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Yorodumi- PDB-1eye: 1.7 ANGSTROM RESOLUTION CRYSTAL STRUCTURE OF 6-HYDROXYMETHYL-7,8-... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1eye | ||||||
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Title | 1.7 ANGSTROM RESOLUTION CRYSTAL STRUCTURE OF 6-HYDROXYMETHYL-7,8-DIHYDROPTEROATE SYNTHASE (DHPS) FROM MYCOBACTERIUM TUBERCULOSIS IN COMPLEX WITH 6-HYDROXYMETHYLPTERIN MONOPHOSPHATE | ||||||
Components | DIHYDROPTEROATE SYNTHASE I | ||||||
Keywords | TRANSFERASE / alpha-beta barrel | ||||||
Function / homology | Function and homology information dihydropteroate synthase / dihydropteroate synthase activity / folic acid biosynthetic process / tetrahydrofolate biosynthetic process / metal ion binding / cytosol Similarity search - Function | ||||||
Biological species | Mycobacterium tuberculosis H37Rv (bacteria) | ||||||
Method | X-RAY DIFFRACTION / Resolution: 1.7 Å | ||||||
Authors | Baca, A.M. / Sirawaraporn, R. / Turley, S. / Sirawaraporn, W. / Hol, W.G.J. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2000 Title: Crystal structure of Mycobacterium tuberculosis 7,8-dihydropteroate synthase in complex with pterin monophosphate: new insight into the enzymatic mechanism and sulfa-drug action. Authors: Baca, A.M. / Sirawaraporn, R. / Turley, S. / Sirawaraporn, W. / Hol, W.G. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1eye.cif.gz | 66.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1eye.ent.gz | 48.5 KB | Display | PDB format |
PDBx/mmJSON format | 1eye.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1eye_validation.pdf.gz | 439.4 KB | Display | wwPDB validaton report |
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Full document | 1eye_full_validation.pdf.gz | 449.7 KB | Display | |
Data in XML | 1eye_validation.xml.gz | 8.2 KB | Display | |
Data in CIF | 1eye_validation.cif.gz | 13.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ey/1eye ftp://data.pdbj.org/pub/pdb/validation_reports/ey/1eye | HTTPS FTP |
-Related structure data
Related structure data | |
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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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Details | The biological assembly is a dimer constructed from chain A a symmetry partner generated by the two-fold. |
-Components
#1: Protein | Mass: 28872.916 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mycobacterium tuberculosis H37Rv (bacteria) Species: Mycobacterium tuberculosis / Strain: H37RV / Plasmid: PKOS007-90 / Production host: Escherichia coli (E. coli) References: UniProt: P0A578, UniProt: P9WND1*PLUS, dihydropteroate synthase |
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#2: Chemical | ChemComp-MG / |
#3: Chemical | ChemComp-PMM / |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.4 Å3/Da / Density % sol: 48.74 % | ||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 5.8 Details: PEG 4000, Sodium Acetate, Ammonium Acetate, para-aminosalicylic acid, 6-hydroxymethl pterin monophosphate, pH 5.8, VAPOR DIFFUSION, SITTING DROP, temperature 298K | ||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 25 ℃ | ||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 140 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 |
Detector | Type: RIGAKU RAXIS IIC / Detector: IMAGE PLATE / Date: Jul 4, 1999 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.7→26.5 Å / Num. all: 136341 / Num. obs: 25211 / % possible obs: 80.5 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 5.4 % / Biso Wilson estimate: 20.649 Å2 / Rmerge(I) obs: 0.043 / Net I/σ(I): 32.411 |
Reflection shell | Resolution: 1.7→1.76 Å / Redundancy: 4.1 % / Rmerge(I) obs: 0.177 / Num. unique all: 2137 / % possible all: 69.9 |
Reflection | *PLUS Num. measured all: 136341 |
Reflection shell | *PLUS % possible obs: 69.9 % |
-Processing
Software |
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Refinement | Resolution: 1.7→20 Å / σ(F): 0 / σ(I): 0 / Stereochemistry target values: TNT default
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Refinement step | Cycle: LAST / Resolution: 1.7→20 Å
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Software | *PLUS Name: TNT / Classification: refinement | |||||||||||||||||||||||||||||||||
Refinement | *PLUS % reflection Rfree: 5 % | |||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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