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- PDB-9ec5: Streptavidin-S112C-L124F bound to Cu(II)dpea cofactor, containing... -

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Basic information

Entry
Database: PDB / ID: 9ec5
TitleStreptavidin-S112C-L124F bound to Cu(II)dpea cofactor, containing S-nitrosocysteine modification
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 / Streptavidin
Similarity search - Component
Biological speciesStreptomyces avidinii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 Å
AuthorsMinnetian, N.M. / 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: To Be Published
Title: S-nitrosylation by artificial copper metalloproteins
Authors: Minnetian, N.M. / Borovik, A.S.
History
DepositionNov 13, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 19, 2025Provider: repository / Type: Initial release

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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)17,3825
Polymers16,6481
Non-polymers7344
Water2,504139
1
A: Streptavidin
hetero molecules

A: Streptavidin
hetero molecules

A: Streptavidin
hetero molecules

A: Streptavidin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,52820
Polymers66,5924
Non-polymers2,93516
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 area14570 Å2
ΔGint-131 kcal/mol
Surface area18290 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.675, 57.675, 183.928
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-303-

HOH

21A-304-

HOH

31A-408-

HOH

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Components

#1: Protein Streptavidin


Mass: 16648.111 Da / Num. of mol.: 1 / Mutation: E14Q, S112C, L124F
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-A1BIA / N-(3-{bis[2-(pyridin-2-yl)ethyl]amino}propyl)-5-[(3aR,4R,6aS)-2-oxohexahydro-1H-thieno[3,4-d]imidazol-4-yl]pentanamide


Mass: 510.695 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C27H38N6O2S / 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 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 139 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

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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: 5.0.1 / Wavelength: 0.97741 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Oct 28, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97741 Å / Relative weight: 1
ReflectionResolution: 1.4→45.98 Å / Num. obs: 31164 / % possible obs: 97.84 % / Redundancy: 20.1 % / Biso Wilson estimate: 9.08 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.1057 / Rpim(I) all: 0.02387 / Net I/σ(I): 23.25
Reflection shellResolution: 1.4→1.45 Å / Rmerge(I) obs: 0.9254 / Mean I/σ(I) obs: 5.82 / Num. unique obs: 3045 / CC1/2: 0.917 / Rpim(I) all: 0.2238 / Rrim(I) all: 0.9528

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Processing

Software
NameVersionClassification
XDSdata reduction
PHENIX1.20.1_4487refinement
PHASERphasing
Aimlessdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.4→45.98 Å / SU ML: 0.1628 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 22.447
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2282 1504 4.93 %
Rwork0.1962 28991 -
obs0.1977 30495 97.84 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 15.48 Å2
Refinement stepCycle: LAST / Resolution: 1.4→45.98 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms933 0 43 139 1115
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00641045
X-RAY DIFFRACTIONf_angle_d1.08511431
X-RAY DIFFRACTIONf_chiral_restr0.0865153
X-RAY DIFFRACTIONf_plane_restr0.0065181
X-RAY DIFFRACTIONf_dihedral_angle_d17.0388343
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.4-1.450.3191500.2882630X-RAY DIFFRACTION99.93
1.45-1.50.27931280.26122635X-RAY DIFFRACTION100
1.5-1.560.26841420.24232650X-RAY DIFFRACTION99.86
1.56-1.630.27091450.23692619X-RAY DIFFRACTION99.42
1.63-1.710.26781200.23392611X-RAY DIFFRACTION98.13
1.71-1.820.24231400.22162611X-RAY DIFFRACTION97.48
1.82-1.960.24661580.21182470X-RAY DIFFRACTION93.26
1.96-2.160.20121300.19372574X-RAY DIFFRACTION95.65
2.16-2.470.18011170.18012644X-RAY DIFFRACTION96.81
2.47-3.110.22761310.17352696X-RAY DIFFRACTION97.96
3.12-45.980.19831430.15922851X-RAY DIFFRACTION97.94

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