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- PDB-8aqj: Hydrophobic probe bound to Streptavidin - 2 -

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Basic information

Entry
Database: PDB / ID: 8aqj
TitleHydrophobic probe bound to Streptavidin - 2
ComponentsStreptavidin
KeywordsUNKNOWN FUNCTION / 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
Chem-N9O / Streptavidin
Similarity search - Component
Biological speciesStreptomyces avidinii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 Å
AuthorsIgareta, N.V. / Ward, T.R.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: Hydrophobic probe bound to Streptavidin - 2
Authors: Igareta, N.V. / Ward, T.R.
History
DepositionAug 12, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 31, 2022Provider: repository / Type: Initial release
Revision 1.1Jan 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: Streptavidin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,9482
Polymers16,4391
Non-polymers5101
Water86548
1
A: Streptavidin
hetero molecules

A: Streptavidin
hetero molecules

A: Streptavidin
hetero molecules

A: Streptavidin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,7948
Polymers65,7554
Non-polymers2,0384
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_665-y+1,-x+1,-z1
crystal symmetry operation10_665-x+1,-y+1,z1
crystal symmetry operation15_555y,x,-z1
Buried area9140 Å2
ΔGint-55 kcal/mol
Surface area19420 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.345, 57.345, 174.447
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number98
Space group name H-MI4122
Components on special symmetry positions
IDModelComponents
11A-317-

HOH

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Components

#1: Protein Streptavidin


Mass: 16438.820 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces avidinii (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: P22629
#2: Chemical ChemComp-N9O / 5-[(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-[6-(dimethylamino)-1,3-bis(oxidanylidene)benzo[de]isoquinolin-2-yl]ethyl]pentanamide


Mass: 509.620 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C26H31N5O4S / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 48 / 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: 2.18 Å3/Da / Density % sol: 43.6 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4 / Details: 25 % w/v PEG 3350 0.1 M sodium acetate pH 4.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1.0000413700317 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jul 2, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0000413700317 Å / Relative weight: 1
ReflectionResolution: 1.85→43.61 Å / Num. obs: 12929 / % possible obs: 100 % / Redundancy: 20 % / CC1/2: 0.999 / Net I/σ(I): 23.1
Reflection shellResolution: 1.85→1.89 Å / Num. unique obs: 750 / CC1/2: 0.993

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Processing

Software
NameVersionClassification
Aimlessdata scaling
REFMAC5.8.0352refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3pk2

3pk2


Resolution: 1.85→43.61 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.927 / SU B: 2.876 / SU ML: 0.085 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.133 / ESU R Free: 0.128 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2341 655 5.1 %RANDOM
Rwork0.1979 ---
obs0.1998 12239 99.87 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 109.13 Å2 / Biso mean: 28.708 Å2 / Biso min: 14.74 Å2
Baniso -1Baniso -2Baniso -3
1--1.41 Å2-0 Å20 Å2
2---1.41 Å20 Å2
3---2.82 Å2
Refinement stepCycle: final / Resolution: 1.85→43.61 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms936 0 36 48 1020
Biso mean--35.16 38.01 -
Num. residues----125
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0111010
X-RAY DIFFRACTIONr_bond_other_d0.0010.016852
X-RAY DIFFRACTIONr_angle_refined_deg1.7511.6411384
X-RAY DIFFRACTIONr_angle_other_deg0.6121.6111975
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.5245126
X-RAY DIFFRACTIONr_dihedral_angle_2_deg4.30355
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.42210136
X-RAY DIFFRACTIONr_chiral_restr0.080.2149
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.021290
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02222
LS refinement shellResolution: 1.85→1.898 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.237 46 -
Rwork0.223 849 -
all-895 -
obs--100 %

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