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Yorodumi- PDB-6ot7: Bimetallic dodecameric cage design 3 (BMC3) from cytochrome cb562 -
+Open data
-Basic information
Entry | Database: PDB / ID: 6ot7 | |||||||||||||||
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Title | Bimetallic dodecameric cage design 3 (BMC3) from cytochrome cb562 | |||||||||||||||
Components | Soluble cytochrome b562 | |||||||||||||||
Keywords | METAL BINDING PROTEIN / Supramolecular assembly / protein cage / bimetallic / metal binding / hydroxamic acid | |||||||||||||||
Function / homology | Function and homology information electron transfer activity / periplasmic space / iron ion binding / heme binding Similarity search - Function | |||||||||||||||
Biological species | Escherichia coli (E. coli) | |||||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 Å | |||||||||||||||
Model details | Keywords: Supramolecular assembly, protein cage, bimetallic, metal binding | |||||||||||||||
Authors | Golub, E. / Esselborn, J. / Bailey, J.B. / Tezcan, F.A. | |||||||||||||||
Funding support | United States, European Union, Germany, 4items
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Citation | Journal: Nature / Year: 2020 Title: Constructing protein polyhedra via orthogonal chemical interactions. Authors: Eyal Golub / Rohit H Subramanian / Julian Esselborn / Robert G Alberstein / Jake B Bailey / Jerika A Chiong / Xiaodong Yan / Timothy Booth / Timothy S Baker / F Akif Tezcan / Abstract: Many proteins exist naturally as symmetrical homooligomers or homopolymers. The emergent structural and functional properties of such protein assemblies have inspired extensive efforts in ...Many proteins exist naturally as symmetrical homooligomers or homopolymers. The emergent structural and functional properties of such protein assemblies have inspired extensive efforts in biomolecular design. As synthesized by ribosomes, proteins are inherently asymmetric. Thus, they must acquire multiple surface patches that selectively associate to generate the different symmetry elements needed to form higher-order architectures-a daunting task for protein design. Here we address this problem using an inorganic chemical approach, whereby multiple modes of protein-protein interactions and symmetry are simultaneously achieved by selective, 'one-pot' coordination of soft and hard metal ions. We show that a monomeric protein (protomer) appropriately modified with biologically inspired hydroxamate groups and zinc-binding motifs assembles through concurrent Fe and Zn coordination into discrete dodecameric and hexameric cages. Our cages closely resemble natural polyhedral protein architectures and are, to our knowledge, unique among designed systems in that they possess tightly packed shells devoid of large apertures. At the same time, they can assemble and disassemble in response to diverse stimuli, owing to their heterobimetallic construction on minimal interprotein-bonding footprints. With stoichiometries ranging from [2 Fe:9 Zn:6 protomers] to [8 Fe:21 Zn:12 protomers], these protein cages represent some of the compositionally most complex protein assemblies-or inorganic coordination complexes-obtained by design. | |||||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6ot7.cif.gz | 147.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6ot7.ent.gz | 93.6 KB | Display | PDB format |
PDBx/mmJSON format | 6ot7.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ot/6ot7 ftp://data.pdbj.org/pub/pdb/validation_reports/ot/6ot7 | HTTPS FTP |
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-Related structure data
Related structure data | 6ot4C 6ot8C 6ot9C 6ovhC 3m4bS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Components on special symmetry positions |
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-Components
-Protein , 1 types, 4 molecules DABC
#1: Protein | Mass: 11809.307 Da / Num. of mol.: 4 Mutation: D5H,E8H,V16H,A24T,Q25T,R34Q,L38Q,Q41W,K42S,K59S,H63C,D66W,I67E,V69I,D73N,D74A,K77H,N80K,E81Q,G82C,R98C,Y101C Source method: isolated from a genetically manipulated source Details: pET20b for expression of BMC2 described here with background of pEC86 to provide machinery for c-type linkage of heme. Source: (gene. exp.) Escherichia coli (E. coli) / Gene: cybC / Plasmid: pET20b-BMC1/pEC86 Details (production host): pET20b for expression of BMC1 described here with background of pEC86 to provide machinery for c-type linkage of heme. Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P0ABE7 |
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-Non-polymers , 6 types, 366 molecules
#2: Chemical | ChemComp-HEC / #3: Chemical | ChemComp-ZN / #4: Chemical | ChemComp-FE / #5: Chemical | ChemComp-HAE / #6: Chemical | ChemComp-1PE / | #7: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.74 Å3/Da / Density % sol: 55.17 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: Protein solution of: 2.2 mM protein with 1.65 mM Fe and 3 mM Zn premixed briefly prior to crystallisation. Drops were 1ul + 1 ul of protein solution and the following mother liquor: 30% ...Details: Protein solution of: 2.2 mM protein with 1.65 mM Fe and 3 mM Zn premixed briefly prior to crystallisation. Drops were 1ul + 1 ul of protein solution and the following mother liquor: 30% PEG400, 0.1 M HEPES pH 7.5, 0.2 M (NH4)2SO4 Temp details: Room temperature |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.11583 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Dec 14, 2018 Details: Primary Mirror: flat internallyerror; Secondary Mirror: uncooled cyllindrical silicon bent into torroid | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: Water-cooled flat double Si(111) Khozu / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1.11583 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.85→91.83 Å / Num. obs: 85783 / % possible obs: 100 % / Redundancy: 10.32 % / Biso Wilson estimate: 35.57 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.096 / Rpim(I) all: 0.031 / Rrim(I) all: 0.101 / Net I/σ(I): 13.7 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1 / % possible all: 100
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3M4B Resolution: 1.85→91.83 Å / SU ML: 0.2609 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 23.447
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 41.52 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.85→91.83 Å
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Refine LS restraints |
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LS refinement shell |
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