 75438 -
obs0.1705 77351 95.22 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 39.06 Å2
Refinement stepCycle: LAST / Resolution: 1.9→35.29 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7510 0 178 442 8130
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00297951
X-RAY DIFFRACTIONf_angle_d0.672310779
X-RAY DIFFRACTIONf_chiral_restr0.06181184
X-RAY DIFFRACTIONf_plane_restr0.00361332
X-RAY DIFFRACTIONf_dihedral_angle_d4.28865523
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9-1.950.28081230.23614854X-RAY DIFFRACTION85.93
1.95-20.25761320.21215031X-RAY DIFFRACTION89.06
2-2.060.23021320.20355136X-RAY DIFFRACTION90.83
2.06-2.130.2171320.19665185X-RAY DIFFRACTION92.5
2.13-2.20.23791360.18615343X-RAY DIFFRACTION94.27
2.2-2.290.25651380.18335369X-RAY DIFFRACTION94.92
2.29-2.390.23161390.17395372X-RAY DIFFRACTION95.41
2.39-2.520.20331370.17345466X-RAY DIFFRACTION96.84
2.52-2.680.20911410.16735538X-RAY DIFFRACTION97.59
2.68-2.880.20531390.17615527X-RAY DIFFRACTION98.2
2.88-3.170.20241410.18175636X-RAY DIFFRACTION98.89
3.17-3.630.21261370.17115629X-RAY DIFFRACTION99.38
3.63-4.580.15731470.14225645X-RAY DIFFRACTION99.76
4.58-35.290.16751390.16295707X-RAY DIFFRACTION99.47

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