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- PDB-6hdv: The crystal structure of intact afifavidin apo form -

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Basic information

Entry
Database: PDB / ID: 6hdv
TitleThe crystal structure of intact afifavidin apo form
ComponentsAfifavidin
Keywordsbiotin binding protein / avidin-biotin system / bacterial avidins / self assembly / dimeric avidins
Function / homology
Function and homology information


biotin binding / extracellular region
Similarity search - Function
Avidin-like / Avidin/streptavidin / Avidin-like superfamily / Avidin family / Avidin-like domain profile. / Lipocalin / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Biological speciesAfifella pfennigii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.16 Å
AuthorsLivnah, O. / Avraham, O.
CitationJournal: FEBS J. / Year: 2018
Title: Crystal structure of afifavidin reveals common features of molecular assemblage in the bacterial dimeric avidins.
Authors: Avraham, O. / Bayer, E.A. / Livnah, O.
History
DepositionAug 20, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 14, 2018Provider: repository / Type: Initial release
Revision 1.1Dec 26, 2018Group: Data collection / Database references
Category: citation / database_PDB_rev ...citation / database_PDB_rev / database_PDB_rev_record / pdbx_database_proc
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Jan 17, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Afifavidin
B: Afifavidin
C: Afifavidin
D: Afifavidin


Theoretical massNumber of molelcules
Total (without water)57,8954
Polymers57,8954
Non-polymers00
Water2,720151
1
A: Afifavidin
D: Afifavidin

A: Afifavidin
D: Afifavidin

B: Afifavidin
C: Afifavidin

B: Afifavidin
C: Afifavidin


Theoretical massNumber of molelcules
Total (without water)115,7918
Polymers115,7918
Non-polymers00
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
crystal symmetry operation4_445y-1/2,-x-1/2,z1
crystal symmetry operation5_445-x-1/2,y-1/2,-z1
Buried area23140 Å2
ΔGint-154 kcal/mol
Surface area41220 Å2
MethodPISA
2
A: Afifavidin
D: Afifavidin


Theoretical massNumber of molelcules
Total (without water)28,9482
Polymers28,9482
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2690 Å2
ΔGint-22 kcal/mol
Surface area13340 Å2
MethodPISA
3
B: Afifavidin
C: Afifavidin


Theoretical massNumber of molelcules
Total (without water)28,9482
Polymers28,9482
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2660 Å2
ΔGint-21 kcal/mol
Surface area13490 Å2
MethodPISA
Unit cell
Length a, b, c (Å)161.986, 161.986, 46.980
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number90
Space group name H-MP4212
Components on special symmetry positions
IDModelComponents
11D-216-

HOH

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Components

#1: Protein
Afifavidin


Mass: 14473.842 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Afifella pfennigii (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: A0A493R6X0*PLUS
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 151 / Source method: isolated from a natural source / Formula: H2O

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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: 2.66 Å3/Da / Density % sol: 53.79 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 1.4M Ammonium Sulfate, 0.1M Bis-Tris pH 7.0, 1% PEG 2000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.97625 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 7, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97625 Å / Relative weight: 1
ReflectionResolution: 2.16→44.93 Å / Num. obs: 32236 / % possible obs: 94.5 % / Redundancy: 5.3 % / Rsym value: 0.089 / Net I/σ(I): 9.2
Reflection shellResolution: 2.16→2.23 Å

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Processing

Software
NameVersionClassification
REFMAC5.8.0230refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3EW1

3ew1


Resolution: 2.16→44.93 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.939 / SU B: 10.115 / SU ML: 0.22 / Cross valid method: THROUGHOUT / ESU R: 0.238 / ESU R Free: 0.209 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25308 1579 4.9 %RANDOM
Rwork0.19478 ---
obs0.19752 30620 94.11 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 46.747 Å2
Baniso -1Baniso -2Baniso -3
1--2.87 Å2-0 Å20 Å2
2---2.87 Å20 Å2
3---5.75 Å2
Refinement stepCycle: 1 / Resolution: 2.16→44.93 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4012 0 0 151 4163
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0144119
X-RAY DIFFRACTIONr_bond_other_d0.0010.0183438
X-RAY DIFFRACTIONr_angle_refined_deg1.7091.6415629
X-RAY DIFFRACTIONr_angle_other_deg1.0151.6448032
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.45539
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.19625.556180
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.90615556
X-RAY DIFFRACTIONr_dihedral_angle_4_deg26.575154
X-RAY DIFFRACTIONr_chiral_restr0.0840.2544
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.024777
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02847
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_it4.6354.6692170
X-RAY DIFFRACTIONr_mcbond_other4.6044.6692169
X-RAY DIFFRACTIONr_mcangle_it6.7546.9862704
X-RAY DIFFRACTIONr_mcangle_other6.7596.9882705
X-RAY DIFFRACTIONr_scbond_it5.1164.9261949
X-RAY DIFFRACTIONr_scbond_other5.1164.9291950
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other7.3547.2112926
X-RAY DIFFRACTIONr_long_range_B_refined9.40652.6824503
X-RAY DIFFRACTIONr_long_range_B_other9.44952.6574480
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.16→2.216 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.382 111 -
Rwork0.37 2149 -
obs--91.61 %

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