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Yorodumi- PDB-1fpm: MONOVALENT CATION BINDING SITES IN N10-FORMYLTETRAHYDROFOLATE SYN... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1fpm | ||||||
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Title | MONOVALENT CATION BINDING SITES IN N10-FORMYLTETRAHYDROFOLATE SYNTHETASE FROM MOORELLA THERMOACETICA | ||||||
Components | FORMATE--TETRAHYDROFOLATE LIGASE | ||||||
Keywords | LIGASE / MONOVALENT CATION / THERMOSTABLE / TETRAMER | ||||||
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 / Resolution: 3 Å | ||||||
Authors | Radfar, R. / Leaphart, A. / Brewer, J.M. / Minor, W. / Odom, J.D. | ||||||
Citation | Journal: Biochemistry / Year: 2000 Title: Cation binding and thermostability of FTHFS monovalent cation binding sites and thermostability of N10-formyltetrahydrofolate synthetase from Moorella thermoacetica. Authors: Radfar, R. / Leaphart, A. / Brewer, J.M. / Minor, W. / Odom, J.D. / Dunlap, R.B. / Lovell, C.R. / Lebioda, L. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1fpm.cif.gz | 220.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1fpm.ent.gz | 176.3 KB | Display | PDB format |
PDBx/mmJSON format | 1fpm.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1fpm_validation.pdf.gz | 401 KB | Display | wwPDB validaton report |
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Full document | 1fpm_full_validation.pdf.gz | 481.4 KB | Display | |
Data in XML | 1fpm_validation.xml.gz | 34 KB | Display | |
Data in CIF | 1fpm_validation.cif.gz | 51.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fp/1fpm ftp://data.pdbj.org/pub/pdb/validation_reports/fp/1fpm | HTTPS FTP |
-Related structure data
-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: 59835.840 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Moorella thermoacetica (bacteria) / Plasmid: PCRL47 S2A / Production host: Escherichia coli (E. coli) References: UniProt: P21164, formate-tetrahydrofolate ligase #2: Chemical | ChemComp-SO4 / #3: Chemical | #4: 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: 53.83 % | ||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7.6 Details: AMMONIUM SULFATE, PEG 1000, POTASSIUM MALEATE, pH 7.6, VAPOR DIFFUSION, HANGING DROP, temperature 295K | ||||||||||||||||||||||||||||||
Crystal grow | *PLUS Method: vapor diffusion | ||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 |
Detector | Type: RIGAKU RAXIS / Detector: IMAGE PLATE / Date: May 15, 1998 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 3→40 Å / Num. all: 137437 / Num. obs: 25025 / % possible obs: 97 % / Observed criterion σ(F): 3 / Observed criterion σ(I): 3 / Rmerge(I) obs: 0.088 |
Reflection shell | Resolution: 2.99→3.1 Å / Rmerge(I) obs: 0.182 / % possible all: 94.7 |
Reflection | *PLUS Lowest resolution: 40 Å / % possible obs: 97 % / Num. measured all: 137437 |
-Processing
Software |
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Refinement | Resolution: 3→40 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 387313.28 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 3 / σ(I): 3
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 23.28 Å2 / ksol: 0.284 e/Å3 | |||||||||||||||||||||||||
Displacement parameters | Biso mean: 35.5 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 3→40 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 3→3.19 Å / Rfactor Rfree error: 0.015 / Total num. of bins used: 6
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Xplor file |
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Software | *PLUS Name: CNS / Version: 1 / Classification: refinement | |||||||||||||||||||||||||
Refinement | *PLUS Lowest resolution: 40 Å / σ(F): 3 / % reflection Rfree: 9.5 % / Rfactor Rfree: 0.315 / Rfactor Rwork: 0.231 | |||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||
Displacement parameters | *PLUS Biso mean: 35.5 Å2 | |||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor Rfree: 0.359 / % reflection Rfree: 9.7 % / Rfactor Rwork: 0.302 |