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- PDB-8qq3: Streptavidin with a Ni-cofactor -

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Basic information

Entry
Database: PDB / ID: 8qq3
TitleStreptavidin with a Ni-cofactor
ComponentsStreptavidin
KeywordsMETAL BINDING PROTEIN / Artificial Metalloenzymes
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
NICKEL (II) ION / : / Streptavidin
Similarity search - Component
Biological speciesStreptomyces avidinii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsZhang, K. / Jakob, R.P. / Ward, T.R.
Funding support Switzerland, 1items
OrganizationGrant numberCountry
Swiss National Science FoundationNCCR Catalysis (Grant Number 180544), a National Centre of Competence Grant Switzerland
CitationJournal: Chem.Commun.(Camb.) / Year: 2024
Title: An artificial nickel chlorinase based on the biotin-streptavidin technology.
Authors: Yu, K. / Zhang, K. / Jakob, R.P. / Maier, T. / Ward, T.R.
History
DepositionOct 3, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 7, 2024Provider: repository / Type: Initial release
Revision 1.1Feb 21, 2024Group: 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

Downloads & links

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Assembly

Deposited unit
A: Streptavidin
B: Streptavidin
C: Streptavidin
D: Streptavidin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,00311
Polymers66,2764
Non-polymers2,7277
Water7,098394
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9670 Å2
ΔGint-92 kcal/mol
Surface area19130 Å2
Unit cell
Length a, b, c (Å)115.028, 88.712, 57.790
Angle α, β, γ (deg.)90.00, 97.13, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11B-359-

HOH

21D-371-

HOH

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Components

#1: Protein
Streptavidin


Mass: 16569.031 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces avidinii (bacteria) / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P22629
#2: Chemical
ChemComp-WKF / 4-[4-[(3~{a}~{S},4~{S},6~{a}~{R})-2-oxidanylidene-1,3,3~{a},4,6,6~{a}-hexahydrothieno[3,4-d]imidazol-4-yl]butylamino]-~{N}1,~{N}1'-di(quinolin-8-yl)cyclohexane-1,1-dicarboxamide


Mass: 637.794 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Formula: C35H39N7O3S / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-NI / NICKEL (II) ION


Mass: 58.693 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Ni
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 394 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.21 Å3/Da / Density % sol: 44.27 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.2 M sodium acetate, 0.1 M Tris, pH 8.5, 30% w/v PEG 4K

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 10, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.6→46.13 Å / Num. obs: 75827 / % possible obs: 99.85 % / Redundancy: 6.9 % / CC1/2: 0.999 / CC star: 1 / Rmerge(I) obs: 0.067 / Rpim(I) all: 0.027 / Rrim(I) all: 0.072 / Net I/σ(I): 14.5
Reflection shellResolution: 1.6→1.657 Å / Rmerge(I) obs: 1.236 / Mean I/σ(I) obs: 1.1 / Num. unique obs: 7553 / CC1/2: 0.735 / CC star: 0.92 / Rpim(I) all: 0.499 / Rrim(I) all: 1.335

