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- PDB-7our: Wilavidin apo form (P1 form) -

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Basic information

Entry
Database: PDB / ID: 7our
TitleWilavidin apo form (P1 form)
Componentswilavidin
KeywordsUNKNOWN FUNCTION / Biotin binding protein
Function / homologyAvidin/streptavidin / Avidin-like superfamily / Avidin family / Avidin-like domain profile. / biotin binding / extracellular region / Avidin
Function and homology information
Biological speciesGammaproteobacteria bacterium (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å
AuthorsAvraham, O. / Livnah, O.
CitationJournal: Febs J. / Year: 2022
Title: Wilavidin - a novel member of the avidin family that forms unique biotin-binding hexamers.
Authors: Avraham, O. / Bayer, E.A. / Livnah, O.
History
DepositionJun 13, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 17, 2021Provider: repository / Type: Initial release
Revision 1.1Mar 23, 2022Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation.year / _citation_author.identifier_ORCID
Revision 1.2Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.3Nov 13, 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: wilavidin
C: wilavidin
D: wilavidin
F: wilavidin
B: wilavidin
E: wilavidin


Theoretical massNumber of molelcules
Total (without water)84,2856
Polymers84,2856
Non-polymers00
Water3,063170
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: light scattering, Wilavidin is hexameric in solution, as verified by IEX-MALS and indicated in the publication.
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area20410 Å2
ΔGint-157 kcal/mol
Surface area24900 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.320, 56.721, 62.641
Angle α, β, γ (deg.)103.530, 110.750, 105.630
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
wilavidin


Mass: 14047.544 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Gammaproteobacteria bacterium (bacteria)
Gene: C4528_07355 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A3A4VWA2
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 170 / 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

CrystalDensity Matthews: 1.78 Å3/Da / Density % sol: 30.82 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 1.6 M sodium citrate tribasic pH 6.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-1 / Wavelength: 0.96546 Å
DetectorType: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Oct 11, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.96546 Å / Relative weight: 1
ReflectionResolution: 1.95→46.7 Å / Num. obs: 40032 / % possible obs: 94.6 % / Redundancy: 1.7 % / CC1/2: 0.91 / Rsym value: 0.112 / Net I/σ(I): 5.6
Reflection shellResolution: 1.95→2 Å / Num. unique obs: 2788 / CC1/2: 0.674

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Processing

Software
NameVersionClassification
Aimlessdata scaling
REFMAC5.8.0238refinement
PDB_EXTRACT3.27data extraction
autoPROCdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7OUQ

7ouq


Resolution: 1.95→46.7 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.921 / SU B: 5.217 / SU ML: 0.142 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.22 / ESU R Free: 0.176 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2259 1971 4.9 %RANDOM
Rwork0.1801 ---
obs0.1823 38031 94.58 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 75.49 Å2 / Biso mean: 17.677 Å2 / Biso min: 1.03 Å2
Baniso -1Baniso -2Baniso -3
1-1.08 Å2-0.52 Å2-0.28 Å2
2---0.04 Å2-0.44 Å2
3---0.03 Å2
Refinement stepCycle: final / Resolution: 1.95→46.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5481 0 0 170 5651
Biso mean---21.24 -
Num. residues----713
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0125631
X-RAY DIFFRACTIONr_bond_other_d0.0010.0184842
X-RAY DIFFRACTIONr_angle_refined_deg1.7211.647705
X-RAY DIFFRACTIONr_angle_other_deg1.3521.56111294
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.3325707
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.18924.85233
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.54515837
X-RAY DIFFRACTIONr_dihedral_angle_4_deg7.566156
X-RAY DIFFRACTIONr_chiral_restr0.0750.2781
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.026319
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021175
LS refinement shellResolution: 1.95→2.001 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.279 141 -
Rwork0.261 2763 -
all-2904 -
obs--94.29 %

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