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- PDB-8ty0: Streptavidin variant S112E-K121H bound to bis-biotinylated Iron-p... -

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Basic information

Entry
Database: PDB / ID: 8ty0
TitleStreptavidin variant S112E-K121H bound to bis-biotinylated Iron-porphyrin
ComponentsStreptavidin
KeywordsMETAL BINDING PROTEIN / Artificial metalloprotein / biotin-binding protein / streptavidin / artificial metalloenzyme
Function / homology
Function and homology information


biotin binding / 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 speciesStreptomyces avidinii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.54 Å
AuthorsFollmer, A.H. / Jakob, R.P. / Mukherjee, M. / Ward, T.R.
Funding support Switzerland, 1items
OrganizationGrant numberCountry
Swiss National Science Foundation Switzerland
CitationJournal: To Be Published
Title: An Artificial Peroxidase based on the Biotin-Streptavidin Technology that Rivals Natural Peroxidases
Authors: Mukherjee, M. / Waser, V. / Igareta, N.V. / Follmer, A.H. / Jakob, R.P. / Maier, T. / Uzumcu, D. / Ward, T.R.
History
DepositionAug 24, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 11, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)68,3146
Polymers65,9594
Non-polymers2,3542
Water10,413578
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10420 Å2
ΔGint-56 kcal/mol
Surface area19100 Å2
MethodPISA
Unit cell
Length a, b, c (Å)192.487, 57.720, 57.770
Angle α, β, γ (deg.)90.000, 107.440, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z

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Components

#1: Protein
Streptavidin


Mass: 16489.824 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces avidinii (bacteria) / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P22629
#2: Chemical ChemComp-SIK / Bis-biotinylated Iron-porphyrin


Mass: 1177.136 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C48H56FeN12O12S4 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 578 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.32 Å3/Da / Density % sol: 47 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4.5
Details: 0.2 M ammonium sulfate, 0.1 M sodium acetate pH 4.5 , 20% PEG 4000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Mar 31, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.54→55.11 Å / Num. obs: 84181 / % possible obs: 94.31 % / Redundancy: 3.6 % / Biso Wilson estimate: 13.17 Å2 / CC1/2: 0.996 / CC star: 0.999 / Rmerge(I) obs: 0.07247 / Rpim(I) all: 0.04319 / Rrim(I) all: 0.08485 / Net I/σ(I): 9.09
Reflection shellResolution: 1.54→1.6 Å / Rmerge(I) obs: 0.408 / Mean I/σ(I) obs: 2.57 / Num. unique obs: 8699 / CC1/2: 0.795 / CC star: 0.941 / Rpim(I) all: 0.2488 / Rrim(I) all: 0.4806 / % possible all: 97.66

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.54→55.11 Å / SU ML: 0.1566 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 18.2301
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1908 3823 4.54 %
Rwork0.1735 80314 -
obs0.1743 84137 94.31 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 19.53 Å2
Refinement stepCycle: LAST / Resolution: 1.54→55.11 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3735 0 154 578 4467
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01574466
X-RAY DIFFRACTIONf_angle_d2.46756228
X-RAY DIFFRACTIONf_chiral_restr0.0988662
X-RAY DIFFRACTIONf_plane_restr0.0105781
X-RAY DIFFRACTIONf_dihedral_angle_d16.89131610
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.54-1.560.2461490.21943101X-RAY DIFFRACTION97.74
1.56-1.580.26051340.21563000X-RAY DIFFRACTION97.57
1.58-1.60.2216650.21533195X-RAY DIFFRACTION97.69
1.6-1.630.21771170.20323024X-RAY DIFFRACTION97.43
1.63-1.650.21531000.19833168X-RAY DIFFRACTION97.06
1.65-1.680.27221840.18792961X-RAY DIFFRACTION96.8
1.68-1.70.21581810.19473030X-RAY DIFFRACTION96.54
1.7-1.730.22131110.19623012X-RAY DIFFRACTION96.51
1.73-1.770.18371090.19533052X-RAY DIFFRACTION95.88
1.77-1.80.21861880.19292946X-RAY DIFFRACTION95.23
1.8-1.840.2441310.19422832X-RAY DIFFRACTION91.59
1.84-1.880.21321580.18063018X-RAY DIFFRACTION95.2
1.88-1.920.18511690.17062991X-RAY DIFFRACTION96.05
1.92-1.970.17481500.16963028X-RAY DIFFRACTION96.13
1.97-2.020.19891560.16973015X-RAY DIFFRACTION95.66
2.02-2.080.12861000.15662989X-RAY DIFFRACTION95.37
2.08-2.150.17961710.16483008X-RAY DIFFRACTION94.67
2.15-2.220.16651570.16422966X-RAY DIFFRACTION94.35
2.22-2.310.17241410.17352959X-RAY DIFFRACTION93.57
2.31-2.420.18771380.1752861X-RAY DIFFRACTION92.88
2.42-2.550.17041230.16822879X-RAY DIFFRACTION90.07
2.55-2.710.16711740.16352908X-RAY DIFFRACTION92.44
2.71-2.910.19541400.16262924X-RAY DIFFRACTION92.99
2.91-3.210.19851290.17152956X-RAY DIFFRACTION92.42
3.21-3.670.19061430.16222896X-RAY DIFFRACTION91.26
3.67-4.620.16451360.15052806X-RAY DIFFRACTION87.87
4.63-55.110.21351690.18572789X-RAY DIFFRACTION86.01

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