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Yorodumi- PDB-1sbq: Crystal Structure of methenyltetrahydrofolate synthetase from Myc... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1sbq | ||||||
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Title | Crystal Structure of methenyltetrahydrofolate synthetase from Mycoplasma pneumoniae at 2.2 resolution | ||||||
Components | 5,10-Methenyltetrahydrofolate synthetase homolog | ||||||
Keywords | LIGASE / 5 / 10-Methenyltetrahydrofolate synthetase / MTHFS / 5-formyltetrahydrofolate cyclo-ligase / Structural Genomics / BSGC structure funded by NIH / Protein Structure Initiative / PSI / Berkeley Structural Genomics Center | ||||||
Function / homology | Function and homology information 5-formyltetrahydrofolate cyclo-ligase / 5-formyltetrahydrofolate cyclo-ligase activity / ATP binding / metal ion binding / cytoplasm Similarity search - Function | ||||||
Biological species | Mycoplasma pneumoniae (Filterable agent of primary atypical pneumonia) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.2 Å | ||||||
Authors | Chen, S. / Shin, D.H. / Pufan, R. / Kim, R. / Kim, S.H. / Berkeley Structural Genomics Center (BSGC) | ||||||
Citation | Journal: Proteins / Year: 2004 Title: Crystal structure of methenyltetrahydrofolate synthetase from Mycoplasma pneumoniae (GI: 13508087) at 2.2 A resolution Authors: Chen, S. / Shin, D.H. / Pufan, R. / Kim, R. / Kim, S.H. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1sbq.cif.gz | 78.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1sbq.ent.gz | 63.3 KB | Display | PDB format |
PDBx/mmJSON format | 1sbq.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/sb/1sbq ftp://data.pdbj.org/pub/pdb/validation_reports/sb/1sbq | HTTPS FTP |
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-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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Details | monomer as the biological assembly |
-Components
#1: Protein | Mass: 22274.486 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mycoplasma pneumoniae (Filterable agent of primary atypical pneumonia) Gene: MPN348, MP488 / Plasmid: pSKB3 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pSJS1244 References: UniProt: P75430, 5-formyltetrahydrofolate cyclo-ligase #2: Chemical | #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: 2.95 Å3/Da / Density % sol: 57.92 % |
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Crystal grow | Temperature: 300 K / Method: vapor diffusion, hanging drop / pH: 4.6 Details: 0.2 M ammonium sulfate, 0.1 M sodium acetate, 25% polyethylene glycol 4000, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 300K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 0.9793 Å |
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Dec 13, 2002 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9793 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→40 Å / Num. all: 23773 / Num. obs: 23677 / % possible obs: 99.6 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 21 Å2 / Rmerge(I) obs: 0.132 / Rsym value: 0.132 / Net I/σ(I): 26.5 |
Reflection shell | Resolution: 2.2→2.34 Å / % possible all: 56.7 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 2.2→40 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 169600.46 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 51.7862 Å2 / ksol: 0.385678 e/Å3 | |||||||||||||||||||||||||
Displacement parameters | Biso mean: 41.8 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.2→40 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.2→2.34 Å / Rfactor Rfree error: 0.019 / Total num. of bins used: 6
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Xplor file |
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