[English] 日本語
Yorodumi
- PDB-4ekv: Streptavidin 8-aa-loop H127C mutein with reversible biotin binding -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4ekv
TitleStreptavidin 8-aa-loop H127C mutein with reversible biotin binding
ComponentsStreptavidin
Keywordsbiotin-binding protein / Beta-barrel / Binding protein / Biotin-binding
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 / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
BIOTIN / Streptavidin
Similarity search - Component
Biological speciesStreptomyces avidinii (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2 Å
AuthorsBarrette-Ng, I.H. / Honetschlaeger, C. / Wong, S.L. / Ng, K.K.S.
CitationJournal: Plos One / Year: 2012
Title: Development of a tetrameric streptavidin mutein with reversible biotin binding capability: engineering a mobile loop as an exit door for biotin.
Authors: O'Sullivan, V.J. / Barrette-Ng, I. / Hommema, E. / Hermanson, G.T. / Schofield, M. / Wu, S.C. / Honetschlaeger, C. / Ng, K.K. / Wong, S.L.
History
DepositionApr 9, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 13, 2012Provider: repository / Type: Initial release
Revision 1.1Nov 15, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.2Sep 13, 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 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Streptavidin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,5663
Polymers16,2861
Non-polymers2802
Water1,26170
1
A: Streptavidin
hetero molecules

A: Streptavidin
hetero molecules

A: Streptavidin
hetero molecules

A: Streptavidin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,26512
Polymers65,1464
Non-polymers1,1198
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
crystal symmetry operation7_555y,x,-z1
crystal symmetry operation8_555-y,-x,-z1
Buried area9110 Å2
ΔGint-74 kcal/mol
Surface area20570 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.066, 57.066, 70.186
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number94
Space group name H-MP42212
Components on special symmetry positions
IDModelComponents
11A-302-

HOH

DetailsThe homotetramer is generated from the single protomer in the asymmetric unit using the four-fold crystallographic symmetry operators.

-
Components

#1: Protein Streptavidin


Mass: 16286.493 Da / Num. of mol.: 1 / Mutation: H151C
Source method: isolated from a genetically manipulated source
Details: Synthetic gene / Source: (gene. exp.) Streptomyces avidinii (bacteria) / Plasmid: pSSAV / Production host: Bacillus subtilis (bacteria) / Strain (production host): WB800 / References: UniProt: P22629
#2: Chemical ChemComp-BTN / BIOTIN


Mass: 244.311 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N2O3S
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 70 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsthe 8-residue loop region was modified from TTEANAWK to DSSNGSDG

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 1.75 Å3/Da / Density % sol: 29.88 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 50% Tacsimate, 10% glycerol, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH3R / Wavelength: 1.5418 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Dec 7, 2010 / Details: Osmic multilayer
RadiationMonochromator: Osmic multilayer / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.95→20 Å / Num. all: 8958 / Num. obs: 8607 / % possible obs: 96.1 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 6.7 % / Biso Wilson estimate: 35.1 Å2 / Rmerge(I) obs: 0.063 / Rsym value: 0.063 / Net I/σ(I): 28.4
Reflection shellResolution: 1.95→2.02 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.496 / Mean I/σ(I) obs: 2.8 / Num. unique all: 776 / Rsym value: 0.0496 / % possible all: 88

-
Phasing

PhasingMethod: molecular replacement

-
Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACT3.11data extraction
MAR345data collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 1SWE

1swe


Resolution: 2→19.39 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.939 / WRfactor Rfree: 0.2252 / WRfactor Rwork: 0.1882 / Occupancy max: 1 / Occupancy min: 0.25 / FOM work R set: 0.8437 / SU B: 4.098 / SU ML: 0.114 / SU R Cruickshank DPI: 0.1995 / SU Rfree: 0.1652 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.199 / ESU R Free: 0.165 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: U VALUES: REFINED INDIVIDUALLY. THE SF DATA DO NOT HAVE FREE SET MARKER.
RfactorNum. reflection% reflectionSelection details
Rfree0.2252 394 4.9 %RANDOM
Rwork0.1882 ---
all0.1902 7585 --
obs0.1902 7585 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso max: 83.47 Å2 / Biso mean: 37.5624 Å2 / Biso min: 21.08 Å2
Baniso -1Baniso -2Baniso -3
1--0.98 Å20 Å20 Å2
2---0.98 Å20 Å2
3---1.96 Å2
Refinement stepCycle: LAST / Resolution: 2→19.39 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms898 0 17 70 985
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.021936
X-RAY DIFFRACTIONr_angle_refined_deg1.2651.9231280
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3635121
X-RAY DIFFRACTIONr_dihedral_angle_2_deg25.78323.88936
X-RAY DIFFRACTIONr_dihedral_angle_3_deg9.97415122
X-RAY DIFFRACTIONr_dihedral_angle_4_deg9.614154
X-RAY DIFFRACTIONr_chiral_restr0.0790.2147
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.02710
X-RAY DIFFRACTIONr_mcbond_it2.0482601
X-RAY DIFFRACTIONr_mcangle_it3.2042.5950
X-RAY DIFFRACTIONr_scbond_it4.2633.5335
X-RAY DIFFRACTIONr_scangle_it5.7674.5330
LS refinement shellResolution: 2→2.052 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.367 23 -
Rwork0.281 404 -
all-427 -
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://pdbjlvh1.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