[English] 日本語
Yorodumi
- PDB-4bx6: trans-divalent streptavidin -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4bx6
Titletrans-divalent streptavidin
Components(STREPTAVIDIN) x 2
KeywordsBIOTIN-BINDING PROTEIN / AVIDIN
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
Biological speciesSTREPTOMYCES AVIDINII (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.595 Å
AuthorsFairhead, M. / Krndija, D. / Lowe, E.D. / Howarth, M.
CitationJournal: J.Mol.Biol. / Year: 2014
Title: Plug-and-Play Pairing Via Defined Divalent Streptavidins.
Authors: Fairhead, M. / Krndija, D. / Lowe, E.D. / Howarth, M.
History
DepositionJul 8, 2013Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 25, 2013Provider: repository / Type: Initial release
Revision 1.1Oct 9, 2013Group: Database references
Revision 1.2Jan 15, 2014Group: Database references
Revision 1.3May 15, 2019Group: Data collection / Experimental preparation / Other
Category: exptl_crystal_grow / pdbx_database_proc / pdbx_database_status
Item: _exptl_crystal_grow.method / _pdbx_database_status.recvd_author_approval
Revision 1.4May 22, 2019Group: Data collection / Experimental preparation / Category: exptl_crystal_grow / Item: _exptl_crystal_grow.temp
Revision 1.5Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 700 SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AA" IN EACH CHAIN ON SHEET RECORDS BELOW ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 8-STRANDED BARREL THIS IS REPRESENTED BY A 9-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEETS PRESENTED AS "BA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 8-STRANDED BARREL THIS IS REPRESENTED BY A 9-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEETS PRESENTED AS "CA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 8-STRANDED BARREL THIS IS REPRESENTED BY A 9-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEETS PRESENTED AS "DA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 8-STRANDED BARREL THIS IS REPRESENTED BY A 9-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL.

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: STREPTAVIDIN
B: STREPTAVIDIN
C: STREPTAVIDIN
D: STREPTAVIDIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,9677
Polymers54,6134
Non-polymers3553
Water8,395466
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9500 Å2
ΔGint-86 kcal/mol
Surface area20780 Å2
MethodPISA
Unit cell
Length a, b, c (Å)47.040, 65.120, 81.590
Angle α, β, γ (deg.)90.00, 95.94, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein STREPTAVIDIN


Mass: 13250.320 Da / Num. of mol.: 2 / Fragment: RESIDUES 37-163 / Mutation: YES
Source method: isolated from a genetically manipulated source
Details: DEAD VARIANT / Source: (gene. exp.) STREPTOMYCES AVIDINII (bacteria) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): RIPL / References: UniProt: P22629
#2: Protein STREPTAVIDIN


Mass: 14056.019 Da / Num. of mol.: 2 / Fragment: RESIDUES 37-163
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) STREPTOMYCES AVIDINII (bacteria) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): RIPL / References: UniProt: P22629
#3: Chemical ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 466 / 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: 2.35 Å3/Da / Density % sol: 47.22 % / Description: NONE
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6
Details: 65% V/V 2-METHYL-2, 4-PENTANEDIOL (MPD), 0.1 M 2-(N-MORPHOLINO)ETHANESULFONIC ACID (MES) PH 6.0. CRYSTALS WERE OBTAINED BY THE SITTING-DROP VAPOR-DIFFUSION METHOD AT 291 K AND REACHED A ...Details: 65% V/V 2-METHYL-2, 4-PENTANEDIOL (MPD), 0.1 M 2-(N-MORPHOLINO)ETHANESULFONIC ACID (MES) PH 6.0. CRYSTALS WERE OBTAINED BY THE SITTING-DROP VAPOR-DIFFUSION METHOD AT 291 K AND REACHED A MAXIMUM SIZE AFTER 10 DAYS AND WERE HARVESTED SOON AFTER

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.92
DetectorType: MARRESEARCH MX-300 / Detector: CCD / Date: Oct 7, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92 Å / Relative weight: 1
ReflectionResolution: 1.6→24.98 Å / Num. obs: 64074 / % possible obs: 98 % / Observed criterion σ(I): 2 / Redundancy: 3.4 % / Biso Wilson estimate: 20.98 Å2 / Rmerge(I) obs: 0.04 / Net I/σ(I): 13.88
Reflection shellResolution: 1.6→1.65 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.64 / Mean I/σ(I) obs: 1.92 / % possible all: 97.3

-
Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3RY1

3ry1


Resolution: 1.595→24.981 Å / SU ML: 0.21 / σ(F): 1.33 / Phase error: 21.11 / Stereochemistry target values: ML / Details: DISORDERED REGIONS WERE MODELED STEREOCHEMICALLY
RfactorNum. reflection% reflection
Rfree0.1866 3246 5.1 %
Rwork0.164 --
obs0.1652 64068 97.99 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 28.4 Å2
Refinement stepCycle: LAST / Resolution: 1.595→24.981 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3574 0 24 466 4064
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0113891
X-RAY DIFFRACTIONf_angle_d1.2765373
X-RAY DIFFRACTIONf_dihedral_angle_d14.0511263
X-RAY DIFFRACTIONf_chiral_restr0.083607
X-RAY DIFFRACTIONf_plane_restr0.005683
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5947-1.61850.32671450.27722663X-RAY DIFFRACTION98
1.6185-1.64380.28251400.27172568X-RAY DIFFRACTION97
1.6438-1.67070.28061510.25492580X-RAY DIFFRACTION95
1.6707-1.69950.35331310.24882588X-RAY DIFFRACTION98
1.6995-1.73040.25021290.23342697X-RAY DIFFRACTION99
1.7304-1.76370.27821460.22182657X-RAY DIFFRACTION99
1.7637-1.79970.26141440.20452650X-RAY DIFFRACTION99
1.7997-1.83880.26241380.20482639X-RAY DIFFRACTION99
1.8388-1.88160.21721360.18962684X-RAY DIFFRACTION99
1.8816-1.92860.20841380.18132650X-RAY DIFFRACTION99
1.9286-1.98070.19431380.17382659X-RAY DIFFRACTION99
1.9807-2.0390.20021490.16762686X-RAY DIFFRACTION99
2.039-2.10480.19021440.16592631X-RAY DIFFRACTION99
2.1048-2.180.20071430.16092656X-RAY DIFFRACTION99
2.18-2.26720.20771340.16612635X-RAY DIFFRACTION97
2.2672-2.37030.19381290.16192575X-RAY DIFFRACTION95
2.3703-2.49520.19391360.16672691X-RAY DIFFRACTION99
2.4952-2.65130.18561510.16062654X-RAY DIFFRACTION99
2.6513-2.85580.20031220.15382692X-RAY DIFFRACTION99
2.8558-3.14270.16321370.14952669X-RAY DIFFRACTION98
3.1427-3.59630.16661620.13892640X-RAY DIFFRACTION98
3.5963-4.52650.13791590.1272580X-RAY DIFFRACTION95
4.5265-24.98410.16531440.16672678X-RAY DIFFRACTION96

+
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