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Yorodumi- PDB-8c3w: Crystal structure of a computationally designed heme binding prot... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8c3w | |||||||||
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Title | Crystal structure of a computationally designed heme binding protein, dnHEM1 | |||||||||
Components | dnHEM1 | |||||||||
Keywords | BIOSYNTHETIC PROTEIN / de novo protein / computational design / heme binding protein | |||||||||
Function / homology | PROTOPORPHYRIN IX CONTAINING FE / IMIDAZOLE / DI(HYDROXYETHYL)ETHER / PHOSPHATE ION Function and homology information | |||||||||
Biological species | synthetic construct (others) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å | |||||||||
Authors | Ortmayer, M. / Levy, C. | |||||||||
Funding support | United Kingdom, European Union, 2items
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Citation | Journal: J.Am.Chem.Soc. / Year: 2023 Title: Design of Heme Enzymes with a Tunable Substrate Binding Pocket Adjacent to an Open Metal Coordination Site. Authors: Kalvet, I. / Ortmayer, M. / Zhao, J. / Crawshaw, R. / Ennist, N.M. / Levy, C. / Roy, A. / Green, A.P. / Baker, D. #1: Journal: Acta Crystallogr D Biol Crystallogr / Year: 2012 Title: Towards automated crystallographic structure refinement with phenix.refine. Authors: Afonine, P.V. / Grosse-Kunstleve, R.W. / Echols, N. / Headd, J.J. / Moriarty, N.W. / Mustyakimov, M. / Terwilliger, T.C. / Urzhumtsev, A. / Zwart, P.H. / Adams, P.D. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8c3w.cif.gz | 118.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8c3w.ent.gz | 74.4 KB | Display | PDB format |
PDBx/mmJSON format | 8c3w.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/c3/8c3w ftp://data.pdbj.org/pub/pdb/validation_reports/c3/8c3w | HTTPS FTP |
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-Related structure data
Related structure data | 4yxxS S: Starting model for refinement |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 24070.592 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) synthetic construct (others) / Production host: Escherichia coli (E. coli) |
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-Non-polymers , 7 types, 122 molecules
#2: Chemical | ChemComp-IMD / | ||||||||
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#3: Chemical | ChemComp-HEM / | ||||||||
#4: Chemical | #5: Chemical | ChemComp-PO4 / | #6: Chemical | ChemComp-PEG / | #7: Chemical | ChemComp-EDO / | #8: Water | ChemComp-HOH / | |
-Details
Has ligand of interest | Y |
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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: 2.69 Å3/Da / Density % sol: 54.25 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop Details: 0.1M HEPES pH 7.7, 70% (4S)-2-methyl-2,4-pentanediol |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9763 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Sep 30, 2022 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9763 Å / Relative weight: 1 |
Reflection | Resolution: 1.6→41.66 Å / Num. obs: 31364 / % possible obs: 97.98 % / Redundancy: 13.4 % / Biso Wilson estimate: 26.8 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.0561 / Net I/σ(I): 22.91 |
Reflection shell | Resolution: 1.6→1.657 Å / Redundancy: 11.7 % / Rmerge(I) obs: 1.036 / Mean I/σ(I) obs: 1.33 / Num. unique obs: 2878 / CC1/2: 0.82 / CC star: 0.949 / % possible all: 92.02 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4yxx Resolution: 1.6→41.66 Å / SU ML: 0.2297 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 21.9696 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 30.65 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.6→41.66 Å
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Refine LS restraints |
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LS refinement shell |
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