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Yorodumi- PDB-1eg7: THE CRYSTAL STRUCTURE OF FORMYLTETRAHYDROFOLATE SYNTHETASE FROM M... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1eg7 | ||||||
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Title | THE CRYSTAL STRUCTURE OF FORMYLTETRAHYDROFOLATE SYNTHETASE FROM MOORELLA THERMOACETICA | ||||||
Components | FORMYLTETRAHYDROFOLATE SYNTHETASE | ||||||
Keywords | LIGASE / Synthetase / Folate Binding / ATP Binding / Formate Binding / Monovalent Cation Binding | ||||||
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 / SYNCHROTRON / Resolution: 2.5 Å | ||||||
Authors | Radfar, R. / Shin, R. / Sheldrick, G.M. / Minor, W. / Lovell, C.R. / Odom, J.D. / Dunlap, R.B. / Lebioda, L. | ||||||
Citation | Journal: Biochemistry / Year: 2000 Title: The crystal structure of N(10)-formyltetrahydrofolate synthetase from Moorella thermoacetica. Authors: Radfar, R. / Shin, R. / Sheldrick, G.M. / Minor, W. / Lovell, C.R. / Odom, J.D. / Dunlap, R.B. / Lebioda, L. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1eg7.cif.gz | 219 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1eg7.ent.gz | 175.7 KB | Display | PDB format |
PDBx/mmJSON format | 1eg7.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1eg7_validation.pdf.gz | 399.7 KB | Display | wwPDB validaton report |
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Full document | 1eg7_full_validation.pdf.gz | 448.4 KB | Display | |
Data in XML | 1eg7_validation.xml.gz | 29 KB | Display | |
Data in CIF | 1eg7_validation.cif.gz | 44.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/eg/1eg7 ftp://data.pdbj.org/pub/pdb/validation_reports/eg/1eg7 | HTTPS FTP |
-Related structure data
Similar structure data |
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-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: 59865.879 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Moorella thermoacetica (bacteria) / Production host: Escherichia coli (E. coli) / Strain (production host): Y1 References: UniProt: P21164, formate-tetrahydrofolate ligase #2: Chemical | ChemComp-SO4 / #3: 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: 53.8 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.6 Details: Ammonium Sulfate, PEG 1000, DTT, Potassium Maleate, pH 7.6, VAPOR DIFFUSION, HANGING DROP, temperature 291K |
Crystal grow | *PLUS Details: Lewinski, K., (1993) J. Mol. Biol., 229, 1153. |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 1.04189 |
Detector | Type: OTHER / Detector: CCD / Date: Mar 21, 1998 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.04189 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→20 Å / Num. all: 194269 / Num. obs: 43717 / % possible obs: 97.2 % / Redundancy: 4.4 % / Biso Wilson estimate: 28 Å2 / Rmerge(I) obs: 0.046 / Net I/σ(I): 12.3 |
Reflection shell | Resolution: 2.49→2.58 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.168 / Num. unique all: 43717 / % possible all: 79.5 |
Reflection | *PLUS Num. measured all: 194269 |
-Processing
Software |
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Refinement | Resolution: 2.5→19.99 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 4734824.3 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 3
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 44.8 Å2 / ksol: 0.345 e/Å3 | |||||||||||||||||||||||||
Displacement parameters | Biso mean: 40.2 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.5→19.99 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.5→2.66 Å / Rfactor Rfree error: 0.021 / Total num. of bins used: 6
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Xplor file |
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Software | *PLUS Name: CNS / Version: 0.9 / Classification: refinement | |||||||||||||||||||||||||
Refinement | *PLUS σ(F): 3 / % reflection Rfree: 5 % | |||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||
Displacement parameters | *PLUS Biso mean: 40.2 Å2 | |||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor Rfree: 0.338 / % reflection Rfree: 5.1 % / Rfactor Rwork: 0.28 |