[English] 日本語
Yorodumi
- PDB-5wqg: Structure of fungal meroterpenoid isomerase Trt14 complexed with ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5wqg
TitleStructure of fungal meroterpenoid isomerase Trt14 complexed with terretonin D
ComponentsIsomerase trt14
KeywordsISOMERASE / meroterpenoid / terretonin
Function / homologyIsomerases / terpenoid biosynthetic process / isomerase activity / methyl / Isomerase trt14
Function and homology information
Biological speciesAspergillus terreus NIH 2624 (mold)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsMori, T. / Matsuda, Y. / Abe, I.
CitationJournal: Nat. Chem. Biol. / Year: 2017
Title: Molecular basis for the unusual ring reconstruction in fungal meroterpenoid biogenesis
Authors: Mori, T. / Iwabuchi, T. / Hoshino, S. / Wang, H. / Matsuda, Y. / Abe, I.
History
DepositionNov 26, 2016Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 26, 2017Provider: repository / Type: Initial release
Revision 1.1Oct 4, 2017Group: Database references / Structure summary / Category: citation
Item: _chem_comp.pdbx_synonyms / _citation.journal_abbrev ..._chem_comp.pdbx_synonyms / _citation.journal_abbrev / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed
Revision 1.2Nov 8, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / entity / pdbx_entity_nonpoly / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
Item: _chem_comp.name / _chem_comp.pdbx_synonyms ..._chem_comp.name / _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _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.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_symmetry / _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.ptnr3_label_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _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.ptnr1_symmetry / _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 / _struct_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Isomerase trt14
B: Isomerase trt14
C: Isomerase trt14
D: Isomerase trt14
E: Isomerase trt14
F: Isomerase trt14
hetero molecules


Theoretical massNumber of molelcules
Total (without water)111,60515
Polymers109,9416
Non-polymers1,6649
Water3,441191
1
A: Isomerase trt14
C: Isomerase trt14
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,2025
Polymers36,6472
Non-polymers5553
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2440 Å2
ΔGint-27 kcal/mol
Surface area13210 Å2
MethodPISA
2
B: Isomerase trt14
D: Isomerase trt14
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,2025
Polymers36,6472
Non-polymers5553
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2440 Å2
ΔGint-26 kcal/mol
Surface area13080 Å2
MethodPISA
3
E: Isomerase trt14
F: Isomerase trt14
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,2025
Polymers36,6472
Non-polymers5553
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2480 Å2
ΔGint-25 kcal/mol
Surface area12900 Å2
MethodPISA
Unit cell
Length a, b, c (Å)99.440, 47.130, 121.130
Angle α, β, γ (deg.)90.00, 107.97, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein
Isomerase trt14 / Terretonin synthesis protein 14


Mass: 18323.566 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aspergillus terreus NIH 2624 (mold) / Strain: NIH 2624 / Gene: trt14, ATEG_10082 / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / References: UniProt: Q0C8A2, Isomerases
#2: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-7MI / methyl (2S,4aR,4bS,5S,6aS,10aS,10bS,12aS)-2,4b,7,7,10a,12a-hexamethyl-12-methylidene-5-oxidanyl-1,4,6,8-tetrakis(oxidanylidene) -5,6a,9,10,10b,11-hexahydro-4aH-naphtho[1,2-h]isochromene-2-carboxylate / methyl (2S,4aR,4bS,5S,6aS,10aS,10bS,12aS)-5-hydroxy-2,4b,7,7,10a,12a-hexamethyl-12-methylene-1,4,6,8-tetraoxohexadecahydro-2H-n aphtho[1,2-h]isochromene-2-carboxylate / Methyl group


Mass: 474.543 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C26H34O8
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 191 / 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: 2.46 Å3/Da / Density % sol: 49.92 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 100mM Imidazole (pH 8.0), 10% PEG 8000, 100mM Ca(OAc)2, 2% 1-propanol

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NE3A / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Nov 30, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.3→50 Å / Num. obs: 47601 / % possible obs: 98.4 % / Redundancy: 3.39 % / CC1/2: 0.998 / Rmerge(I) obs: 0.07 / Net I/σ(I): 12.37
Reflection shellResolution: 2.3→2.44 Å / Redundancy: 3.4 % / Num. unique obs: 7487 / CC1/2: 0.826 / % possible all: 96.7

-
Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5WQF

5wqf


Resolution: 2.3→36.478 Å / SU ML: 0.31 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 27.54
RfactorNum. reflection% reflection
Rfree0.2452 2378 5 %
Rwork0.1957 --
obs0.1981 47576 98.49 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.3→36.478 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6681 0 108 191 6980
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0086915
X-RAY DIFFRACTIONf_angle_d0.9919393
X-RAY DIFFRACTIONf_dihedral_angle_d20.6712802
X-RAY DIFFRACTIONf_chiral_restr0.0611074
X-RAY DIFFRACTIONf_plane_restr0.0051200
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2977-2.34460.31791310.27152494X-RAY DIFFRACTION93
2.3446-2.39560.36421370.2562608X-RAY DIFFRACTION98
2.3956-2.45130.32591400.25812659X-RAY DIFFRACTION99
2.4513-2.51260.28941360.24612591X-RAY DIFFRACTION97
2.5126-2.58050.3231400.22912661X-RAY DIFFRACTION100
2.5805-2.65640.30381390.22472631X-RAY DIFFRACTION98
2.6564-2.74210.30381410.2352680X-RAY DIFFRACTION100
2.7421-2.84010.31091390.21072642X-RAY DIFFRACTION98
2.8401-2.95380.261400.20092654X-RAY DIFFRACTION98
2.9538-3.08810.2581390.22362651X-RAY DIFFRACTION100
3.0881-3.25090.311400.21792659X-RAY DIFFRACTION99
3.2509-3.45440.2911400.19452665X-RAY DIFFRACTION99
3.4544-3.72090.20781410.1852672X-RAY DIFFRACTION99
3.7209-4.09490.21621410.17542686X-RAY DIFFRACTION99
4.0949-4.68630.17441430.15782718X-RAY DIFFRACTION99
4.6863-5.90030.21711440.18442720X-RAY DIFFRACTION99
5.9003-36.4830.21611470.17552807X-RAY DIFFRACTION99

+
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://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