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- PDB-8an6: The Crystal structure of wt apo agroavidin - biotin complex -

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Basic information

Entry
Database: PDB / ID: 8an6
TitleThe Crystal structure of wt apo 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: 1.9 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 4, 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 1.3Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,2028
Polymers59,2254
Non-polymers9774
Water1,08160
1
A: Agroavidin
B: Agroavidin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,1014
Polymers29,6132
Non-polymers4892
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3650 Å2
ΔGint-12 kcal/mol
Surface area11060 Å2
MethodPISA
2
C: Agroavidin
D: Agroavidin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,1014
Polymers29,6132
Non-polymers4892
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3490 Å2
ΔGint-13 kcal/mol
Surface area10830 Å2
MethodPISA
Unit cell
Length a, b, c (Å)80.089, 82.340, 67.314
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: 14806.284 Da / Num. of mol.: 4
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


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.: 60 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
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: 1.87 Å3/Da / Density % sol: 34.36 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 25% PEG 3350, 0.1 M MgCl2 and 0.1 M Bis Tris pH 6.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.972 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 8, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.972 Å / Relative weight: 1
ReflectionResolution: 1.9→43.72 Å / Num. obs: 35567 / % possible obs: 99.5 % / Redundancy: 3.9 % / CC1/2: 0.99 / Rmerge(I) obs: 0.084 / Net I/σ(I): 8.3
Reflection shellResolution: 1.9→1.94 Å / Redundancy: 4.1 % / Rmerge(I) obs: 0.978 / Num. unique obs: 2247 / CC1/2: 0.64 / % possible all: 99.7

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Processing

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

Resolution: 1.9→43.72 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.924 / SU B: 5.958 / SU ML: 0.161 / Cross valid method: THROUGHOUT / ESU R: 0.194 / ESU R Free: 0.182 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.274 1711 5 %RANDOM
Rwork0.21488 ---
obs0.21773 32452 95.49 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 33.817 Å2
Baniso -1Baniso -2Baniso -3
1--0.04 Å20 Å2-0 Å2
2--0.02 Å20 Å2
3---0.02 Å2
Refinement stepCycle: 1 / Resolution: 1.9→43.72 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3596 0 64 60 3720
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0133764
X-RAY DIFFRACTIONr_bond_other_d0.0050.0153346
X-RAY DIFFRACTIONr_angle_refined_deg1.5491.6345120
X-RAY DIFFRACTIONr_angle_other_deg1.3271.5817678
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.6755485
X-RAY DIFFRACTIONr_dihedral_angle_2_deg25.921.685178
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.16215515
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.3111516
X-RAY DIFFRACTIONr_chiral_restr0.0650.2492
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.024402
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02950
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_it2.5983.5171940
X-RAY DIFFRACTIONr_mcbond_other2.5953.5161939
X-RAY DIFFRACTIONr_mcangle_it3.9235.2632419
X-RAY DIFFRACTIONr_mcangle_other3.9225.2642420
X-RAY DIFFRACTIONr_scbond_it2.7613.6821824
X-RAY DIFFRACTIONr_scbond_other2.763.6811825
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.1655.3922700
X-RAY DIFFRACTIONr_long_range_B_refined5.91240.1124020
X-RAY DIFFRACTIONr_long_range_B_other5.91340.1014019
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.9→1.949 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.453 107 -
Rwork0.406 2376 -
obs--95.76 %

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