+Open data
-Basic information
Entry | Database: PDB / ID: 3tye | ||||||
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Title | Dihydropteroate Synthase in complex with DHP-STZ | ||||||
Components | Dihydropteroate synthase | ||||||
Keywords | TRANSFERASE / anthracis / folate biosynthesis / dihydropteroate / pterine / tim 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 | Bacillus anthracis (anthrax bacterium) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å | ||||||
Authors | Yun, M.-K. / White, S.W. | ||||||
Citation | Journal: Science / Year: 2012 Title: Catalysis and sulfa drug resistance in dihydropteroate synthase. Authors: Yun, M.K. / Wu, Y. / Li, Z. / Zhao, Y. / Waddell, M.B. / Ferreira, A.M. / Lee, R.E. / Bashford, D. / White, S.W. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3tye.cif.gz | 225.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3tye.ent.gz | 183.6 KB | Display | PDB format |
PDBx/mmJSON format | 3tye.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3tye_validation.pdf.gz | 988.5 KB | Display | wwPDB validaton report |
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Full document | 3tye_full_validation.pdf.gz | 1000.1 KB | Display | |
Data in XML | 3tye_validation.xml.gz | 23.1 KB | Display | |
Data in CIF | 3tye_validation.cif.gz | 31.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ty/3tye ftp://data.pdbj.org/pub/pdb/validation_reports/ty/3tye | HTTPS FTP |
-Related structure data
Related structure data | 3tyaC 3tybC 3tycC 3tydC 3tyuC 3tyzC 3tzfC 3tznC 3v5oC 1twsS 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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2 |
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Unit cell |
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-Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 32883.734 Da / Num. of mol.: 2 / Fragment: DIHYDROPTEROATE SYNTHASE Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacillus anthracis (anthrax bacterium) / Strain: A2012 / Gene: folP, BAS0071, BA_0071, GBAA_0071 / Plasmid: PET-28A / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q81VW8, dihydropteroate synthase |
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-Non-polymers , 5 types, 96 molecules
#2: Chemical | ChemComp-XTZ / | ||||||
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#3: Chemical | ChemComp-SO4 / #4: Chemical | ChemComp-XHP / | #5: Chemical | ChemComp-YTZ / | #6: 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: 2.74 Å3/Da / Density % sol: 55.15 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 9 Details: LITHIUM SULFATE, Bis-Tris propane, pH 9.0, VAPOR DIFFUSION, HANGING DROP, temperature 291.0K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å |
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Dec 3, 2010 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→50 Å / Num. obs: 32382 / % possible obs: 95.2 % / Observed criterion σ(I): -3 / Redundancy: 9.2 % / Rsym value: 0.062 / Net I/σ(I): 30.5 |
Reflection shell | Resolution: 2.3→2.38 Å / Redundancy: 8.9 % / Mean I/σ(I) obs: 5 / Num. unique all: 2520 / Rsym value: 0.219 / % possible all: 76 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1TWS Resolution: 2.3→45.66 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.93 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 33.846 / SU ML: 0.325 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.341 / ESU R Free: 0.262 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 166.69 Å2 / Biso mean: 78.2592 Å2 / Biso min: 2 Å2
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Refinement step | Cycle: LAST / Resolution: 2.3→45.66 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.3→2.36 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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