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- PDB-9edg: Streptavidin-WT bound to Cu(II)dpea cofactor -

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Basic information

Entry
Database: PDB / ID: 9edg
TitleStreptavidin-WT 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
: / ACETATE ION / COPPER (II) ION / Streptavidin
Similarity search - Component
Biological speciesStreptomyces avidinii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 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)17,3636
Polymers16,5701
Non-polymers7935
Water1,62190
1
A: Streptavidin
hetero molecules

A: Streptavidin
hetero molecules

A: Streptavidin
hetero molecules

A: Streptavidin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,45224
Polymers66,2804
Non-polymers3,17220
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 area9490 Å2
ΔGint-86 kcal/mol
Surface area20340 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.510, 57.510, 183.900
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-205-

SO4

21A-303-

HOH

31A-316-

HOH

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Streptavidin


Mass: 16570.018 Da / Num. of mol.: 1 / Fragment: UNP residues 33-183
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces avidinii (bacteria) / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: P22629

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Non-polymers , 5 types, 95 molecules

#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-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2 / Feature type: SUBJECT OF INVESTIGATION
#4: 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
#5: Chemical ChemComp-SO4 / SULFATE ION


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


Mass: 18.015 Da / Num. of mol.: 90 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 5.0.2 / Wavelength: 0.99987 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 27, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99987 Å / Relative weight: 1
ReflectionResolution: 1.75→54.89 Å / Num. obs: 15226 / % possible obs: 94.9 % / Redundancy: 7.3 % / Biso Wilson estimate: 14.36 Å2 / CC1/2: 0.995 / Rmerge(I) obs: 0.101 / Rpim(I) all: 0.037 / Net I/σ(I): 11.8
Reflection shellResolution: 1.75→1.78 Å / Rmerge(I) obs: 0.495 / Num. unique obs: 796 / CC1/2: 0.883 / Rpim(I) all: 0.191

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Processing

Software
NameVersionClassification
PHASERphasing
PHENIX1.20.1_4487refinement
iMOSFLMdata reduction
Aimlessdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.75→54.89 Å / SU ML: 0.1753 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 18.2283
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1969 734 4.83 %
Rwork0.1731 14460 -
obs0.1742 15194 94.22 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 17.4 Å2
Refinement stepCycle: LAST / Resolution: 1.75→54.89 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms936 0 47 90 1073
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00931041
X-RAY DIFFRACTIONf_angle_d1.12181423
X-RAY DIFFRACTIONf_chiral_restr0.0639153
X-RAY DIFFRACTIONf_plane_restr0.0103180
X-RAY DIFFRACTIONf_dihedral_angle_d14.8505158
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.75-1.890.23951260.20792750X-RAY DIFFRACTION91.24
1.89-2.070.21271550.16742822X-RAY DIFFRACTION94.54
2.08-2.380.22781580.1782918X-RAY DIFFRACTION96.46
2.38-2.990.19161450.17352917X-RAY DIFFRACTION94.65
2.99-54.890.17111500.16483053X-RAY DIFFRACTION94.18

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