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- PDB-6avk: Streptavidin bound to peptide-like compound KPM-6 -

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Basic information

Entry
Database: PDB / ID: 6avk
TitleStreptavidin bound to peptide-like compound KPM-6
ComponentsStreptavidin
KeywordsBIOTIN BINDING PROTEIN / streptavidin
Function / homology
Function and homology information


biotin binding / extracellular region
Similarity search - Function
Avidin-like / Avidin-like, conserved site / Avidin-like domain signature. / Avidin / Avidin/streptavidin / Avidin-like superfamily / Avidin family / Avidin-like domain profile. / Lipocalin / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Chem-BZ4 / 1-hydroxydodecan-4-one / Streptavidin
Similarity search - Component
Biological speciesStreptomyces avidinii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 Å
AuthorsPark, H. / Shamim, R. / McEnaney, P. / Kodadek, T.
CitationJournal: To be Published
Title: Efficient Workflow for Screening DNA-encoded One Bead One Compound Libraries Using a Flow Cytometer
Authors: McEnaney, P. / Dickson, P. / Dang, V. / MacConnell, A. / Cavett, V. / Reza, S. / Park, H. / Paegel, B. / Kodadek, T.
History
DepositionSep 2, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 8, 2018Provider: repository / Type: Initial release
Revision 1.1Oct 4, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Streptavidin
B: Streptavidin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,8074
Polymers25,9302
Non-polymers8772
Water5,441302
1
A: Streptavidin
B: Streptavidin
hetero molecules

A: Streptavidin
B: Streptavidin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,6158
Polymers51,8604
Non-polymers1,7554
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_655-x+1,y,-z1
Buried area9120 Å2
ΔGint-54 kcal/mol
Surface area19430 Å2
MethodPISA
Unit cell
Length a, b, c (Å)47.310, 93.520, 104.450
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222
Components on special symmetry positions
IDModelComponents
11B-22-

TYR

21B-349-

HOH

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Components

#1: Protein Streptavidin


Mass: 12965.025 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Streptomyces avidinii (bacteria) / References: UniProt: P22629
#2: Chemical ChemComp-BZ4 / N-[(2H-1,3-benzodioxol-5-yl)methyl]-2-({[(2H-1,3-benzodioxol-5-yl)methyl][2-(chloromethyl)-1,3-oxazole-4-carbonyl]amino}methyl)-N-[(4-carbamoyl-1,3-oxazol-2-yl)methyl]-1,3-oxazole-4-carboxamide


Mass: 677.017 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C31H25ClN6O10
#3: Chemical ChemComp-HDO / 1-hydroxydodecan-4-one


Mass: 200.318 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C12H24O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 302 / Source method: isolated from a natural source / Formula: H2O

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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: 2.23 Å3/Da / Density % sol: 44.79 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop / Details: 0.2 M potassium iodide, 20% PEG3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.1 / Wavelength: 0.9774 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Aug 16, 2017
RadiationMonochromator: Si(220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9774 Å / Relative weight: 1
ReflectionResolution: 1.4→69.65 Å / Num. obs: 45941 / % possible obs: 99.99 % / Redundancy: 5.8 % / Biso Wilson estimate: 16.07 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.042 / Rpim(I) all: 0.027 / Rrim(I) all: 0.05 / Net I/σ(I): 18
Reflection shellResolution: 1.4→1.42 Å / Redundancy: 4.5 % / Rmerge(I) obs: 0.337 / Mean I/σ(I) obs: 3.4 / Num. unique all: 9975 / Num. unique obs: 2212 / CC1/2: 0.861 / Rpim(I) all: 0.239 / Rrim(I) all: 0.416 / % possible all: 98.3

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Processing

Software
NameVersionClassification
BUSTER2.10.2refinement
iMOSFLMdata reduction
SCALAdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1VWA

1vwa


Resolution: 1.4→69.67 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.962 / Rfactor Rfree error: 0 / SU R Cruickshank DPI: 0.06 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.065 / SU Rfree Blow DPI: 0.061 / SU Rfree Cruickshank DPI: 0.058
RfactorNum. reflection% reflectionSelection details
Rfree0.186 2251 4.9 %RANDOM
Rwork0.174 ---
obs0.174 45903 99.8 %-
Displacement parametersBiso mean: 20.78 Å2
Baniso -1Baniso -2Baniso -3
1--0.6945 Å20 Å20 Å2
2--0.2473 Å20 Å2
3---0.4472 Å2
Refine analyzeLuzzati coordinate error obs: 0.16 Å
Refinement stepCycle: 1 / Resolution: 1.4→69.67 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1808 0 62 303 2173
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.012046HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.112857HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d635SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes37HARMONIC2
X-RAY DIFFRACTIONt_gen_planes303HARMONIC5
X-RAY DIFFRACTIONt_it2046HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion4.76
X-RAY DIFFRACTIONt_other_torsion13.27
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion261SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact2675SEMIHARMONIC4
LS refinement shellResolution: 1.4→1.44 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.23 151 4.56 %
Rwork0.201 3163 -
all0.203 3314 -
obs--98.71 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.6697-0.2438-0.47131.31650.46211.0381-0.0149-0.00030.0461-0.00060.00060.0626-0.1776-0.04080.0143-0.0208-0.0032-0.0021-0.04260.0022-0.038315.913629.327511.5698
20.6066-0.257-0.35940.99470.09591.1157-0.0802-0.0402-0.12410.11330.01150.09540.07220.04390.0687-0.0299-0.00090.0122-0.0480.0086-0.025321.320913.761513.6698
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{ A|* }
2X-RAY DIFFRACTION2{ B|* }

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