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- PDB-9cst: Streptavidin-E101Q-K121A bound to Cu(II)-biotin-ethyl-dipicolylam... -

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Basic information

Entry
Database: PDB / ID: 9cst
TitleStreptavidin-E101Q-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
COPPER (II) ION / Chem-QG7 / Streptavidin
Similarity search - Component
Biological speciesStreptomyces avidinii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.13 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)17,2346
Polymers16,5111
Non-polymers7235
Water2,324129
1
A: Streptavidin
hetero molecules

A: Streptavidin
hetero molecules

A: Streptavidin
hetero molecules

A: Streptavidin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,93524
Polymers66,0444
Non-polymers2,89120
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 area11710 Å2
ΔGint-234 kcal/mol
Surface area18090 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.820, 57.820, 184.139
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: 16510.930 Da / Num. of mol.: 1 / Mutation: E101Q, K121A
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.: 4 / Source method: obtained synthetically / Formula: Cu
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 129 / 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: 2.33 Å3/Da / Density % sol: 47.22 %
Crystal growTemperature: 293 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: SSRL / Beamline: BL12-2 / Wavelength: 0.8856 Å
DetectorType: DECTRIS EIGER2 S 16M / Detector: PIXEL / Date: Mar 19, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8856 Å / Relative weight: 1
ReflectionResolution: 1.13→42.09 Å / Num. obs: 58555 / % possible obs: 99.7 % / Redundancy: 79.7 % / Biso Wilson estimate: 13.62 Å2 / CC1/2: 0.946 / Rpim(I) all: 0.08369 / Rrim(I) all: 0.764 / Net I/σ(I): 60.09
Reflection shellResolution: 1.13→1.172 Å / Rmerge(I) obs: 3.208 / Mean I/σ(I) obs: 2.15 / Num. unique obs: 5764 / CC1/2: 0.784 / Rpim(I) all: 0.3621 / Rrim(I) all: 3.229 / % possible all: 99.88

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Processing

Software
NameVersionClassification
MOSFLM7.4.0data reduction
Aimlessdata scaling
PHASERphasing
PHENIX1.20.1-4487-000refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.13→42.09 Å / SU ML: 0.1368 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 15.8117
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1604 5620 5.07 %
Rwork0.1415 105180 -
obs0.1425 58555 99.69 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 20.09 Å2
Refinement stepCycle: LAST / Resolution: 1.13→42.09 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms924 0 37 129 1090
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01431018
X-RAY DIFFRACTIONf_angle_d1.47351398
X-RAY DIFFRACTIONf_chiral_restr0.1061155
X-RAY DIFFRACTIONf_plane_restr0.0198176
X-RAY DIFFRACTIONf_dihedral_angle_d8.1498159
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.13-1.140.331670.34983525X-RAY DIFFRACTION99.84
1.14-1.160.32041740.31843582X-RAY DIFFRACTION99.95
1.16-1.170.33741990.29313456X-RAY DIFFRACTION99.92
1.17-1.190.25622020.27293491X-RAY DIFFRACTION99.92
1.19-1.20.2981700.23283525X-RAY DIFFRACTION99.92
1.2-1.220.27131920.24223490X-RAY DIFFRACTION99.7
1.22-1.240.24071750.23433559X-RAY DIFFRACTION99.87
1.24-1.260.21911910.2023510X-RAY DIFFRACTION99.81
1.26-1.270.24872050.21663437X-RAY DIFFRACTION99.21
1.27-1.30.2121560.17963551X-RAY DIFFRACTION99.62
1.3-1.320.23992100.19843401X-RAY DIFFRACTION97.75
1.32-1.340.20251880.18793544X-RAY DIFFRACTION100
1.34-1.370.20871830.17993490X-RAY DIFFRACTION100
1.37-1.40.2222160.18773506X-RAY DIFFRACTION100
1.4-1.430.21271720.17973514X-RAY DIFFRACTION100
1.43-1.460.16921870.14863519X-RAY DIFFRACTION99.95
1.46-1.50.13641930.12463482X-RAY DIFFRACTION99.92
1.5-1.540.14312130.10743518X-RAY DIFFRACTION99.95
1.54-1.580.11611920.09223522X-RAY DIFFRACTION100
1.58-1.630.12821800.09343504X-RAY DIFFRACTION100
1.63-1.690.13551780.09943534X-RAY DIFFRACTION100
1.69-1.760.13351600.11043525X-RAY DIFFRACTION99.3
1.76-1.840.10861560.09443517X-RAY DIFFRACTION99.57
1.84-1.940.14151990.11293478X-RAY DIFFRACTION98.45
1.94-2.060.11642030.10753494X-RAY DIFFRACTION99.92
2.06-2.220.12881730.10783515X-RAY DIFFRACTION99.86
2.22-2.440.16211690.13043476X-RAY DIFFRACTION98.62
2.44-2.790.14841760.14043537X-RAY DIFFRACTION99.97
2.79-3.520.15872090.14143487X-RAY DIFFRACTION99.76
3.52-42.090.15872320.15243491X-RAY DIFFRACTION99.92

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