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- PDB-9csv: Streptavidin-E101Q-S112Y-K121A bound to Cu(II)-biotin-ethyl-dipic... -

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Basic information

Entry
Database: PDB / ID: 9csv
TitleStreptavidin-E101Q-S112Y-K121A bound to Cu(II)-biotin-ethyl-dipicolylamine cofactor, oxidized by hydrogen peroxide
ComponentsStreptavidin
KeywordsMETAL BINDING PROTEIN / biotin-streptavidin complex / artificial metalloprotein
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
COPPER (II) ION / Chem-QG7 / Streptavidin
Similarity search - Component
Biological speciesStreptomyces avidinii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsUyeda, K.S. / Follmer, A.H. / Borovik, A.S.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM120349 United States
CitationJournal: Chem Sci / Year: 2024
Title: Selective oxidation of active site aromatic residues in engineered Cu proteins.
Authors: Uyeda, K.S. / Follmer, A.H. / Borovik, A.S.
History
DepositionJul 24, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 11, 2024Provider: repository / Type: Initial release
Revision 1.1Dec 18, 2024Group: Database references / Category: citation / citation_author
Item: _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI ..._citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
Revision 1.2Jan 1, 2025Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID

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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)17,1193
Polymers16,5871
Non-polymers5322
Water1,72996
1
A: Streptavidin
hetero molecules

A: Streptavidin
hetero molecules

A: Streptavidin
hetero molecules

A: Streptavidin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,47712
Polymers66,3484
Non-polymers2,1298
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 area10040 Å2
ΔGint-96 kcal/mol
Surface area18660 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.550, 57.550, 177.730
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number98
Space group name H-MI4122
Space group name HallI4bw2bw
Symmetry operation#1: x,y,z
#2: -y+1/2,x,z+3/4
#3: y+1/2,-x,z+3/4
#4: x+1/2,-y,-z+3/4
#5: -x+1/2,y,-z+3/4
#6: -x,-y,z
#7: y,x,-z
#8: -y,-x,-z
#9: x+1/2,y+1/2,z+1/2
#10: -y+1,x+1/2,z+5/4
#11: y+1,-x+1/2,z+5/4
#12: x+1,-y+1/2,-z+5/4
#13: -x+1,y+1/2,-z+5/4
#14: -x+1/2,-y+1/2,z+1/2
#15: y+1/2,x+1/2,-z+1/2
#16: -y+1/2,-x+1/2,-z+1/2
Components on special symmetry positions
IDModelComponents
11A-318-

HOH

21A-322-

HOH

31A-379-

HOH

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Components

#1: Protein Streptavidin


Mass: 16587.025 Da / Num. of mol.: 1 / Mutation: E101Q, S112Y, K121A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces avidinii (bacteria) / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: P22629
#2: Chemical ChemComp-QG7 / N-(2-{bis[(pyridin-2-yl)methyl]amino}ethyl)-5-[(3aS,4S,6aR)-2-oxohexahydro-1H-thieno[3,4-d]imidazol-4-yl]pentanamide


Mass: 468.615 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C24H32N6O2S / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-CU / COPPER (II) ION


Mass: 63.546 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cu
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 96 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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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: 2.22 Å3/Da / Density % sol: 44.54 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6 / Details: ammonium sulfate, sodium acetate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 0.9999 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Oct 27, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9999 Å / Relative weight: 1
ReflectionResolution: 1.6→27.38 Å / Num. obs: 20125 / % possible obs: 99.12 % / Redundancy: 6.7 % / Biso Wilson estimate: 22.06 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.09639 / Rpim(I) all: 0.03725 / Rrim(I) all: 0.1037 / Net I/σ(I): 9
Reflection shellResolution: 1.6→1.657 Å / Rmerge(I) obs: 1.151 / Mean I/σ(I) obs: 1.42 / Num. unique obs: 1984 / CC1/2: 0.561 / Rpim(I) all: 0.4666 / Rrim(I) all: 1.246

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
MOSFLM7.4.0data reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.6→27.38 Å / SU ML: 0.2017 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 26.6103
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.234 972 4.83 %
Rwork0.2061 19136 -
obs0.2074 20108 99.16 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 30.25 Å2
Refinement stepCycle: LAST / Resolution: 1.6→27.38 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms926 0 34 96 1056
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00741036
X-RAY DIFFRACTIONf_angle_d0.9471428
X-RAY DIFFRACTIONf_chiral_restr0.0541159
X-RAY DIFFRACTIONf_plane_restr0.0057180
X-RAY DIFFRACTIONf_dihedral_angle_d15.0713348
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6-1.680.35991630.34132676X-RAY DIFFRACTION99.93
1.68-1.790.28041310.28172695X-RAY DIFFRACTION99.75
1.79-1.930.23921220.25142723X-RAY DIFFRACTION99.72
1.93-2.120.22911530.22432702X-RAY DIFFRACTION99.83
2.12-2.430.26331420.21412721X-RAY DIFFRACTION99.2
2.43-3.060.20971170.20162781X-RAY DIFFRACTION99.11
3.06-27.380.21491440.17492838X-RAY DIFFRACTION96.79

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