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- PDB-7qc9: HisF-C9A-D11E-V33A_L50H_I52H mutant in complex with Ni(II) from T... -
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Open data
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Basic information
Entry | Database: PDB / ID: 7qc9 | ||||||
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Title | HisF-C9A-D11E-V33A_L50H_I52H mutant in complex with Ni(II) from T. maritima | ||||||
![]() | Imidazole glycerol phosphate synthase subunit HisF | ||||||
![]() | METAL BINDING PROTEIN / BETA BARREL / ARTIFICIAL METALLOENZYME / PROTEIN DESIGN / OXIDOREDUCTASE | ||||||
Function / homology | ![]() imidazole glycerol-phosphate synthase / imidazoleglycerol-phosphate synthase activity / L-histidine biosynthetic process / lyase activity / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Beaumet, M. / Dose, A. / Braeuer, A. / Mahy, J. / Ghattas, W. / Groll, M. / Hess, C. | ||||||
Funding support | European Union, 1items
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![]() | ![]() Title: An artificial metalloprotein with metal-adaptive coordination sites and Ni-dependent quercetinase activity. Authors: Beaumet, M. / Dose, A. / Brauer, A. / Mahy, J.P. / Ghattas, W. / Groll, M. / Hess, C.R. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 119.1 KB | Display | ![]() |
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PDB format | ![]() | 91.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 618.3 KB | Display | ![]() |
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Full document | ![]() | 619.1 KB | Display | |
Data in XML | ![]() | 12.8 KB | Display | |
Data in CIF | ![]() | 18.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7qc3SC ![]() 7qc6C ![]() 7qc7C ![]() 7qc8C S: Starting model for refinement C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components on special symmetry positions |
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Components
#1: Protein | Mass: 27741.691 Da / Num. of mol.: 1 / Mutation: C9A, D11E, L50H, I52H Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Strain: ATCC 43589 / DSM 3109 / JCM 10099 / NBRC 100826 / MSB8 Gene: hisF, TM_1036 / Production host: ![]() ![]() References: UniProt: Q9X0C6, imidazole glycerol-phosphate synthase | ||||
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#2: Chemical | ChemComp-NI / | ||||
#3: Chemical | ChemComp-SO4 / | ||||
#4: Chemical | #5: Water | ChemComp-HOH / | Has ligand of interest | Y | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal grow | Temperature: 292 K / Method: vapor diffusion, sitting drop / pH: 8.3 / Details: 100 mM TRIS, 23% PEG 3350 |
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-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Aug 29, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→30 Å / Num. obs: 40563 / % possible obs: 99.9 % / Redundancy: 10.8 % / Rmerge(I) obs: 0.063 / Net I/σ(I): 19.4 |
Reflection shell | Resolution: 1.8→1.9 Å / Rmerge(I) obs: 0.639 / Mean I/σ(I) obs: 3 / Num. unique obs: 5948 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 7QC3 Resolution: 1.8→30 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.958 / SU B: 3.503 / SU ML: 0.049 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.091 / ESU R Free: 0.081 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 119.76 Å2 / Biso mean: 39.202 Å2 / Biso min: 22.19 Å2
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Refinement step | Cycle: final / Resolution: 1.8→30 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.8→1.847 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Origin x: 17.0746 Å / Origin y: -20.2519 Å / Origin z: 10.866 Å
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