[English] 日本語
Yorodumi
- PDB-3ry2: Wild-type core streptavidin-biotin complex at atomic resolution -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3ry2
TitleWild-type core streptavidin-biotin complex at atomic resolution
ComponentsStreptavidin
KeywordsBiotin-binding protein / biotin
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
BIOTIN / Streptavidin
Similarity search - Component
Biological speciesStreptomyces avidinii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / isomorphous to previous structure / Resolution: 0.95 Å
AuthorsStenkamp, R.E. / Le Trong, I. / Stayton, P.S. / Lybrand, T.P.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2011
Title: Streptavidin and its biotin complex at atomic resolution.
Authors: Le Trong, I. / Wang, Z. / Hyre, D.E. / Lybrand, T.P. / Stayton, P.S. / Stenkamp, R.E.
History
DepositionMay 10, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 24, 2011Provider: repository / Type: Initial release
Revision 1.1Jun 19, 2013Group: Database references
Revision 1.2Nov 8, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.3Sep 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 / pdbx_struct_special_symmetry / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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
B: Streptavidin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,3287
Polymers26,5632
Non-polymers7655
Water5,026279
1
A: Streptavidin
B: Streptavidin
hetero molecules

A: Streptavidin
B: Streptavidin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,65514
Polymers53,1254
Non-polymers1,53010
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_655-x+1,y,-z1
Buried area12720 Å2
ΔGint-44 kcal/mol
Surface area19090 Å2
MethodPISA
Unit cell
Length a, b, c (Å)46.426, 94.062, 104.608
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number23
Space group name H-MI222
Components on special symmetry positions
IDModelComponents
11A-22-

TYR

-
Components

#1: Protein Streptavidin


Mass: 13281.336 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces avidinii (bacteria) / Plasmid: PET21A / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: P22629
#2: Chemical ChemComp-BTN / BIOTIN


Mass: 244.311 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H16N2O3S
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 279 / 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: 2.15 Å3/Da / Density % sol: 42.78 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 4.5
Details: 30% saturated ammonium sulfate, 0.1 M sodium acetate, 0.2 M sodium chloride, pH 4.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 0.9794 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Mar 18, 2003
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9794 Å / Relative weight: 1
ReflectionResolution: 0.88→70.01 Å / Num. all: 150014 / Num. obs: 150014 / % possible obs: 83.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Rmerge(I) obs: 0.049 / Χ2: 1.26 / Net I/σ(I): 49.14
Reflection shell
Resolution (Å)Num. unique allΧ2Diffraction-ID% possible allRmerge(I) obs
0.88-0.98360.96819.4
0.9-0.9124271.027127.2
0.91-0.9338671.076143.4
0.93-0.9551481.162157.8
0.95-0.9762901.164170.2
0.97-0.9969171.216177.80.804
0.99-1.0277031.225186.20.571
1.02-1.0484321.238194.20.447
1.04-1.0789321.252199.80.345
1.07-1.1189481.29111000.232
1.11-1.1589501.31511000.178
1.15-1.1989991.32611000.145
1.19-1.2589431.29411000.13
1.25-1.3189751.20111000.11
1.31-1.490281.17711000.093
1.4-1.590081.15511000.075
1.5-1.6690371.36311000.089
1.66-1.990681.64411000.096
1.9-2.3991451.30511000.055
2.39-5093610.616199.40.032

-
Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACT3.1data extraction
Blu-Icedata collection
Fccalculationphasing
RefinementMethod to determine structure: isomorphous to previous structure
Starting model: PDB entry 1MK5

1mk5


Resolution: 0.95→50 Å / Cor.coef. Fo:Fc: 0.984 / Cor.coef. Fo:Fc free: 0.979 / WRfactor Rfree: 0.1217 / WRfactor Rwork: 0.1067 / Occupancy max: 1 / Occupancy min: 0.2 / FOM work R set: 0.9228 / SU B: 0.404 / SU ML: 0.01 / SU R Cruickshank DPI: 0.0168 / SU Rfree: 0.0174 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R Free: 0.017 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.1313 6914 5 %RANDOM
Rwork0.1153 ---
all0.1161 137368 --
obs0.1161 137368 95.62 %-
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: 107.67 Å2 / Biso mean: 16.25 Å2 / Biso min: 7.79 Å2
Baniso -1Baniso -2Baniso -3
1--0.19 Å20 Å20 Å2
2--0.94 Å20 Å2
3----0.74 Å2
Refinement stepCycle: LAST / Resolution: 0.95→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1814 0 50 279 2143
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0212124
X-RAY DIFFRACTIONr_bond_other_d0.0010.021346
X-RAY DIFFRACTIONr_angle_refined_deg1.7611.9222910
X-RAY DIFFRACTIONr_angle_other_deg2.80333292
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.4225266
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.33123.67887
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.35615300
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.6581510
X-RAY DIFFRACTIONr_chiral_restr0.1260.2332
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.022386
X-RAY DIFFRACTIONr_gen_planes_other0.0050.02452
X-RAY DIFFRACTIONr_mcbond_it6.24141291
X-RAY DIFFRACTIONr_mcbond_other5.3524549
X-RAY DIFFRACTIONr_mcangle_it7.22662086
X-RAY DIFFRACTIONr_scbond_it9.1656833
X-RAY DIFFRACTIONr_scangle_it11.03310824
X-RAY DIFFRACTIONr_rigid_bond_restr5.06633469
X-RAY DIFFRACTIONr_sphericity_free23.0523279
X-RAY DIFFRACTIONr_sphericity_bonded9.84833417
LS refinement shellResolution: 0.95→0.975 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.371 356 -
Rwork0.347 7137 -
all-7493 -
obs--71.14 %

+
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