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- PDB-8avp: Structure of short biotin complexed agroavidin with the Hoef tail. -

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Basic information

Entry
Database: PDB / ID: 8avp
TitleStructure of short biotin complexed 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 / BIOTIN / Avidin
Function and homology information
Biological speciesRhizobium sp. AAP43 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.87 Å
AuthorsLivnah, O. / Bana, J. / Warar, 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
F: agroavCH
G: agroavCH
H: agroavCH
I: agroavCH
J: agroavCH
K: agroavCH
L: agroavCH
M: agroavCH
N: agroavCH
O: agroavCH
P: agroavCH
S: agroavCH
T: agroavCH
Q: agroavCH
R: agroavCH
hetero molecules


Theoretical massNumber of molelcules
Total (without water)279,91040
Polymers275,02320
Non-polymers4,88620
Water00
1
A: agroavCH
B: agroavCH
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,9914
Polymers27,5022
Non-polymers4892
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3460 Å2
ΔGint-13 kcal/mol
Surface area11260 Å2
MethodPISA
2
C: agroavCH
D: agroavCH
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,9914
Polymers27,5022
Non-polymers4892
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3500 Å2
ΔGint-11 kcal/mol
Surface area11140 Å2
MethodPISA
3
E: agroavCH
F: agroavCH
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,9914
Polymers27,5022
Non-polymers4892
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3460 Å2
ΔGint-13 kcal/mol
Surface area11200 Å2
MethodPISA
4
G: agroavCH
H: agroavCH
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,9914
Polymers27,5022
Non-polymers4892
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3510 Å2
ΔGint-12 kcal/mol
Surface area11070 Å2
MethodPISA
5
I: agroavCH
J: agroavCH
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,9914
Polymers27,5022
Non-polymers4892
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3590 Å2
ΔGint-12 kcal/mol
Surface area11250 Å2
MethodPISA
6
K: agroavCH
L: agroavCH
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,9914
Polymers27,5022
Non-polymers4892
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3500 Å2
ΔGint-14 kcal/mol
Surface area11170 Å2
MethodPISA
7
M: agroavCH
N: agroavCH
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,9914
Polymers27,5022
Non-polymers4892
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3550 Å2
ΔGint-14 kcal/mol
Surface area11210 Å2
MethodPISA
8
O: agroavCH
P: agroavCH
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,9914
Polymers27,5022
Non-polymers4892
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3500 Å2
ΔGint-13 kcal/mol
Surface area11430 Å2
MethodPISA
9
S: agroavCH
T: agroavCH
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,9914
Polymers27,5022
Non-polymers4892
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3560 Å2
ΔGint-12 kcal/mol
Surface area11020 Å2
MethodPISA
10
Q: agroavCH
R: agroavCH
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,9914
Polymers27,5022
Non-polymers4892
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3540 Å2
ΔGint-13 kcal/mol
Surface area11410 Å2
MethodPISA
Unit cell
Length a, b, c (Å)143.106, 81.576, 170.050
Angle α, β, γ (deg.)90.00, 114.87, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
agroavCH


Mass: 13751.172 Da / Num. of mol.: 20
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.: 20 / Source method: obtained synthetically / Formula: C10H16N2O3S / Feature type: SUBJECT OF INVESTIGATION
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: 3.27 Å3/Da / Density % sol: 62.44 %
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: 2.87→50 Å / Num. obs: 74109 / % possible obs: 99.3 % / Redundancy: 3.35 % / CC1/2: 0.993 / Rmerge(I) obs: 0.089 / Net I/σ(I): 6.8
Reflection shellResolution: 2.87→2.96 Å / Rmerge(I) obs: 0.932 / Num. unique obs: 4436 / CC1/2: 0.465

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Processing

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

8ast


Resolution: 2.87→50 Å / Cor.coef. Fo:Fc: 0.922 / Cor.coef. Fo:Fc free: 0.868 / SU B: 21.557 / SU ML: 0.387 / Cross valid method: THROUGHOUT / ESU R Free: 0.437 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.29716 4024 5.2 %RANDOM
Rwork0.23103 ---
obs0.23446 74109 94.99 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--0.1 Å2-0 Å20.01 Å2
2--0.02 Å2-0 Å2
3---0.04 Å2
Refinement stepCycle: 1 / Resolution: 2.87→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms17840 0 320 0 18160
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.01318634
X-RAY DIFFRACTIONr_bond_other_d0.0040.01516593
X-RAY DIFFRACTIONr_angle_refined_deg1.6341.63625361
X-RAY DIFFRACTIONr_angle_other_deg1.2231.58138069
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.9452402
X-RAY DIFFRACTIONr_dihedral_angle_2_deg28.26921.626861
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.236152541
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.2681580
X-RAY DIFFRACTIONr_chiral_restr0.0610.22461
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0221757
X-RAY DIFFRACTIONr_gen_planes_other0.0010.024611
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_it6.1977.4639665
X-RAY DIFFRACTIONr_mcbond_other6.197.4639664
X-RAY DIFFRACTIONr_mcangle_it9.62311.16512048
X-RAY DIFFRACTIONr_mcangle_other9.62311.16512049
X-RAY DIFFRACTIONr_scbond_it5.8467.648969
X-RAY DIFFRACTIONr_scbond_other5.8457.648970
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other9.05811.30213314
X-RAY DIFFRACTIONr_long_range_B_refined14.89972909
X-RAY DIFFRACTIONr_long_range_B_other14.89972910
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.87→2.94 Å
RfactorNum. reflection% reflection
Rfree0.449 294 -
Rwork0.41 5060 -
obs--88.44 %

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