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- PDB-9csw: Streptavidin-E101Q-S112A-K121Y bound to Cu(II)-biotin-ethyl-dipic... -

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Basic information

Entry
Database: PDB / ID: 9csw
TitleStreptavidin-E101Q-S112A-K121Y 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: 1.3 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)17,2435
Polymers16,5871
Non-polymers6564
Water1,856103
1
A: Streptavidin
hetero molecules

A: Streptavidin
hetero molecules

A: Streptavidin
hetero molecules

A: Streptavidin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,97120
Polymers66,3484
Non-polymers2,62316
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 area10370 Å2
ΔGint-135 kcal/mol
Surface area18990 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.770, 57.770, 184.250
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-314-

HOH

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Components

#1: Protein Streptavidin


Mass: 16587.025 Da / Num. of mol.: 1 / Mutation: E101Q, S112A, K121Y
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.: 2 / Source method: obtained synthetically / Formula: Cu
#4: Chemical ChemComp-ACY / ACETIC ACID


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


Mass: 18.015 Da / Num. of mol.: 103 / 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: 2.32 Å3/Da / Density % sol: 46.91 %
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: SSRL / Beamline: BL12-1 / Wavelength: 0.9795 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jul 6, 2024
RadiationProtocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.3→42.08 Å / Num. obs: 38754 / % possible obs: 99.33 % / Redundancy: 47.5 % / Biso Wilson estimate: 17.17 Å2 / CC1/2: 0.957 / Rmerge(I) obs: 0.6465 / Rpim(I) all: 0.09512 / Rrim(I) all: 0.6537 / Net I/σ(I): 62.91
Reflection shellResolution: 1.3→1.349 Å / Redundancy: 48.2 % / Rmerge(I) obs: 3.806 / Mean I/σ(I) obs: 1.26 / Num. unique obs: 3812 / CC1/2: 0.607 / Rpim(I) all: 0.5524 / Rrim(I) all: 3.847 / % possible all: 99.08

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Processing

Software
NameVersionClassification
MOSFLM7.4.0data reduction
PHENIX1.20.1_4487-000refinement
PHASERphasing
Aimlessdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.3→42.08 Å / SU ML: 0.168 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 19.9139
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1886 3707 5.13 %
Rwork0.166 68494 -
obs0.1672 38754 98.91 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 22.91 Å2
Refinement stepCycle: LAST / Resolution: 1.3→42.08 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms926 0 39 103 1068
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0081025
X-RAY DIFFRACTIONf_angle_d1.05351409
X-RAY DIFFRACTIONf_chiral_restr0.0921157
X-RAY DIFFRACTIONf_plane_restr0.0073177
X-RAY DIFFRACTIONf_dihedral_angle_d21.6488158
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.3-1.320.49071110.36552373X-RAY DIFFRACTION88.15
1.32-1.340.3141560.30372660X-RAY DIFFRACTION99.68
1.34-1.360.27641370.27812639X-RAY DIFFRACTION99.89
1.36-1.380.29111380.27222673X-RAY DIFFRACTION100
1.38-1.40.30531320.24632677X-RAY DIFFRACTION99.93
1.4-1.420.28891470.26152644X-RAY DIFFRACTION99.93
1.42-1.450.29571300.24552675X-RAY DIFFRACTION99.36
1.45-1.470.28621640.2172606X-RAY DIFFRACTION99.14
1.47-1.50.26461300.21082657X-RAY DIFFRACTION99.29
1.5-1.530.19281660.18752645X-RAY DIFFRACTION99.86
1.53-1.560.16071470.14012668X-RAY DIFFRACTION100
1.56-1.60.16721310.1362703X-RAY DIFFRACTION99.96
1.6-1.640.17921470.13442620X-RAY DIFFRACTION100
1.64-1.680.16541320.13692687X-RAY DIFFRACTION99.96
1.68-1.730.19631400.14042640X-RAY DIFFRACTION100
1.73-1.790.17561440.1422663X-RAY DIFFRACTION99.89
1.79-1.850.17531600.13282652X-RAY DIFFRACTION99.93
1.85-1.930.19111370.20442544X-RAY DIFFRACTION95.75
1.93-2.020.21751180.15472609X-RAY DIFFRACTION97.18
2.02-2.120.1841600.14282603X-RAY DIFFRACTION98.75
2.12-2.260.19891620.1792594X-RAY DIFFRACTION97.73
2.26-2.430.16851470.1592604X-RAY DIFFRACTION98.25
2.43-2.670.16541450.15952663X-RAY DIFFRACTION99.96
2.67-3.060.14421360.16472675X-RAY DIFFRACTION99.89
3.06-3.860.18821170.15512684X-RAY DIFFRACTION99.54
3.86-42.080.1771730.15252636X-RAY DIFFRACTION99.89

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