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- PDB-9e6z: Streptavidin-E101Q-S112F-K121A bound to Cu(II)-biotin-ethyl-dipic... -

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Basic information

Entry
Database: PDB / ID: 9e6z
TitleStreptavidin-E101Q-S112F-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: 1.7 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
DepositionOct 31, 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)17,1634
Polymers16,5711
Non-polymers5923
Water1,36976
1
A: Streptavidin
hetero molecules

A: Streptavidin
hetero molecules

A: Streptavidin
hetero molecules

A: Streptavidin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,65316
Polymers66,2844
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 area9860 Å2
ΔGint-107 kcal/mol
Surface area19060 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.536, 57.536, 176.282
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-307-

HOH

21A-365-

HOH

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Components

#1: Protein Streptavidin


Mass: 16571.025 Da / Num. of mol.: 1 / Mutation: E101Q, S112F, K121A
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-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
#3: Chemical ChemComp-ACY / ACETIC ACID


Mass: 60.052 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H4O2 / 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
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 76 / 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: 2.2 Å3/Da / Density % sol: 44.12 %
Crystal growTemperature: 296 K / Method: vapor diffusion, sitting drop / pH: 4 / 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: 5.0.1 / Wavelength: 0.97741 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 4, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97741 Å / Relative weight: 1
ReflectionResolution: 1.7→41.11 Å / Num. obs: 16842 / % possible obs: 99.92 % / Redundancy: 14.1 % / Biso Wilson estimate: 16.12 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.2381 / Rpim(I) all: 0.06501 / Rrim(I) all: 0.247 / Net I/σ(I): 8.98
Reflection shellResolution: 1.7→1.761 Å / Rmerge(I) obs: 2.023 / Mean I/σ(I) obs: 1.33 / Num. unique obs: 1647 / CC1/2: 0.524 / Rpim(I) all: 0.5481 / Rrim(I) all: 2.097 / % possible all: 100

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Processing

Software
NameVersionClassification
XDS1.20.1_4487data reduction
Aimlessdata scaling
PHASERphasing
PHENIX1.20.1-4487-000refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.7→41.11 Å / SU ML: 0.1836 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 22.6577
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2194 1491 4.79 %
Rwork0.2011 29626 -
obs0.202 31117 99.94 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 20.26 Å2
Refinement stepCycle: LAST / Resolution: 1.7→41.11 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms925 0 38 76 1039
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01381026
X-RAY DIFFRACTIONf_angle_d1.33941406
X-RAY DIFFRACTIONf_chiral_restr0.08153
X-RAY DIFFRACTIONf_plane_restr0.0206179
X-RAY DIFFRACTIONf_dihedral_angle_d21.3293342
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7-1.750.3281360.31052692X-RAY DIFFRACTION100
1.75-1.820.26651480.26542686X-RAY DIFFRACTION100
1.82-1.890.26731260.25022699X-RAY DIFFRACTION100
1.89-1.980.26621380.2412708X-RAY DIFFRACTION100
1.98-2.080.25861460.20912658X-RAY DIFFRACTION100
2.08-2.210.23421310.19532708X-RAY DIFFRACTION99.89
2.21-2.380.2041470.19822677X-RAY DIFFRACTION100
2.38-2.620.21521310.19652713X-RAY DIFFRACTION100
2.62-30.2091190.20082694X-RAY DIFFRACTION99.96
3-3.780.20781290.17712694X-RAY DIFFRACTION99.75
3.78-41.110.17011400.17262697X-RAY DIFFRACTION99.72

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