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Yorodumi- PDB-4iol: N10-formyltetrahydrofolate synthetase from Moorella thermoacetica... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4iol | ||||||
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Title | N10-formyltetrahydrofolate synthetase from Moorella thermoacetica with ADP/ZD9 and XPO | ||||||
Components | Formate--tetrahydrofolate ligase | ||||||
Keywords | LIGASE/LIGASE INHIBITOR / alpha/beta / enzyme / LIGASE-LIGASE INHIBITOR complex | ||||||
Function / homology | Function and homology information formate-tetrahydrofolate ligase / formate-tetrahydrofolate ligase activity / tetrahydrofolate interconversion / ATP binding Similarity search - Function | ||||||
Biological species | Moorella thermoacetica (bacteria) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.563 Å | ||||||
Authors | Stec, B. | ||||||
Citation | Journal: Protein Sci. / Year: 2012 Title: Mechanism of N10-formyltetrahydrofolate synthetase derived from complexes with intermediates and inhibitors. Authors: Celeste, L.R. / Chai, G. / Bielak, M. / Minor, W. / Lovelace, L.L. / Lebioda, L. | ||||||
History |
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Remark 0 | THIS ENTRY 4IOL REFLECTS AN ALTERNATIVE MODELING OF THE ORIGINAL STRUCTURAL DATA R3PZXSF DETERMINED ...THIS ENTRY 4IOL REFLECTS AN ALTERNATIVE MODELING OF THE ORIGINAL STRUCTURAL DATA R3PZXSF DETERMINED BY AUTHORS OF THE PDB ENTRY 3SIN: L.R. CELESTE, G. CHAI, M. BIELAK, W. MINOR, L.L. LOVELACE, L. LEBIODA | ||||||
Remark 200 | AUTHOR USED THE SF DATA FROM ENTRY 3SIN. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4iol.cif.gz | 223.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4iol.ent.gz | 179 KB | Display | PDB format |
PDBx/mmJSON format | 4iol.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/io/4iol ftp://data.pdbj.org/pub/pdb/validation_reports/io/4iol | HTTPS FTP |
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-Related structure data
Related structure data | 4iojC 4iokC 4iomC 3sin S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Components on special symmetry positions |
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-Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 60011.980 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Moorella thermoacetica (bacteria) / Strain: ATCC 39073 / Gene: fhs, Moth_0109 / Production host: Escherichia coli (E. coli) References: UniProt: Q2RM91, formate-tetrahydrofolate ligase |
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-Non-polymers , 5 types, 173 molecules
#2: Chemical | ChemComp-SO4 / #3: Chemical | #4: Chemical | ChemComp-ZD9 / | #5: Chemical | ChemComp-XPO / | #6: Water | ChemComp-HOH / | |
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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: 2.66 Å3/Da / Density % sol: 53.77 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 18 to 22% (w/v) PEG 6-8K, 0.2M AS, 1 mM DTT, 75 mM KMB pH 7.0-8.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Relative weight: 1 |
Reflection | Resolution: 2.56→122.3 Å / Num. obs: 79627 / % possible obs: 91.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.5 % / Rmerge(I) obs: 0.049 / Net I/σ(I): 9.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 3SIN 3sin Resolution: 2.563→122.3 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.906 / SU B: 14.909 / SU ML: 0.304 / Cross valid method: THROUGHOUT / ESU R Free: 0.38 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
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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 mean: 63.713 Å2
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Refinement step | Cycle: LAST / Resolution: 2.563→122.3 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.563→2.63 Å / Total num. of bins used: 20
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