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- PDB-8asu: The Crystal structure of short F46Y agroavidin - biotin complex -

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Basic information

Entry
Database: PDB / ID: 8asu
TitleThe Crystal structure of short F46Y agroavidin - biotin complex
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 / BIOTIN / Avidin
Function and homology information
Biological speciesRhizobium sp. AAP43 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.52 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 21, 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 1.2Feb 7, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)56,1548
Polymers55,1774
Non-polymers9774
Water34219
1
A: Agroavidin
C: Agroavidin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,0774
Polymers27,5882
Non-polymers4892
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3480 Å2
ΔGint-12 kcal/mol
Surface area11040 Å2
MethodPISA
2
B: Agroavidin
D: Agroavidin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,0774
Polymers27,5882
Non-polymers4892
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3650 Å2
ΔGint-14 kcal/mol
Surface area10860 Å2
MethodPISA
Unit cell
Length a, b, c (Å)81.365, 81.973, 68.123
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein
Agroavidin


Mass: 13794.177 Da / Num. of mol.: 4 / Mutation: F46Y
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rhizobium sp. AAP43 (bacteria) / Gene: IP76_08565 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A0N1ABZ3
#2: Chemical
ChemComp-BTN / BIOTIN / 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 / Water


Mass: 18.015 Da / Num. of mol.: 19 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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Experimental details

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Experiment

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

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Sample preparation

CrystalDensity Matthews: 2.06 Å3/Da / Density % sol: 40.25 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 20% PEG 3350, 0.1 M Bis Tris

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 1.0723 Å
DetectorType: DECTRIS EIGER2 S 16M / Detector: PIXEL / Date: Nov 23, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0723 Å / Relative weight: 1
ReflectionResolution: 2.52→57.75 Å / Num. obs: 15697 / % possible obs: 98.5 % / Redundancy: 4.6 % / CC1/2: 0.998 / Net I/σ(I): 11.2
Reflection shellResolution: 2.52→2.59 Å / Redundancy: 4.7 % / Num. unique obs: 1118 / CC1/2: 0.507 / Rsym value: 0.923 / % possible all: 98.5

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 8ASS

8ass


Resolution: 2.52→44.09 Å / Cor.coef. Fo:Fc: 0.938 / Cor.coef. Fo:Fc free: 0.922 / SU B: 14.969 / SU ML: 0.317 / Cross valid method: THROUGHOUT / ESU R: 1.2 / ESU R Free: 0.344 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.27309 670 4.3 %RANDOM
Rwork0.20435 ---
obs0.20762 15024 98.38 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 59.054 Å2
Baniso -1Baniso -2Baniso -3
1--0.15 Å2-0 Å20 Å2
2--0.1 Å2-0 Å2
3---0.06 Å2
Refinement stepCycle: 1 / Resolution: 2.52→44.09 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3520 0 64 19 3603
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0133676
X-RAY DIFFRACTIONr_bond_other_d0.0010.0183204
X-RAY DIFFRACTIONr_angle_refined_deg1.7271.6555000
X-RAY DIFFRACTIONr_angle_other_deg1.2721.6077408
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.7085472
X-RAY DIFFRACTIONr_dihedral_angle_2_deg26.95122.195164
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.79115504
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.0481516
X-RAY DIFFRACTIONr_chiral_restr0.0650.2480
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.024244
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02852
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_it5.0916.221900
X-RAY DIFFRACTIONr_mcbond_other5.0886.2171899
X-RAY DIFFRACTIONr_mcangle_it7.699.3122368
X-RAY DIFFRACTIONr_mcangle_other7.6919.3152369
X-RAY DIFFRACTIONr_scbond_it5.1316.4881776
X-RAY DIFFRACTIONr_scbond_other5.1236.4881774
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other7.7289.5012632
X-RAY DIFFRACTIONr_long_range_B_refined10.77170.3933876
X-RAY DIFFRACTIONr_long_range_B_other10.7770.3953877
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.52→2.585 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.361 64 -
Rwork0.328 1051 -
obs--96.62 %

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