[English] 日本語
Yorodumi
- PDB-8amh: The Crystal structure of wt apo agroavidin -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8amh
TitleThe Crystal structure of wt apo agroavidin
ComponentsAgroavidin
KeywordsUNKNOWN FUNCTION / BIOTIN BINDING PROTEIN / avidin / biotin / high affinity systems
Function / homologyAvidin/streptavidin / Avidin-like superfamily / Avidin family / Avidin-like domain profile. / biotin binding / extracellular region / Avidin
Function and homology information
Biological speciesRhizobium sp. AAP43 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.73 Å
AuthorsLivnah, O. / Bana, J.
Funding support Israel, 1items
OrganizationGrant numberCountry
Israel Science Foundation Israel
CitationJournal: Febs J. / Year: 2023
Title: Self-assembly of a dimeric avidin into unique higher-order oligomers.
Authors: Bana, J. / Warwar, J. / Bayer, E.A. / Livnah, O.
History
DepositionAug 3, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 12, 2023Provider: repository / Type: Initial release
Revision 1.1Aug 2, 2023Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.2May 1, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.3Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Agroavidin
B: Agroavidin
C: Agroavidin
D: Agroavidin


Theoretical massNumber of molelcules
Total (without water)59,2254
Polymers59,2254
Non-polymers00
Water2,846158
1
A: Agroavidin
B: Agroavidin


Theoretical massNumber of molelcules
Total (without water)29,6132
Polymers29,6132
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2480 Å2
ΔGint-22 kcal/mol
Surface area11640 Å2
MethodPISA
2
C: Agroavidin
D: Agroavidin


Theoretical massNumber of molelcules
Total (without water)29,6132
Polymers29,6132
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2380 Å2
ΔGint-23 kcal/mol
Surface area11910 Å2
MethodPISA
Unit cell
Length a, b, c (Å)82.853, 83.639, 67.781
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

-
Components

#1: Protein
Agroavidin


Mass: 14806.284 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Details: Agroavidin / Source: (gene. exp.) Rhizobium sp. AAP43 (bacteria) / Gene: IP76_08565 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A0N1ABZ3
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 158 / 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

CrystalDensity Matthews: 1.98 Å3/Da / Density % sol: 37.96 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 25% PEG 3350, 0.1 M MgCl2, 0.1 M Bis-Tris pH 6

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID09 / Wavelength: 1.072 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 19, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.072 Å / Relative weight: 1
ReflectionResolution: 1.73→44.44 Å / Num. obs: 47014 / % possible obs: 99.5 % / Redundancy: 5.1 % / CC1/2: 0.99 / Rmerge(I) obs: 0.061 / Net I/σ(I): 13.8
Reflection shellResolution: 1.73→1.79 Å / Rmerge(I) obs: 1.09 / Num. unique obs: 4789 / CC1/2: 0.639 / % possible all: 99.1

-
Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: rhizavidin

Resolution: 1.73→44.44 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.955 / SU B: 3.006 / SU ML: 0.092 / Cross valid method: THROUGHOUT / ESU R: 0.118 / ESU R Free: 0.11 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21836 2548 5.1 %RANDOM
Rwork0.19235 ---
obs0.19374 47014 99.37 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 28.28 Å2
Baniso -1Baniso -2Baniso -3
1-0.02 Å2-0 Å2-0 Å2
2---0.02 Å2-0 Å2
3----0 Å2
Refinement stepCycle: 1 / Resolution: 1.73→44.44 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3666 0 0 158 3824
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0123767
X-RAY DIFFRACTIONr_bond_other_d0.0050.0153346
X-RAY DIFFRACTIONr_angle_refined_deg1.6871.6315123
X-RAY DIFFRACTIONr_angle_other_deg1.4741.5827661
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.0395491
X-RAY DIFFRACTIONr_dihedral_angle_2_deg28.24222.299174
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.59215521
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.3381516
X-RAY DIFFRACTIONr_chiral_restr0.080.2489
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.024440
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02964
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_it2.532.8111976
X-RAY DIFFRACTIONr_mcbond_other2.522.8091975
X-RAY DIFFRACTIONr_mcangle_it3.6194.2012463
X-RAY DIFFRACTIONr_mcangle_other3.6194.2032464
X-RAY DIFFRACTIONr_scbond_it3.4263.1411791
X-RAY DIFFRACTIONr_scbond_other3.4253.1421792
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.1554.5462661
X-RAY DIFFRACTIONr_long_range_B_refined6.53132.4454039
X-RAY DIFFRACTIONr_long_range_B_other6.53132.4074027
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.73→1.775 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.349 180 -
Rwork0.327 3413 -
obs--99.01 %

+
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