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

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Basic information

Entry
Database: PDB / ID: 9csu
TitleStreptavidin-E101Q-S112Y-K121A bound to Cu(II)-biotin-ethyl-dipicolylamine cofactor
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
ACETIC ACID / 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)17,1794
Polymers16,5871
Non-polymers5923
Water1,51384
1
A: Streptavidin
hetero molecules

A: Streptavidin
hetero molecules

A: Streptavidin
hetero molecules

A: Streptavidin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,71716
Polymers66,3484
Non-polymers2,36912
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 area9430 Å2
ΔGint-56 kcal/mol
Surface area19050 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.700, 57.700, 178.050
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-308-

HOH

21A-373-

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-ACY / ACETIC ACID


Mass: 60.052 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H4O2 / Feature type: SUBJECT OF INVESTIGATION
#3: 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
#4: Chemical ChemComp-CU / COPPER (II) ION


Mass: 63.546 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cu / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 84 / 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: 2.23 Å3/Da / Density % sol: 44.93 %
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: 1 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: 1 Å / Relative weight: 1
ReflectionResolution: 1.6→54.72 Å / Num. obs: 20131 / % possible obs: 99.49 % / Redundancy: 36.9 % / Biso Wilson estimate: 18.24 Å2 / CC1/2: 0.968 / Rmerge(I) obs: 0.7085 / Rpim(I) all: 0.1116 / Rrim(I) all: 0.7177 / Net I/σ(I): 13.47
Reflection shellResolution: 1.6→1.657 Å / Redundancy: 37.1 % / Rmerge(I) obs: 4.619 / Mean I/σ(I) obs: 0.91 / Num. unique obs: 1966 / CC1/2: 0.309 / Rpim(I) all: 0.7681 / Rrim(I) all: 4.685 / % possible all: 97.31

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Processing

Software
NameVersionClassification
MOSFLM7.4.0data reduction
Aimlessdata scaling
PHASERphasing
PHENIX1.20.1-4487-000refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.6→54.72 Å / SU ML: 0.227 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 22.096
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2071 1014 5.05 %
Rwork0.1753 19052 -
obs0.1769 20066 98.3 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 24.9 Å2
Refinement stepCycle: LAST / Resolution: 1.6→54.72 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms926 0 38 84 1048
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00571037
X-RAY DIFFRACTIONf_angle_d0.77371428
X-RAY DIFFRACTIONf_chiral_restr0.0719159
X-RAY DIFFRACTIONf_plane_restr0.0038180
X-RAY DIFFRACTIONf_dihedral_angle_d10.0209162
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6-1.680.34641360.2832520X-RAY DIFFRACTION93.59
1.68-1.790.31771550.26282660X-RAY DIFFRACTION98.25
1.79-1.930.27221320.20362697X-RAY DIFFRACTION98.33
1.93-2.120.20521480.17432736X-RAY DIFFRACTION100
2.12-2.430.23611080.17782759X-RAY DIFFRACTION99.2
2.43-3.060.21791660.16152779X-RAY DIFFRACTION100
3.06-54.720.15521690.15032901X-RAY DIFFRACTION98.62

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