[English] 日本語
Yorodumi
- PDB-5dxo: Structure of Aspergillus fumigatus trehalose-6-phosphate phosphat... -

+
Open data


ID or keywords:

Loading...

-
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 / hyphal growth / 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 / fungal-type cell wall organization / trehalose metabolism in response to stress / positive regulation of autophagy ...asexual sporulation resulting in formation of a cellular spore / hyphal growth / 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 / fungal-type cell wall organization / trehalose metabolism in response to stress / positive regulation of autophagy / cellular response to heat / metal ion binding / cytosol
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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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

-
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

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
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

-
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

-
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

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbjlvh1.pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more