[English] 日本語
Yorodumi
- PDB-6hdt: crystal structure of short afifavidin - biotin complex -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6hdt
Titlecrystal structure of short afifavidin - biotin complex
ComponentsShort afifavidin
Keywordsbiotin binding protein / avidin / biotin / high affinity systems / dimeric avidins
Function / homology
Function and homology information


biotin binding / extracellular region
Similarity search - Function
Avidin-like / Avidin/streptavidin / Avidin-like superfamily / Avidin family / Avidin-like domain profile. / Lipocalin / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Biological speciesAfifella pfennigii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.54 Å
AuthorsLivnah, O. / Avraham, O.
CitationJournal: FEBS J. / Year: 2018
Title: Crystal structure of afifavidin reveals common features of molecular assemblage in the bacterial dimeric avidins.
Authors: Avraham, O. / Bayer, E.A. / Livnah, O.
History
DepositionAug 19, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 14, 2018Provider: repository / Type: Initial release
Revision 1.1Dec 26, 2018Group: Data collection / Database references
Category: citation / database_PDB_rev ...citation / database_PDB_rev / database_PDB_rev_record / pdbx_database_proc
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Jan 17, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.3Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Short afifavidin
B: Short afifavidin
C: Short afifavidin
D: Short afifavidin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,5228
Polymers55,5454
Non-polymers9774
Water2,198122
1
A: Short afifavidin
C: Short afifavidin
hetero molecules


  • defined by author&software
  • Evidence: light scattering
  • 28.3 kDa, 2 polymers
Theoretical massNumber of molelcules
Total (without water)28,2614
Polymers27,7722
Non-polymers4892
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2720 Å2
ΔGint-21 kcal/mol
Surface area10980 Å2
MethodPISA
2
B: Short afifavidin
D: Short afifavidin
hetero molecules


  • defined by author&software
  • 28.3 kDa, 2 polymers
Theoretical massNumber of molelcules
Total (without water)28,2614
Polymers27,7722
Non-polymers4892
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2600 Å2
ΔGint-22 kcal/mol
Surface area10650 Å2
MethodPISA
Unit cell
Length a, b, c (Å)42.131, 65.218, 67.738
Angle α, β, γ (deg.)90.00, 100.25, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein
Short afifavidin


Mass: 13886.132 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Afifella pfennigii (bacteria) / Production host: Escherichia coli (E. coli)
#2: Chemical
ChemComp-BTN / BIOTIN


Mass: 244.311 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H16N2O3S / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 122 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5 / Details: 1.3-1.5M Ammonium Sulfate, 0.1M Acetate pH 5.0

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Nov 22, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.53→46.62 Å / Num. obs: 52210 / % possible obs: 95.8 % / Redundancy: 3 % / Rsym value: 0.081 / Net I/σ(I): 7
Reflection shellResolution: 1.53→1.59 Å

-
Processing

Software
NameVersionClassification
REFMAC5.8.0071refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6HDS

6hds


Resolution: 1.54→46.62 Å / Cor.coef. Fo:Fc: 0.973 / Cor.coef. Fo:Fc free: 0.957 / SU B: 7.208 / SU ML: 0.103 / Cross valid method: THROUGHOUT / ESU R: 0.128 / ESU R Free: 0.096 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22012 2608 5 %RANDOM
Rwork0.16282 ---
obs0.16571 49575 96.67 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 24.1 Å2
Baniso -1Baniso -2Baniso -3
1-3.48 Å20 Å20.83 Å2
2---1.76 Å2-0 Å2
3----1.9 Å2
Refinement stepCycle: 1 / Resolution: 1.54→46.62 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3600 0 64 122 3786
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.023798
X-RAY DIFFRACTIONr_bond_other_d0.0010.023243
X-RAY DIFFRACTIONr_angle_refined_deg1.6451.9095219
X-RAY DIFFRACTIONr_angle_other_deg0.84137454
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6885498
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.38525.732164
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.13415455
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.609153
X-RAY DIFFRACTIONr_chiral_restr0.0910.2573
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.024579
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02960
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it3.3222.291974
X-RAY DIFFRACTIONr_mcbond_other3.3152.2891973
X-RAY DIFFRACTIONr_mcangle_it4.1853.4452463
X-RAY DIFFRACTIONr_mcangle_other4.1863.4462464
X-RAY DIFFRACTIONr_scbond_it3.8912.4621824
X-RAY DIFFRACTIONr_scbond_other3.8932.4621822
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.5743.5922751
X-RAY DIFFRACTIONr_long_range_B_refined4.80218.9024203
X-RAY DIFFRACTIONr_long_range_B_other4.76618.8264173
X-RAY DIFFRACTIONr_rigid_bond_restr5.02537041
X-RAY DIFFRACTIONr_sphericity_free26.747532
X-RAY DIFFRACTIONr_sphericity_bonded16.70157019
LS refinement shellResolution: 1.535→1.575 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.363 177 -
Rwork0.318 3360 -
obs--88.74 %

+
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