+Open data
-Basic information
Entry | Database: PDB / ID: 7xzo | ||||||
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Title | Formate-tetrahydrofolate ligase in complex with ATP | ||||||
Components | Formate--tetrahydrofolate ligase | ||||||
Keywords | LIGASE / Formate tetrahydrofolate ligase / ATP | ||||||
Function / homology | Function and homology information formate-tetrahydrofolate ligase / formate-tetrahydrofolate ligase activity / tetrahydrofolate interconversion / ATP binding Similarity search - Function | ||||||
Biological species | Peptostreptococcus anaerobius (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.31 Å | ||||||
Authors | Fang, C.L. / Zhang, Y. | ||||||
Funding support | China, 1items
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Citation | Journal: Bmc Biol. / Year: 2023 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7xzo.cif.gz | 421.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7xzo.ent.gz | 343.1 KB | Display | PDB format |
PDBx/mmJSON format | 7xzo.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7xzo_validation.pdf.gz | 1.7 MB | Display | wwPDB validaton report |
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Full document | 7xzo_full_validation.pdf.gz | 1.8 MB | Display | |
Data in XML | 7xzo_validation.xml.gz | 74.5 KB | Display | |
Data in CIF | 7xzo_validation.cif.gz | 98.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xz/7xzo ftp://data.pdbj.org/pub/pdb/validation_reports/xz/7xzo | HTTPS FTP |
-Related structure data
Related structure data | 7xznC 7xzpC 5a4jS S: Starting model for refinement C: citing same article (ref.) |
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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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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 60583.137 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Peptostreptococcus anaerobius (bacteria) Gene: fhs, NCTC11460_01517 / Production host: Escherichia coli (E. coli) References: UniProt: A0A379CIH2, formate-tetrahydrofolate ligase #2: Chemical | ChemComp-K / #3: Chemical | ChemComp-ATP / #4: Chemical | ChemComp-BU3 / ( #5: Water | ChemComp-HOH / | Has ligand of interest | N | |
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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: 2.72 Å3/Da / Density % sol: 54.76 % |
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Crystal grow | Temperature: 295.15 K / Method: vapor diffusion, hanging drop / Details: 20% w/v PEG 3350, 200mM potassium formate |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL02U1 / Wavelength: 0.9791 Å |
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: 2.31→32.48 Å / Num. obs: 113515 / % possible obs: 99.9 % / Redundancy: 6.9 % / CC1/2: 0.995 / Net I/σ(I): 5.6 |
Reflection shell | Resolution: 2.31→2.37 Å / Mean I/σ(I) obs: 1.2 / Num. unique obs: 8382 / CC1/2: 0.523 / % possible all: 99.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5a4j Resolution: 2.31→30.029 Å / SU ML: 0.35 / Cross valid method: THROUGHOUT / σ(F): 1.4 / Phase error: 34.9 / 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: 104.84 Å2 / Biso mean: 42.4203 Å2 / Biso min: 13.57 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.31→30.029 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0
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