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Open data
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Basic information
Entry | Database: PDB / ID: 8fm6 | ||||||
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Title | Dri1 hemoprotein variant H21A with a zinc-mirror heme site | ||||||
![]() | Ssr1698 protein | ||||||
![]() | METAL BINDING PROTEIN / ![]() | ||||||
Function / homology | Domain of unknown function DUF2470 / Domain of unknown function (DUF2470) / Haem oxygenase HugZ-like superfamily / HEME B/C / Ssr1698 protein![]() | ||||||
Biological species | ![]() ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Yee, E.F. / Blaby-Haas, C. | ||||||
Funding support | 1items
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![]() | ![]() Title: A hemoprotein with a zinc-mirror heme site ties heme availability to carbon metabolism in cyanobacteria. Authors: Grosjean, N. / Yee, E.F. / Kumaran, D. / Chopra, K. / Abernathy, M. / Biswas, S. / Byrnes, J. / Kreitler, D.F. / Cheng, J.F. / Ghosh, A. / Almo, S.C. / Iwai, M. / Niyogi, K.K. / Pakrasi, H.B. ...Authors: Grosjean, N. / Yee, E.F. / Kumaran, D. / Chopra, K. / Abernathy, M. / Biswas, S. / Byrnes, J. / Kreitler, D.F. / Cheng, J.F. / Ghosh, A. / Almo, S.C. / Iwai, M. / Niyogi, K.K. / Pakrasi, H.B. / Sarangi, R. / van Dam, H. / Yang, L. / Blaby, I.K. / Blaby-Haas, C.E. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 102.2 KB | Display | ![]() |
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PDB format | ![]() | 69.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 8gbkC ![]() 8gdwC ![]() 8gf4C C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
Other databases |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments:
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Components
#1: Protein | Mass: 11239.646 Da / Num. of mol.: 2 / Mutation: H21A Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() ![]() #2: Chemical | ChemComp-HEB / | Has ligand of interest | Y | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.78 Å3/Da / Density % sol: 67.45 % |
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Crystal grow![]() | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5 Details: 0.1 M sodium citrate, 0.1 M potassium phosphate, 34% PEG8000 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Oct 16, 2022 / Details: KB bimorph mirrors |
Radiation | Monochromator: Si(111) DCM / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 2.85→36.76 Å / Num. obs: 8771 / % possible obs: 81.64 % / Redundancy: 10 % / Biso Wilson estimate: 81.6 Å2 / CC1/2: 0.998 / CC star: 1 / Rmerge(I) obs: 0.148 / Rpim(I) all: 0.049 / Rrim(I) all: 0.156 / Net I/σ(I): 10.7 |
Reflection shell | Resolution: 2.851→3.05 Å / Redundancy: 12.8 % / Rmerge(I) obs: 2.395 / Mean I/σ(I) obs: 1.2 / Num. unique obs: 106 / CC1/2: 0.436 / Rpim(I) all: 0.691 / Rrim(I) all: 2.495 / % possible all: 63.7 |
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Processing
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Refinement | Method to determine structure![]() ![]() Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 77.57 Å2 | ||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.85→36.76 Å
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Refine LS restraints |
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Refine LS restraints NCS | Type: Torsion NCS / Rms dev position: 0.921678426611 Å | ||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
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Refinement TLS params. | Method: refined / Origin x: -26.9976013583 Å / Origin y: 19.4440202137 Å / Origin z: -1.77762991529 Å
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Refinement TLS group | Selection details: all |