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Processing

Software
NameVersionClassification
PHENIX(1.17.1_3660: ???)refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.6→46.13 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 21.91 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1906 3835 5.06 %
Rwork0.1616 --
obs0.163 75725 99.85 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.6→46.13 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3758 0 156 394 4308
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0114162
X-RAY DIFFRACTIONf_angle_d1.2155722
X-RAY DIFFRACTIONf_dihedral_angle_d14.27767
X-RAY DIFFRACTIONf_chiral_restr0.065614
X-RAY DIFFRACTIONf_plane_restr0.007762
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6-1.620.33781510.3322659X-RAY DIFFRACTION100
1.62-1.640.3221530.31182615X-RAY DIFFRACTION100
1.64-1.660.32291510.29442646X-RAY DIFFRACTION100
1.66-1.690.2961470.26752637X-RAY DIFFRACTION100
1.69-1.710.29941360.25292661X-RAY DIFFRACTION100
1.71-1.740.27321500.25022634X-RAY DIFFRACTION100
1.74-1.770.29081380.22662666X-RAY DIFFRACTION100
1.77-1.80.28641400.22672650X-RAY DIFFRACTION100
1.8-1.830.28211440.2142632X-RAY DIFFRACTION100
1.83-1.870.21421530.1962673X-RAY DIFFRACTION100
1.87-1.90.20281460.17772630X-RAY DIFFRACTION100
1.9-1.950.19251620.1692627X-RAY DIFFRACTION100
1.95-1.990.18471470.15792654X-RAY DIFFRACTION100
1.99-2.040.18671170.15592672X-RAY DIFFRACTION100
2.04-2.10.21741520.1562662X-RAY DIFFRACTION100
2.1-2.160.17721390.15652675X-RAY DIFFRACTION100
2.16-2.230.17121440.15352638X-RAY DIFFRACTION100
2.23-2.310.18661300.15642690X-RAY DIFFRACTION100
2.31-2.40.19631380.16022671X-RAY DIFFRACTION100
2.4-2.510.21491110.15812706X-RAY DIFFRACTION100
2.51-2.640.16181430.15172651X-RAY DIFFRACTION100
2.64-2.810.18381600.14592621X-RAY DIFFRACTION100
2.81-3.020.16281370.14522734X-RAY DIFFRACTION100
3.02-3.330.16931210.14832669X-RAY DIFFRACTION100
3.33-3.810.19181320.14622695X-RAY DIFFRACTION100
3.81-4.80.15321420.12492701X-RAY DIFFRACTION100
4.8-46.130.17971510.1742721X-RAY DIFFRACTION100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
14.50251.24580.77377.5169-1.77517.51030.1973-0.3469-0.98370.31970.0064-0.38231.19540.3086-0.15040.37550.0922-0.03230.52860.07110.472148.7344-35.060434.2955
22.9290.2469-0.01291.57430.72162.4620.10110.05940.1252-0.0476-0.0491-0.2334-0.22160.1869-0.02710.19790.00960.01650.26810.01320.298246.3047-21.654131.9547
33.55253.4333-1.20624.0406-0.56030.92930.10140.64280.17250.1588-0.5489-0.1198-0.3105-0.26890.31370.54420.01390.08980.51890.09690.603443.0523-8.099530.4872
42.0909-1.14060.38472.7293-0.3891.48140.04070.04980.0593-0.0341-0.1137-0.19870.01010.11280.01660.1972-0.01480.03220.2126-0.01030.215636.4226-20.786831.5291
58.0254-3.2469-0.69293.32380.98173.17010.1410.49440.3607-0.0748-0.1273-0.3754-0.01060.4107-0.03880.2205-0.00620.04170.24360.0380.229640.2948-20.42523.106
61.45451.2431.62021.60582.01192.5306-0.38070.75461.3396-0.4453-0.06930.3743-1.16210.1630.57930.6770.1136-0.00380.57360.12030.555522.9274-10.2685-0.6425
72.8684-0.56430.17212.208-0.39693.3639-0.00810.1382-0.3498-0.00880.06110.02850.29150.07750.00570.27920.03040.00820.2797-0.04190.20623.3136-26.96334.0337
81.8860.4886-0.10383.0425-0.80331.96690.10220.1034-0.0754-0.1548-0.0887-0.04010.0660.0481-0.03240.22540.02460.0070.2168-0.02780.199821.2982-24.098912.9431
93.451.5839-1.37222.518-1.16920.7066-0.2590.1255-0.243-0.31710.1275-0.19960.69480.34230.21960.29270.02410.0280.2937-0.04770.239530.5838-25.171411.2704
107.0642-4.51440.73827.218-4.63488.58940.4219-0.1752-0.6871-0.73260.50831.24391.1222-0.3504-0.88160.4452-0.1014-0.07960.45430.03770.50850.5029-31.024415.5599
112.08850.0178-0.26941.90120.01541.62580.06990.0390.0413-0.0814-0.06290.24530.0121-0.2861-0.00120.19220.00640.00130.2495-0.0150.22349.3409-17.983816.9834
121.4656-1.3479-0.42151.3930.53113.82290.1315-0.2924-0.04060.2405-0.14610.35320.2098-0.43340.04460.1915-0.03190.02610.2682-0.0110.219312.3421-21.735324.7795
136.47192.6713-0.83022.9337-0.77452.5390.0938-0.37010.2983-0.0541-0.1135-0.0234-0.14510.059-0.01190.20410.01250.00980.1419-0.02950.181719.5473-14.209423.0079
143.3234-0.25410.30444.59350.50043.4483-0.0333-0.39070.31480.23740.1093-0.1627-0.31760.0047-0.08380.30550.0180.0560.3301-0.02880.238924.6043-19.229347.7868
151.6248-0.2808-0.06682.8361-0.14541.46170.0157-0.23620.0660.21480.00880.0849-0.0515-0.047-0.030.2306-0.01350.01850.2489-0.01620.186928.8348-24.470341.5313
162.8897-1.74740.78474.38411.69352.66160.1339-0.0008-0.1587-0.0641-0.05050.08450.2412-0.24210.04870.2103-0.0396-0.0110.14530.02430.187425.1944-29.404431.4166
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'D' and (resid 10 through 17 )
2X-RAY DIFFRACTION2chain 'D' and (resid 18 through 44 )
3X-RAY DIFFRACTION3chain 'D' and (resid 45 through 53 )
4X-RAY DIFFRACTION4chain 'D' and (resid 54 through 122 )
5X-RAY DIFFRACTION5chain 'D' and (resid 123 through 134 )
6X-RAY DIFFRACTION6chain 'A' and (resid 10 through 17 )
7X-RAY DIFFRACTION7chain 'A' and (resid 18 through 53 )
8X-RAY DIFFRACTION8chain 'A' and (resid 54 through 122 )
9X-RAY DIFFRACTION9chain 'A' and (resid 123 through 134 )
10X-RAY DIFFRACTION10chain 'B' and (resid 10 through 17 )
11X-RAY DIFFRACTION11chain 'B' and (resid 18 through 97 )
12X-RAY DIFFRACTION12chain 'B' and (resid 98 through 112 )
13X-RAY DIFFRACTION13chain 'B' and (resid 113 through 135 )
14X-RAY DIFFRACTION14chain 'C' and (resid 10 through 27 )
15X-RAY DIFFRACTION15chain 'C' and (resid 28 through 112 )
16X-RAY DIFFRACTION16chain 'C' and (resid 113 through 135 )

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