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Open data
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Basic information
Entry | Database: PDB / ID: 7xzp | ||||||
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Title | Formate-tetrahydrofolate ligase in complex with berberine | ||||||
![]() | Formate--tetrahydrofolate ligase | ||||||
![]() | LIGASE / Formate tetrahydrofolate ligase / Berberine | ||||||
Function / homology | ![]() formate-tetrahydrofolate ligase / formate-tetrahydrofolate ligase activity / tetrahydrofolate interconversion / ATP binding Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Fang, C.L. / Zhang, Y. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Identification of FtfL as a novel target of berberine in intestinal bacteria. Authors: Yan, J. / Fang, C. / Yang, G. / Li, J. / Liu, Y. / Zhang, L. / Yang, P. / Fang, J. / Gu, Y. / Zhang, Y. / Jiang, W. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 221.3 KB | Display | ![]() |
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PDB format | ![]() | 176.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.4 MB | Display | ![]() |
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Full document | ![]() | 1.5 MB | Display | |
Data in XML | ![]() | 39.8 KB | Display | |
Data in CIF | ![]() | 53.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7xznC ![]() 7xzoC ![]() 5a4jS 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
#1: Protein | Mass: 60583.137 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Gene: fhs, NCTC11460_01517 / Production host: ![]() ![]() References: UniProt: A0A379CIH2, formate-tetrahydrofolate ligase #2: Chemical | ChemComp-BER / #3: Chemical | #4: Chemical | ChemComp-PRO / #5: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.1 Å3/Da / Density % sol: 60.38 % |
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Crystal grow | Temperature: 295.15 K / Method: vapor diffusion, sitting drop / Details: 0.1M HEPES pH 7.5, 2.0M Ammonium sulfate |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS EIGER2 S 9M / Detector: PIXEL / Date: Oct 10, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9791 Å / Relative weight: 1 |
Reflection | Resolution: 2.56→50.2 Å / Num. obs: 48875 / % possible obs: 100 % / Redundancy: 8 % / CC1/2: 0.978 / Rpim(I) all: 0.124 / Rrim(I) all: 0.339 / Χ2: 1.02 / Net I/σ(I): 8.8 |
Reflection shell | Resolution: 2.56→2.63 Å / Redundancy: 8.2 % / Num. unique obs: 3564 / CC1/2: 0.288 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 5A4J Resolution: 2.56→47.651 Å / SU ML: 0.41 / Cross valid method: THROUGHOUT / σ(F): 1.39 / Phase error: 26.85 / Stereochemistry target values: ML
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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 max: 111.68 Å2 / Biso mean: 54.6661 Å2 / Biso min: 27.49 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.56→47.651 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0
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