[English] 日本語
Yorodumi
- PDB-5f2b: Expanding Nature's Catalytic Repertoire -Directed Evolution of an... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5f2b
TitleExpanding Nature's Catalytic Repertoire -Directed Evolution of an Artificial Metalloenzyme for In Vivo Metathesis
ComponentsStreptavidin
Keywordsbiotin-binding protein / beta barrel / metathesis / organometallic complex
Function / homology
Function and homology information


biotin binding / extracellular region
Similarity search - Function
Avidin-like / Avidin-like, conserved site / Avidin-like domain signature. / Avidin / : / Avidin/streptavidin / Avidin-like superfamily / Avidin family / Avidin-like domain profile. / Lipocalin ...Avidin-like / Avidin-like, conserved site / Avidin-like domain signature. / Avidin / : / Avidin/streptavidin / Avidin-like superfamily / Avidin family / Avidin-like domain profile. / Lipocalin / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Chem-9RU / Streptavidin
Similarity search - Component
Biological speciesStreptomyces avidinii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.7 Å
AuthorsHeinisch, T. / Jeschek, M. / Reuter, R. / Trindler, C. / Panke, S. / Ward, T.R.
CitationJournal: Nature / Year: 2016
Title: Directed evolution of artificial metalloenzymes for in vivo metathesis.
Authors: Jeschek, M. / Reuter, R. / Heinisch, T. / Trindler, C. / Klehr, J. / Panke, S. / Ward, T.R.
History
DepositionDec 1, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Aug 31, 2016Provider: repository / Type: Initial release
Revision 1.1Sep 7, 2016Group: Database references
Revision 1.2Oct 5, 2016Group: Database references
Revision 1.3Jan 10, 2024Group: 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 / diffrn_radiation_wavelength / pdbx_initial_refinement_model / pdbx_struct_special_symmetry
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Streptavidin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,4143
Polymers16,5981
Non-polymers8162
Water99155
1
A: Streptavidin
hetero molecules

A: Streptavidin
hetero molecules

A: Streptavidin
hetero molecules

A: Streptavidin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,65512
Polymers66,3924
Non-polymers3,2638
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_665-y+1,-x+1,-z1
crystal symmetry operation10_665-x+1,-y+1,z1
crystal symmetry operation15_555y,x,-z1
Unit cell
Length a, b, c (Å)57.465, 57.465, 173.564
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number98
Space group name H-MI4122
Components on special symmetry positions
IDModelComponents
11A-323-

HOH

-
Components

#1: Protein Streptavidin


Mass: 16598.053 Da / Num. of mol.: 1 / Mutation: V47A,N49K,T114Q,A119G,K121R
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces avidinii (bacteria) / Plasmid: pET30b / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Top10 / References: UniProt: P22629
#2: Chemical ChemComp-9RU / [1-[4-[[5-[(3~{a}~{S},4~{S},6~{a}~{R})-2-oxidanylidene-1,3,3~{a},4,6,6~{a}-hexahydrothieno[3,4-d]imidazol-4-yl]pentanoylamino]methyl]-2,6-dimethyl-phenyl]-3-(2,4,6-trimethylphenyl)-4,5-dihydroimidazol-1-ium-2-yl]-bis(chloranyl)ruthenium


Mass: 719.731 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C31H41Cl2N5O2RuS
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 55 / 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: 2.16 Å3/Da / Density % sol: 43.01 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4 / Details: 1.5 M ammonium sulfate, 0.1 M sodium acetate

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Oct 17, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.7→54.553 Å / Num. obs: 16547 / % possible obs: 100 % / Redundancy: 12.6 % / CC1/2: 0.998 / Rmerge(I) obs: 0.103 / Rpim(I) all: 0.03 / Net I/σ(I): 12.6 / Num. measured all: 208507 / Scaling rejects: 5
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allCC1/2Rpim(I) all% possible all
1.7-1.73132.0181.3109008370.5090.577100
9-40.779.80.06135.214871510.9970.01999.3

-
Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation5.03 Å40.77 Å
Translation5.03 Å40.77 Å

-
Processing

Software
NameVersionClassification
Aimless0.5.15data scaling
PHASER2.5.7phasing
REFMAC5.8.0135refinement
PDB_EXTRACT3.15data extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2QCB

2qcb


Resolution: 1.7→54.55 Å / Cor.coef. Fo:Fc: 0.974 / Cor.coef. Fo:Fc free: 0.958 / WRfactor Rfree: 0.2017 / WRfactor Rwork: 0.1378 / FOM work R set: 0.7593 / SU B: 5.793 / SU ML: 0.078 / SU R Cruickshank DPI: 0.098 / SU Rfree: 0.0905 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.098 / ESU R Free: 0.091 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2058 760 4.6 %RANDOM
Rwork0.1437 ---
obs0.1465 15764 99.97 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 168.39 Å2 / Biso mean: 37.888 Å2 / Biso min: 19.43 Å2
Baniso -1Baniso -2Baniso -3
1--2.32 Å20 Å20 Å2
2---2.32 Å20 Å2
3---4.64 Å2
Refinement stepCycle: final / Resolution: 1.7→54.55 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms915 0 53 55 1023
Biso mean--38.27 53.54 -
Num. residues----122
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0320.02994
X-RAY DIFFRACTIONr_bond_other_d0.0020.02825
X-RAY DIFFRACTIONr_angle_refined_deg2.621.9531361
X-RAY DIFFRACTIONr_angle_other_deg1.32231884
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.4585121
X-RAY DIFFRACTIONr_dihedral_angle_2_deg26.32723.65941
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.99915129
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.942155
X-RAY DIFFRACTIONr_chiral_restr0.1710.2140
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.021149
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02238
X-RAY DIFFRACTIONr_mcbond_it7.063.381487
X-RAY DIFFRACTIONr_mcbond_other6.9633.375486
X-RAY DIFFRACTIONr_mcangle_it8.3625.063607
X-RAY DIFFRACTIONr_rigid_bond_restr6.45231814
X-RAY DIFFRACTIONr_sphericity_free65.16515
X-RAY DIFFRACTIONr_sphericity_bonded25.53951833
LS refinement shellResolution: 1.7→1.744 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.357 67 -
Rwork0.275 1119 -
all-1186 -
obs--100 %

+
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