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- PDB-8asr: The Crystal structure of F46Y mutant of apo agroavidin -

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Basic information

Entry
Database: PDB / ID: 8asr
TitleThe Crystal structure of F46Y mutant of 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: 1.66 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
Revision 1.3Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)59,2894
Polymers59,2894
Non-polymers00
Water6,305350
1
A: Agroavidin
B: Agroavidin


Theoretical massNumber of molelcules
Total (without water)29,6452
Polymers29,6452
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2490 Å2
ΔGint-22 kcal/mol
Surface area11870 Å2
MethodPISA
2
C: Agroavidin
D: Agroavidin


Theoretical massNumber of molelcules
Total (without water)29,6452
Polymers29,6452
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2390 Å2
ΔGint-23 kcal/mol
Surface area12460 Å2
MethodPISA
Unit cell
Length a, b, c (Å)83.322, 84.781, 67.915
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: 14822.284 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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 350 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.02 Å3/Da / Density % sol: 39.2 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 18% pentaerythritol ethoxylate, 0.05 M Bis Tris pH 5.9-6.0, 0.05 M ammonium sulphate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID09 / Wavelength: 1.0723 Å
DetectorType: DECTRIS EIGER2 S 16M / Detector: PIXEL / Date: Feb 2, 2018 / Details: optical hatch
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0723 Å / Relative weight: 1
ReflectionResolution: 1.66→44.76 Å / Num. obs: 53732 / % possible obs: 98.6 % / Redundancy: 4.3 % / CC1/2: 0.99 / Net I/σ(I): 15.5
Reflection shellResolution: 1.66→1.72 Å / Rmerge(I) obs: 0.778 / Num. unique obs: 5477 / CC1/2: 0.794

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3ew1

3ew1


Resolution: 1.66→44.76 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.953 / SU B: 2.261 / SU ML: 0.074 / Cross valid method: THROUGHOUT / ESU R: 0.101 / ESU R Free: 0.101 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21467 2735 4.8 %RANDOM
Rwork0.17851 ---
obs0.18033 53763 98.2 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 24.271 Å2
Baniso -1Baniso -2Baniso -3
1-0.01 Å20 Å20 Å2
2--0.02 Å2-0 Å2
3----0.04 Å2
Refinement stepCycle: 1 / Resolution: 1.66→44.76 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3771 0 0 350 4121
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0123904
X-RAY DIFFRACTIONr_bond_other_d0.0010.0183355
X-RAY DIFFRACTIONr_angle_refined_deg1.6931.6325320
X-RAY DIFFRACTIONr_angle_other_deg1.5391.5767758
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9335516
X-RAY DIFFRACTIONr_dihedral_angle_2_deg27.20622.376181
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.79315534
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.1681516
X-RAY DIFFRACTIONr_chiral_restr0.0880.2504
X-RAY DIFFRACTIONr_gen_planes_refined0.010.024576
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02920
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_it2.452.4072049
X-RAY DIFFRACTIONr_mcbond_other2.452.4062048
X-RAY DIFFRACTIONr_mcangle_it3.5663.5932561
X-RAY DIFFRACTIONr_mcangle_other3.5653.5942562
X-RAY DIFFRACTIONr_scbond_it3.0652.6941855
X-RAY DIFFRACTIONr_scbond_other3.0652.6951856
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.7133.8872757
X-RAY DIFFRACTIONr_long_range_B_refined6.2228.1084256
X-RAY DIFFRACTIONr_long_range_B_other6.18127.7864196
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.66→1.703 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.378 218 -
Rwork0.338 3913 -
obs--98.1 %

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