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- PDB-7zn1: Avidin + Biotin-Tempo -

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ID or keywords:

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Basic information

Entry
Database: PDB / ID: 7zn1
TitleAvidin + Biotin-Tempo
ComponentsAvidin
KeywordsPROTEIN BINDING / Avidin / Biotin / TEMPO free radical
Function / homology
Function and homology information


biotin binding / antibacterial humoral response / extracellular region
Similarity search - Function
Avidin-like, conserved site / Avidin-like domain signature. / Avidin / : / Avidin/streptavidin / Avidin-like superfamily / Avidin family / Avidin-like domain profile.
Similarity search - Domain/homology
Biological speciesGallus gallus (chicken)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.33 Å
AuthorsMilani, J. / Lau, K. / Pojer, F. / Ansermet, J.P. / Saenz, F.
Funding support1items
OrganizationGrant numberCountry
Other government
CitationJournal: To Be Published
Title: Avidin + Biotin-Tempo
Authors: Milani, J. / Lau, K. / Pojer, F. / Ansermet, J.P. / Saenz, F.
History
DepositionApr 20, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 10, 2023Provider: repository / Type: Initial release
Revision 1.1Feb 7, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond
Revision 1.2Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)70,24120
Polymers67,1494
Non-polymers3,09216
Water77543
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12390 Å2
ΔGint-223 kcal/mol
Surface area18680 Å2
MethodPISA
Unit cell
Length a, b, c (Å)59.353, 80.952, 60.951
Angle α, β, γ (deg.)90.000, 119.079, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

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Protein , 1 types, 4 molecules ABCD

#1: Protein
Avidin


Mass: 16787.193 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Gallus gallus (chicken) / References: UniProt: P02701

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Sugars , 2 types, 4 molecules

#2: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}LINUCSPDB-CARE
#3: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 4 types, 55 molecules

#4: Chemical
ChemComp-KFL / 6-[(3~{a}~{S},4~{S},6~{a}~{R})-2-oxidanylidene-1,3,3~{a},4,6,6~{a}-hexahydrothieno[3,4-d]imidazol-4-yl]-~{N}-(2,2,6,6-tetramethyl-1-oxidanyl-piperidin-4-yl)hexanamide


Mass: 412.590 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C20H36N4O3S / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#6: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Formula: Na
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 43 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
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: 1.91 Å3/Da / Density % sol: 35.46 %
Crystal growTemperature: 298.15 K / Method: vapor diffusion, sitting drop / Details: 0.2 M Zinc Acetate dihydrate 22% w/v PEG3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Dec 10, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.33→44.5 Å / Num. obs: 40645 / % possible obs: 95.9 % / Redundancy: 2.13 % / Biso Wilson estimate: 44.79 Å2 / CC1/2: 0.995 / Net I/σ(I): 5.13
Reflection shellResolution: 2.33→2.48 Å / Num. unique obs: 6570 / CC1/2: 0.609

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Processing

Software
NameVersionClassification
PHENIXdev_4827refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1rav

1rav


Resolution: 2.33→44.5 Å / SU ML: 0.3528 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 36.7179
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2788 1057 4.99 %
Rwork0.2264 20110 -
obs0.2289 21167 98.28 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 50.84 Å2
Refinement stepCycle: LAST / Resolution: 2.33→44.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3690 0 190 43 3923
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00313949
X-RAY DIFFRACTIONf_angle_d0.50035366
X-RAY DIFFRACTIONf_chiral_restr0.0382631
X-RAY DIFFRACTIONf_plane_restr0.0036650
X-RAY DIFFRACTIONf_dihedral_angle_d19.17221403
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.33-2.440.39931290.34422468X-RAY DIFFRACTION96.47
2.44-2.570.34821330.33122519X-RAY DIFFRACTION99.25
2.57-2.730.3921310.30532527X-RAY DIFFRACTION99.33
2.73-2.940.30891320.26522512X-RAY DIFFRACTION99.21
2.94-3.240.33421330.24032533X-RAY DIFFRACTION99.03
3.24-3.710.28161330.2072510X-RAY DIFFRACTION97.96
3.71-4.670.23161320.18112496X-RAY DIFFRACTION97.33
4.67-44.50.22171340.19962545X-RAY DIFFRACTION97.74

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