[English] 日本語
Yorodumi
- PDB-6fhe: Highly active enzymes by automated modular backbone assembly and ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6fhe
TitleHighly active enzymes by automated modular backbone assembly and sequence design
ComponentsSynthetic construct
KeywordsArtificial enzyme / Design
Function / homologyGlycosidases / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.93 Å
AuthorsLapidot, G. / Khersonsky, O. / Lipsh, R. / Dym, O. / Albeck, S. / Rogotner, S. / Fleishman, J.S.
CitationJournal: Nat Commun / Year: 2018
Title: Highly active enzymes by automated combinatorial backbone assembly and sequence design.
Authors: Lapidoth, G. / Khersonsky, O. / Lipsh, R. / Dym, O. / Albeck, S. / Rogotner, S. / Fleishman, S.J.
History
DepositionJan 14, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 25, 2018Provider: repository / Type: Initial release
Revision 1.1Aug 1, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.2Jan 17, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Synthetic construct


Theoretical massNumber of molelcules
Total (without water)39,0391
Polymers39,0391
Non-polymers00
Water1,27971
1


  • Idetical with deposited unit
  • defined by software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area270 Å2
ΔGint-26 kcal/mol
Surface area13670 Å2
MethodPISA
Unit cell
Length a, b, c (Å)51.020, 51.020, 296.379
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

-
Components

#1: Protein Synthetic construct


Mass: 39038.512 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Production host: Escherichia coli (E. coli)
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 71 / 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: 2.47 Å3/Da / Density % sol: 50.21 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / Details: 8% PEG 3,350 0.05M Tri-sodium cidrate pH=5.8

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH3R / Wavelength: 1.541 Å
DetectorType: RIGAKU / Detector: AREA DETECTOR / Date: Jul 12, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.541 Å / Relative weight: 1
ReflectionResolution: 1.93→51.02 Å / Num. obs: 30737 / % possible obs: 99 % / Observed criterion σ(F): 0 / Redundancy: 6.4 % / Biso Wilson estimate: 37.6 Å2 / Rsym value: 0.047 / Net I/σ(I): 7.6
Reflection shellResolution: 1.93→1.97 Å / Redundancy: 6.3 % / Mean I/σ(I) obs: 1 / Num. unique obs: 2057 / Rsym value: 0.66 / % possible all: 99.9

-
Processing

Software
NameVersionClassification
PHENIX(1.11.1-2575_1692: ???)refinement
iMOSFLMdata reduction
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3W2F

3w2f


Resolution: 1.93→42.02 Å / Cross valid method: FREE R-VALUE
RfactorNum. reflection% reflection
Rfree0.275 -5 %
Rwork0.242 --
obs-29092 98.7 %
Displacement parametersBiso mean: 44.26 Å2
Refinement stepCycle: LAST / Resolution: 1.93→42.02 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2540 0 0 71 2611

+
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