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- PDB-8avj: Structure of short apo agroavidin with the Hoef tail. -

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Basic information

Entry
Database: PDB / ID: 8avj
TitleStructure of short apo agroavidin with the Hoef tail.
ComponentsagroavCH
KeywordsUNKNOWN FUNCTION / avidin / streptavidin / high-affinity systems / dimeric avidins / multimers
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: 2.1 Å
AuthorsLivnah, O. / Bana, J. / Warwar, 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 26, 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: agroavCH
B: agroavCH
C: agroavCH
D: agroavCH
E: agroavCH
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,43916
Polymers68,7565
Non-polymers68311
Water3,153175
1
A: agroavCH
B: agroavCH
C: agroavCH
D: agroavCH
E: agroavCH
hetero molecules

A: agroavCH
B: agroavCH
C: agroavCH
D: agroavCH
E: agroavCH
hetero molecules


Theoretical massNumber of molelcules
Total (without water)138,87732
Polymers137,51210
Non-polymers1,36522
Water18010
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_554x-y,-y,-z-2/31
Buried area30140 Å2
ΔGint-153 kcal/mol
Surface area53670 Å2
MethodPISA
Unit cell
Length a, b, c (Å)116.697, 116.697, 147.889
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221
Components on special symmetry positions
IDModelComponents
11A-309-

HOH

21A-314-

HOH

31B-333-

HOH

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Components

#1: Protein
agroavCH


Mass: 13751.172 Da / Num. of mol.: 5
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-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: C2H6O2 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 175 / 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: 4.23 Å3/Da / Density % sol: 70.91 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 20% ethylene glycol 0.05M acetic acid pH 3.2

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID30B / Wavelength: 0.965 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Oct 10, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.965 Å / Relative weight: 1
ReflectionResolution: 2.1→49.3 Å / Num. obs: 64372 / % possible obs: 99.3 % / Redundancy: 5.2 % / CC1/2: 0.998 / Rmerge(I) obs: 0.051 / Net I/σ(I): 0.998
Reflection shellResolution: 2.1→2.134 Å / Rmerge(I) obs: 0.613 / Num. unique obs: 16884 / CC1/2: 0.729

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
MOSFLMdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 8ASU

8asu


Resolution: 2.1→49.3 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.946 / SU B: 3.843 / SU ML: 0.099 / Cross valid method: THROUGHOUT / ESU R: 0.145 / ESU R Free: 0.137 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23029 3432 5.1 %RANDOM
Rwork0.20258 ---
obs0.20398 64372 99.07 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 44.211 Å2
Baniso -1Baniso -2Baniso -3
1--0 Å2-0 Å2-0 Å2
2---0 Å2-0 Å2
3---0.01 Å2
Refinement stepCycle: 1 / Resolution: 2.1→49.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4760 0 44 175 4979
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0134903
X-RAY DIFFRACTIONr_bond_other_d0.0020.0154415
X-RAY DIFFRACTIONr_angle_refined_deg1.7781.6356652
X-RAY DIFFRACTIONr_angle_other_deg1.4251.57810121
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.735640
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.29922.558215
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.08615695
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.9351520
X-RAY DIFFRACTIONr_chiral_restr0.0810.2645
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.025695
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021185
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_it4.2074.542575
X-RAY DIFFRACTIONr_mcbond_other4.2034.5392574
X-RAY DIFFRACTIONr_mcangle_it5.6846.7853210
X-RAY DIFFRACTIONr_mcangle_other5.6856.7873211
X-RAY DIFFRACTIONr_scbond_it4.9474.8692328
X-RAY DIFFRACTIONr_scbond_other4.9464.872329
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other6.9767.0893443
X-RAY DIFFRACTIONr_long_range_B_refined8.25251.025195
X-RAY DIFFRACTIONr_long_range_B_other8.25251.0295196
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.1→2.154 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.32 258 -
Rwork0.28 4631 -
obs--97.43 %

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