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- PDB-6hds: Crystal Structure of apo short afifavidin -

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Basic information

Entry
Database: PDB / ID: 6hds
TitleCrystal Structure of apo short afifavidin
Componentsshort afifavidin
Keywordsbiotin binding protein / avidin / biotin / protein assembly / 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
Biological speciesAfifella pfennigii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.74 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
Revision 1.3Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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


Theoretical massNumber of molelcules
Total (without water)55,5454
Polymers55,5454
Non-polymers00
Water2,450136
1
A: short afifavidin
C: short afifavidin


Theoretical massNumber of molelcules
Total (without water)27,7722
Polymers27,7722
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2640 Å2
ΔGint-21 kcal/mol
Surface area10620 Å2
MethodPISA
2
B: short afifavidin
D: short afifavidin


Theoretical massNumber of molelcules
Total (without water)27,7722
Polymers27,7722
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2570 Å2
ΔGint-22 kcal/mol
Surface area10050 Å2
MethodPISA
Unit cell
Length a, b, c (Å)41.991, 64.952, 68.114
Angle α, β, γ (deg.)90.00, 100.07, 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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 136 / Source method: isolated from a natural source / Formula: H2O
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

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 PILATUS 6M-F / 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: 1.74→67.06 Å / Num. obs: 35450 / % possible obs: 95.7 % / Redundancy: 2.7 % / Rsym value: 0.043 / Net I/σ(I): 11.6
Reflection shellResolution: 1.74→1.77 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: 1.74→46.7 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.945 / SU B: 3.468 / SU ML: 0.107 / Cross valid method: THROUGHOUT / ESU R: 0.148 / ESU R Free: 0.138 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23066 1775 5 %RANDOM
Rwork0.18448 ---
obs0.18679 33657 95.51 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 24.983 Å2
Baniso -1Baniso -2Baniso -3
1-0.4 Å20 Å2-0.04 Å2
2--0.48 Å20 Å2
3----0.81 Å2
Refinement stepCycle: 1 / Resolution: 1.74→46.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3603 0 0 136 3739
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0143714
X-RAY DIFFRACTIONr_bond_other_d0.0010.0183029
X-RAY DIFFRACTIONr_angle_refined_deg1.5591.6325100
X-RAY DIFFRACTIONr_angle_other_deg1.0551.6417056
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.3885492
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.20625.394165
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.57115452
X-RAY DIFFRACTIONr_dihedral_angle_4_deg4.202153
X-RAY DIFFRACTIONr_chiral_restr0.0790.2490
X-RAY DIFFRACTIONr_gen_planes_refined0.010.024370
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02802
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_it2.3522.461968
X-RAY DIFFRACTIONr_mcbond_other2.3492.461967
X-RAY DIFFRACTIONr_mcangle_it3.5043.6772454
X-RAY DIFFRACTIONr_mcangle_other3.5043.6772455
X-RAY DIFFRACTIONr_scbond_it2.8092.6551746
X-RAY DIFFRACTIONr_scbond_other2.8082.6561747
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.1623.8822645
X-RAY DIFFRACTIONr_long_range_B_refined5.53729.2944179
X-RAY DIFFRACTIONr_long_range_B_other5.52329.1944148
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.74→1.785 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.346 130 -
Rwork0.284 2518 -
obs--97.21 %

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