[English] 日本語
Yorodumi
- PDB-5d37: Directed evolutionary changes in Kemp Eliminase KE07 - Crystal 16... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5d37
TitleDirected evolutionary changes in Kemp Eliminase KE07 - Crystal 16 round 7
ComponentsDe novo kemp eliminase KE07 round 7
KeywordsDE NOVO PROTEIN / LYASE / Kemp Eliminase / Directed Evolution / KE07
Function / homologyAldolase class I / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.04 Å
AuthorsJackson, C.J. / Hong, N.-S. / Carr, P.D.
CitationJournal: To Be Published
Title: Directed evolutionary changes in Kemp Eliminase KE07 - Crystal 16 round 7
Authors: Hong, N.-S. / Jackson, C.J. / Carr, P.D.
History
DepositionAug 6, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 7, 2016Provider: repository / Type: Initial release
Revision 1.1Sep 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_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: De novo kemp eliminase KE07 round 7
B: De novo kemp eliminase KE07 round 7


Theoretical massNumber of molelcules
Total (without water)58,2242
Polymers58,2242
Non-polymers00
Water10,467581
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)39.357, 83.480, 171.305
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein De novo kemp eliminase KE07 round 7


Mass: 29112.182 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Plasmid: pET29b (+) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3)
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 581 / 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: 2.42 Å3/Da / Density % sol: 49.1 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop
Details: 11% (W/V) PEG 3350, 0.1M BIS-TRIS PROPANE, PH 8.5, 0.2M NAF

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SEALED TUBE / Type: OTHER / Wavelength: 1.5418 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Aug 19, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.04→42.83 Å / Num. obs: 36939 / % possible obs: 99.94 % / Redundancy: 6.9 % / Rmerge(I) obs: 0.1246 / Net I/σ(I): 11.53

-
Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3IIV

3iiv


Resolution: 2.04→42.826 Å / SU ML: 0.36 / Cross valid method: FREE R-VALUE / σ(F): 0.53 / Phase error: 29.99 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.3177 1845 5 %
Rwork0.2344 --
obs0.2386 36918 99.88 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.04→42.826 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4031 0 0 581 4612
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0084107
X-RAY DIFFRACTIONf_angle_d1.0955541
X-RAY DIFFRACTIONf_dihedral_angle_d15.0881517
X-RAY DIFFRACTIONf_chiral_restr0.043638
X-RAY DIFFRACTIONf_plane_restr0.004711
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.04-2.09520.39881230.2962680X-RAY DIFFRACTION100
2.0952-2.15680.32071550.2612599X-RAY DIFFRACTION100
2.1568-2.22640.36871370.25592660X-RAY DIFFRACTION100
2.2264-2.3060.33941330.24192696X-RAY DIFFRACTION100
2.306-2.39830.30851320.25462644X-RAY DIFFRACTION100
2.3983-2.50740.35231290.24932682X-RAY DIFFRACTION100
2.5074-2.63960.3471470.24852695X-RAY DIFFRACTION100
2.6396-2.8050.35681570.23572666X-RAY DIFFRACTION100
2.805-3.02150.33321420.23582687X-RAY DIFFRACTION100
3.0215-3.32550.30941450.22662696X-RAY DIFFRACTION100
3.3255-3.80640.30011410.22092732X-RAY DIFFRACTION100
3.8064-4.79470.30021450.1982754X-RAY DIFFRACTION100
4.7947-42.83570.27211590.24512882X-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