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- PDB-9edk: Streptavidin-S112C-T114V bound to Cu(II)dpea cofactor -

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Basic information

Entry
Database: PDB / ID: 9edk
TitleStreptavidin-S112C-T114V bound to Cu(II)dpea 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
: / COPPER (II) ION / Streptavidin
Similarity search - Component
Biological speciesStreptomyces avidinii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.45 Å
AuthorsMinnetian, N.M. / Borovik, A.S. / Follmer, A.H.
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: Tuning the active site geometry and spectroscopic properties of artificial blue copper proteins
Authors: Minnetian, N.M. / Follmer, A.H. / Borovik, A.S.
History
DepositionNov 17, 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)17,4457
Polymers16,5841
Non-polymers8616
Water1,964109
1
A: Streptavidin
hetero molecules

A: Streptavidin
hetero molecules

A: Streptavidin
hetero molecules

A: Streptavidin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,78028
Polymers66,3364
Non-polymers3,44424
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 area16370 Å2
ΔGint-237 kcal/mol
Surface area17380 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.760, 57.760, 183.960
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-310-

HOH

21A-311-

HOH

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Components

#1: Protein Streptavidin


Mass: 16584.109 Da / Num. of mol.: 1 / Mutation: S112C, T114V
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.: 4 / 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.: 109 / 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: 298 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: 8.2.1 / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: May 19, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.45→45.99 Å / Num. obs: 27339 / % possible obs: 97.2 % / Redundancy: 3.5 % / Biso Wilson estimate: 15.59 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.059 / Rpim(I) all: 0.034 / Net I/σ(I): 10.4
Reflection shellResolution: 1.45→1.47 Å / Rmerge(I) obs: 0.643 / Mean I/σ(I) obs: 1.6 / Num. unique obs: 1329 / CC1/2: 0.656 / Rpim(I) all: 0.385 / Rrim(I) all: 0.755 / % possible all: 96.8

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Processing

Software
NameVersionClassification
PHASERphasing
PHENIX1.20.1_4487refinement
iMOSFLMdata reduction
Aimlessdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.45→45.99 Å / SU ML: 0.1641 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 18.4778
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1896 1376 5.04 %
Rwork0.1812 25930 -
obs0.1816 27306 96.81 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 20.58 Å2
Refinement stepCycle: LAST / Resolution: 1.45→45.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms927 0 45 109 1081
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01011079
X-RAY DIFFRACTIONf_angle_d1.56911477
X-RAY DIFFRACTIONf_chiral_restr0.0914158
X-RAY DIFFRACTIONf_plane_restr0.0063185
X-RAY DIFFRACTIONf_dihedral_angle_d20.0425357
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.45-1.50.26581280.25072553X-RAY DIFFRACTION96.86
1.5-1.560.24991460.22652551X-RAY DIFFRACTION97.15
1.56-1.630.28271330.24372547X-RAY DIFFRACTION97.24
1.63-1.720.19941400.19652538X-RAY DIFFRACTION96.4
1.72-1.830.19071290.18062578X-RAY DIFFRACTION96.68
1.83-1.970.20211360.18812589X-RAY DIFFRACTION97.81
1.97-2.170.18241380.16112629X-RAY DIFFRACTION98.57
2.17-2.480.17191310.17142642X-RAY DIFFRACTION97.81
2.48-3.120.17221400.17672639X-RAY DIFFRACTION97.27
3.12-45.990.17951550.17132664X-RAY DIFFRACTION92.61

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