[English] 日本語
Yorodumi
- PDB-6c7t: Directed evolutionary changes in Kemp Eliminase KE07 - Crystal 20... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6c7t
TitleDirected evolutionary changes in Kemp Eliminase KE07 - Crystal 20 round 5
ComponentsKemp Eliminase KE07
KeywordsLYASE / Kemp Eliminase / Directed Evolution / KE07 / DE NOVO PROTEIN
Function / homologyAldolase class I / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.83 Å
AuthorsJackson, C.J. / Hong, N.-S. / Carr, P.D.
CitationJournal: Nat Commun / Year: 2018
Title: The evolution of multiple active site configurations in a designed enzyme.
Authors: Hong, N.S. / Petrovic, D. / Lee, R. / Gryn'ova, G. / Purg, M. / Saunders, J. / Bauer, P. / Carr, P.D. / Lin, C.Y. / Mabbitt, P.D. / Zhang, W. / Altamore, T. / Easton, C. / Coote, M.L. / ...Authors: Hong, N.S. / Petrovic, D. / Lee, R. / Gryn'ova, G. / Purg, M. / Saunders, J. / Bauer, P. / Carr, P.D. / Lin, C.Y. / Mabbitt, P.D. / Zhang, W. / Altamore, T. / Easton, C. / Coote, M.L. / Kamerlin, S.C.L. / Jackson, C.J.
History
DepositionJan 23, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 1, 2018Provider: repository / Type: Initial release
Revision 1.1Feb 13, 2019Group: Data collection / 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.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Oct 4, 2023Group: 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: Kemp Eliminase KE07


Theoretical massNumber of molelcules
Total (without water)29,3291
Polymers29,3291
Non-polymers00
Water4,197233
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)97.765, 97.765, 157.027
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122
Components on special symmetry positions
IDModelComponents
11A-523-

HOH

-
Components

#1: Protein Kemp Eliminase KE07


Mass: 29328.545 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Production host: Escherichia coli BL21(DE3) (bacteria)
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 233 / 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: 3.69 Å3/Da / Density % sol: 66.7 %
Crystal growTemperature: 277 K / Method: slow cooling / pH: 7.25 / Details: 25 mM HEPES pH 7.25, 100 mM NaCl

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9537 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 30, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 1.83→42.33 Å / Num. obs: 39775 / % possible obs: 99.96 % / Redundancy: 2 % / Biso Wilson estimate: 32.39 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.022 / Rrim(I) all: 0.0306 / Net I/σ(I): 14.73
Reflection shellResolution: 1.83→1.895 Å / Redundancy: 2 % / Rmerge(I) obs: 0.87 / Num. unique obs: 3871 / CC1/2: 0.49 / Rrim(I) all: 1.23 / % possible all: 99.87

-
Processing

Software
NameVersionClassification
PHENIX(1.12_2829: ???)refinement
XDSVERSION Jun 1, 2017data reduction
Aimlessversion 0.5.32data scaling
MOLREPVers 11.5.05phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5D30

5d30


Resolution: 1.83→42.33 Å / SU ML: 0.23 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 22.56
RfactorNum. reflection% reflection
Rfree0.216 1931 4.86 %
Rwork0.1997 --
obs0.2005 39769 99.98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.83→42.33 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1963 0 0 233 2196
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0082071
X-RAY DIFFRACTIONf_angle_d0.8332801
X-RAY DIFFRACTIONf_dihedral_angle_d21.881774
X-RAY DIFFRACTIONf_chiral_restr0.295316
X-RAY DIFFRACTIONf_plane_restr0.004365
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.83-1.87580.35231330.32442649X-RAY DIFFRACTION100
1.8758-1.92650.42581210.35672663X-RAY DIFFRACTION100
1.9265-1.98320.31811290.28842645X-RAY DIFFRACTION100
1.9832-2.04720.27221460.24452631X-RAY DIFFRACTION100
2.0472-2.12040.25521570.22742669X-RAY DIFFRACTION100
2.1204-2.20530.23731370.20912643X-RAY DIFFRACTION100
2.2053-2.30560.25551260.23412670X-RAY DIFFRACTION100
2.3056-2.42720.24361470.19752670X-RAY DIFFRACTION100
2.4272-2.57920.22921500.1962681X-RAY DIFFRACTION100
2.5792-2.77830.21551430.19892690X-RAY DIFFRACTION100
2.7783-3.05790.22511310.18162728X-RAY DIFFRACTION100
3.0579-3.50020.19831170.18822768X-RAY DIFFRACTION100
3.5002-4.40930.18121470.16692761X-RAY DIFFRACTION100
4.4093-44.53460.18611470.19232970X-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