[English] 日本語
Yorodumi
- PDB-7e5u: Crystal structure of Phm7 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7e5u
TitleCrystal structure of Phm7
ComponentsDiels-Alderase
KeywordsBIOSYNTHETIC PROTEIN / cyclase / diels-alderase / diels alder / [4+2] / cycloaddition
Function / homology: / Diels-Alderase, C-terminal domain / Diels-Alderase N-terminal domain / Isomerases; Intramolecular lyases / isomerase activity / Diels-Alderase phm7
Function and homology information
Biological speciesPyrenochaetopsis sp. (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.62 Å
AuthorsFujiyama, K. / Kato, N. / Kinugasa, K. / Hino, T. / Takahashi, S. / Nagano, S.
Funding support Japan, 3items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)19H04665 Japan
Japan Society for the Promotion of Science (JSPS)19H05780 Japan
Japan Society for the Promotion of Science (JSPS)19H04658 Japan
CitationJournal: Angew.Chem.Int.Ed.Engl. / Year: 2021
Title: Molecular Basis for Two Stereoselective Diels-Alderases that Produce Decalin Skeletons*.
Authors: Fujiyama, K. / Kato, N. / Re, S. / Kinugasa, K. / Watanabe, K. / Takita, R. / Nogawa, T. / Hino, T. / Osada, H. / Sugita, Y. / Takahashi, S. / Nagano, S.
History
DepositionFeb 20, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 30, 2021Provider: repository / Type: Initial release
Revision 1.1Oct 13, 2021Group: Database references / Category: citation / citation_author / database_2
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation_author.identifier_ORCID / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Apr 3, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Diels-Alderase
B: Diels-Alderase
C: Diels-Alderase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)128,23036
Polymers125,2563
Non-polymers2,97333
Water14,772820
1
A: Diels-Alderase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,95714
Polymers41,7521
Non-polymers1,20513
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Diels-Alderase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,76013
Polymers41,7521
Non-polymers1,00812
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Diels-Alderase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,5139
Polymers41,7521
Non-polymers7618
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)91.206, 150.481, 99.333
Angle α, β, γ (deg.)90.00, 97.35, 90.00
Int Tables number5
Space group name H-MC121
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z

-
Components

#1: Protein Diels-Alderase


Mass: 41752.055 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pyrenochaetopsis sp. (fungus) / Gene: phm7 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A2Z5XAU0
#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 19 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 820 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.81 Å3/Da / Density % sol: 56.19 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 1.54-1.62M Ammonium sulfate, 0.10M Tris HCl, 14-19% (v/v) Glycerol

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL32XU / Wavelength: 0.999994 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Jan 12, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.999994 Å / Relative weight: 1
ReflectionResolution: 1.62→43.867242414 Å / Num. obs: 167533 / % possible obs: 99.76 % / Redundancy: 3.5 % / Biso Wilson estimate: 20.2922462934 Å2 / CC1/2: 0.988 / Net I/σ(I): 6.9
Reflection shellResolution: 1.62→1.678 Å / Num. unique obs: 16704 / CC1/2: 0.674

-
Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575: ???)refinement
XDSdata reduction
XDSdata scaling
pointless1.11.6data scaling
Aimless0.5.32data scaling
PHASER2.7.17phasing
Coot0.8.9.2model building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: SeMet derivative

Resolution: 1.62→43.867 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 23.1 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2215 8357 4.99 %
Rwork0.1894 --
obs0.191 167511 99.76 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.62→43.867 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8506 0 176 820 9502
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0149057
X-RAY DIFFRACTIONf_angle_d1.26112339
X-RAY DIFFRACTIONf_dihedral_angle_d15.145164
X-RAY DIFFRACTIONf_chiral_restr0.0921281
X-RAY DIFFRACTIONf_plane_restr0.0091612
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.62-1.63840.31532710.27775301X-RAY DIFFRACTION100
1.6384-1.65770.29292770.26895346X-RAY DIFFRACTION100
1.6577-1.67790.29072730.26235236X-RAY DIFFRACTION100
1.6779-1.69910.31632780.26135275X-RAY DIFFRACTION100
1.6991-1.72150.28562660.24965372X-RAY DIFFRACTION100
1.7215-1.74510.29072640.23835251X-RAY DIFFRACTION100
1.7451-1.770.26512450.23545321X-RAY DIFFRACTION100
1.77-1.79640.25982600.21755317X-RAY DIFFRACTION100
1.7964-1.82450.25822690.21695299X-RAY DIFFRACTION100
1.8245-1.85440.25462420.20745323X-RAY DIFFRACTION99
1.8544-1.88640.24532640.20175287X-RAY DIFFRACTION100
1.8864-1.92070.23452460.20395302X-RAY DIFFRACTION100
1.9207-1.95760.23122570.20455360X-RAY DIFFRACTION100
1.9576-1.99760.25912490.19995326X-RAY DIFFRACTION100
1.9976-2.0410.22672430.20085351X-RAY DIFFRACTION100
2.041-2.08850.24673080.19595258X-RAY DIFFRACTION100
2.0885-2.14070.20653090.19175304X-RAY DIFFRACTION100
2.1407-2.19860.22982820.18955266X-RAY DIFFRACTION100
2.1986-2.26330.23673540.18725211X-RAY DIFFRACTION100
2.2633-2.33640.22162960.1885326X-RAY DIFFRACTION100
2.3364-2.41990.24053230.18915247X-RAY DIFFRACTION100
2.4199-2.51670.2282710.20015337X-RAY DIFFRACTION100
2.5167-2.63130.22762560.19175301X-RAY DIFFRACTION100
2.6313-2.770.24222720.19345332X-RAY DIFFRACTION100
2.77-2.94350.22793070.19495294X-RAY DIFFRACTION100
2.9435-3.17070.22433010.18715286X-RAY DIFFRACTION100
3.1707-3.48970.19233120.1735283X-RAY DIFFRACTION100
3.4897-3.99430.18613140.16435315X-RAY DIFFRACTION100
3.9943-5.03130.17722110.15055393X-RAY DIFFRACTION100
5.0313-43.8670.2073370.19025334X-RAY DIFFRACTION100

+
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