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- PDB-6hdt: crystal structure of short afifavidin - biotin complex -

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Basic information

Entry
Database: PDB / ID: 6hdt
Titlecrystal structure of short afifavidin - biotin complex
ComponentsShort afifavidin
Keywordsbiotin binding protein / avidin / biotin / high affinity systems / 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
BIOTIN / Short afifavidin
Similarity search - Component
Biological speciesAfifella pfennigii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.54 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 19, 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

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Assembly

Deposited unit
A: Short afifavidin
B: Short afifavidin
C: Short afifavidin
D: Short afifavidin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,5228
Polymers55,5454
Non-polymers9774
Water2,198122
1
A: Short afifavidin
C: Short afifavidin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,2614
Polymers27,7722
Non-polymers4892
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2720 Å2
ΔGint-21 kcal/mol
Surface area10980 Å2
MethodPISA
2
B: Short afifavidin
D: Short afifavidin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,2614
Polymers27,7722
Non-polymers4892
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2600 Å2
ΔGint-22 kcal/mol
Surface area10650 Å2
MethodPISA
Unit cell
Length a, b, c (Å)42.131, 65.218, 67.738
Angle α, β, γ (deg.)90.00, 100.25, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Short afifavidin


Mass: 13886.132 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: A0A493R6W9*PLUS
#2: Chemical
ChemComp-BTN / BIOTIN / 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 / Water


Mass: 18.015 Da / Num. of mol.: 122 / 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

Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5 / Details: 1.3-1.5M Ammonium Sulfate, 0.1M Acetate pH 5.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Nov 22, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.53→46.62 Å / Num. obs: 52210 / % possible obs: 95.8 % / Redundancy: 3 % / Rsym value: 0.081 / Net I/σ(I): 7
Reflection shellResolution: 1.53→1.59 Å

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Processing

Software
NameVersionClassification
REFMAC5.8.0071refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6HDS

6hds


Resolution: 1.54→46.62 Å / Cor.coef. Fo:Fc: 0.973 / Cor.coef. Fo:Fc free: 0.957 / SU B: 7.208 / SU ML: 0.103 / Cross valid method: THROUGHOUT / ESU R: 0.128 / ESU R Free: 0.096 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22012 2608 5 %RANDOM
Rwork0.16282 ---
obs0.16571 49575 96.67 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 24.1 Å2
Baniso -1Baniso -2Baniso -3
1-3.48 Å20 Å20.83 Å2
2---1.76 Å2-0 Å2
3----1.9 Å2
Refinement stepCycle: 1 / Resolution: 1.54→46.62 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3600 0 64 122 3786
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.023798
X-RAY DIFFRACTIONr_bond_other_d0.0010.023243
X-RAY DIFFRACTIONr_angle_refined_deg1.6451.9095219
X-RAY DIFFRACTIONr_angle_other_deg0.84137454
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6885498
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.38525.732164
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.13415455
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.609153
X-RAY DIFFRACTIONr_chiral_restr0.0910.2573
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.024579
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02960
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_it3.3222.291974
X-RAY DIFFRACTIONr_mcbond_other3.3152.2891973
X-RAY DIFFRACTIONr_mcangle_it4.1853.4452463
X-RAY DIFFRACTIONr_mcangle_other4.1863.4462464
X-RAY DIFFRACTIONr_scbond_it3.8912.4621824
X-RAY DIFFRACTIONr_scbond_other3.8932.4621822
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.5743.5922751
X-RAY DIFFRACTIONr_long_range_B_refined4.80218.9024203
X-RAY DIFFRACTIONr_long_range_B_other4.76618.8264173
X-RAY DIFFRACTIONr_rigid_bond_restr5.02537041
X-RAY DIFFRACTIONr_sphericity_free26.747532
X-RAY DIFFRACTIONr_sphericity_bonded16.70157019
LS refinement shellResolution: 1.535→1.575 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.363 177 -
Rwork0.318 3360 -
obs--88.74 %

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