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- PDB-7p8y: Short wilavidin apo form -

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Basic information

Entry
Database: PDB / ID: 7p8y
TitleShort wilavidin apo form
ComponentsWilavidin
KeywordsUNKNOWN FUNCTION / Biotin binding protein / avidin / biotechnology
Function / homologyAvidin/streptavidin / Avidin-like superfamily / Avidin family / Avidin-like domain profile. / biotin binding / extracellular region / DI(HYDROXYETHYL)ETHER / TRIETHYLENE GLYCOL / Avidin
Function and homology information
Biological speciesGammaproteobacteria bacterium (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.18 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
DepositionJul 23, 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Wilavidin
B: Wilavidin
C: Wilavidin
D: Wilavidin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,96316
Polymers51,1484
Non-polymers2,81512
Water3,045169
1
A: Wilavidin
D: Wilavidin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,6777
Polymers25,5742
Non-polymers1,1035
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Wilavidin
C: Wilavidin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,2869
Polymers25,5742
Non-polymers1,7127
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)89.675, 67.687, 77.512
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212

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Components

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Protein , 1 types, 4 molecules ABCD

#1: Protein
Wilavidin


Mass: 12786.995 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Details: short wilavidin
Source: (gene. exp.) Gammaproteobacteria bacterium (bacteria)
Gene: C4528_07355 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A3A4VWA2

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Non-polymers , 5 types, 181 molecules

#2: Chemical
ChemComp-1PE / PENTAETHYLENE GLYCOL / PEG400


Mass: 238.278 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C10H22O6 / Comment: precipitant*YM
#3: Chemical
ChemComp-P6G / HEXAETHYLENE GLYCOL / POLYETHYLENE GLYCOL PEG400


Mass: 282.331 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C12H26O7 / Comment: precipitant*YM
#4: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#5: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 169 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN

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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: 2.3 Å3/Da / Density % sol: 46.51 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 1.5-1.7 M ammonium sulfate 0.1 M HEPES at pH 7.5 2-3% PEG 400

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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: Dec 2, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.96546 Å / Relative weight: 1
ReflectionResolution: 2.18→58.71 Å / Num. obs: 25250 / % possible obs: 99.5 % / Redundancy: 4.6 % / CC1/2: 0.993 / Rmerge(I) obs: 0.129 / Net I/σ(I): 9.3
Reflection shellResolution: 2.18→2.266 Å / Redundancy: 4.6 % / Num. unique obs: 2805 / CC1/2: 0.984 / % possible all: 99.9

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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: 2.18→58.71 Å / Cor.coef. Fo:Fc: 0.938 / Cor.coef. Fo:Fc free: 0.913 / SU B: 5.962 / SU ML: 0.158 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.343 / ESU R Free: 0.264 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.306 1282 5.1 %RANDOM
Rwork0.2491 ---
obs0.252 23971 99.44 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 69.39 Å2 / Biso mean: 18.496 Å2 / Biso min: 7.55 Å2
Baniso -1Baniso -2Baniso -3
1--0.89 Å2-0 Å2-0 Å2
2---0.96 Å20 Å2
3---1.85 Å2
Refinement stepCycle: final / Resolution: 2.18→58.71 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3276 0 189 169 3634
Biso mean--37.26 27.35 -
Num. residues----426
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0133553
X-RAY DIFFRACTIONr_bond_other_d0.0010.0183062
X-RAY DIFFRACTIONr_angle_refined_deg1.8661.6834807
X-RAY DIFFRACTIONr_angle_other_deg1.3381.6657152
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.4785422
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.04724.444144
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.64615456
X-RAY DIFFRACTIONr_dihedral_angle_4_deg5.822154
X-RAY DIFFRACTIONr_chiral_restr0.080.2470
X-RAY DIFFRACTIONr_gen_planes_refined0.010.023854
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02734
LS refinement shellResolution: 2.18→2.233 Å / Rfactor Rfree error: 0
RfactorNum. reflection% reflection
Rfree0.441 73 -
Rwork0.259 1758 -
obs--99.84 %

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