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Yorodumi- PDB-2rh9: Tryptophan synthase complexed with IGP, internal aldimine, pH 9.0 -
+Open data
-Basic information
Entry | Database: PDB / ID: 2rh9 | ||||||
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Title | Tryptophan synthase complexed with IGP, internal aldimine, pH 9.0 | ||||||
Components | (Tryptophan synthase ...) x 2 | ||||||
Keywords | LYASE / AROMATIC AMINO ACID BIOSYNTHESIS / TRYPTOPHAN BIOSYNTHESIS / CARBON-OXYGEN LYASE / AMINOACID BIOSYNTHESIS / ALLOSTERIC ENZYME / PYRIDOXAL PHOSPHATE / Amino-acid biosynthesis | ||||||
Function / homology | Function and homology information tryptophan synthase / tryptophan synthase activity / tryptophan biosynthetic process / identical protein binding / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | Salmonella typhimurium (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.7 Å | ||||||
Authors | Kulik, V. / Barends, T.R.M. / Schlichting, I. | ||||||
Citation | Journal: To be Published Title: Tryptophan synthase complexed with IGP, internal aldimine, pH 9.0. Authors: Kulik, V. / Barends, T.R.M. / Schlichting, I. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2rh9.cif.gz | 141.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2rh9.ent.gz | 115 KB | Display | PDB format |
PDBx/mmJSON format | 2rh9.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2rh9_validation.pdf.gz | 777.1 KB | Display | wwPDB validaton report |
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Full document | 2rh9_full_validation.pdf.gz | 781.7 KB | Display | |
Data in XML | 2rh9_validation.xml.gz | 29.2 KB | Display | |
Data in CIF | 2rh9_validation.cif.gz | 44 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/rh/2rh9 ftp://data.pdbj.org/pub/pdb/validation_reports/rh/2rh9 | 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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Unit cell |
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-Components
-Tryptophan synthase ... , 2 types, 2 molecules AB
#1: Protein | Mass: 28698.797 Da / Num. of mol.: 1 / Fragment: tryptophan synthase, alpha chain Source method: isolated from a genetically manipulated source Source: (gene. exp.) Salmonella typhimurium (bacteria) / Gene: trpA, STM1727 / Plasmid: pSTB7 / Production host: Escherichia coli (E. coli) / Strain (production host): CB149 / References: UniProt: P00929, tryptophan synthase |
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#2: Protein | Mass: 42918.879 Da / Num. of mol.: 1 / Fragment: tryptophan synthase, beta chain Source method: isolated from a genetically manipulated source Source: (gene. exp.) Salmonella typhimurium (bacteria) / Gene: trpB, STM1726 / Plasmid: pSTB7 / Production host: Escherichia coli (E. coli) / Strain (production host): CB149 / References: UniProt: P0A2K1, tryptophan synthase |
-Non-polymers , 4 types, 486 molecules
#3: Chemical | ChemComp-IGP / |
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#4: Chemical | ChemComp-NA / |
#5: Chemical | ChemComp-PLP / |
#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: 2.54 Å3/Da / Density % sol: 51.63 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 9 Details: Protein: 50 mM Bicine pH 7.8, 10 mM Na-EDTA, 1 mM DTE, 20 uM PLP. Reservoir: 50 mM Bicine pH 7.8, 5 mM DTE, 5 mM Na-EDTA, 0.1 M PLP, 2 mM Spermine, 2 mM NaN3, 8-12% PEG 8000. Crystal soaked ...Details: Protein: 50 mM Bicine pH 7.8, 10 mM Na-EDTA, 1 mM DTE, 20 uM PLP. Reservoir: 50 mM Bicine pH 7.8, 5 mM DTE, 5 mM Na-EDTA, 0.1 M PLP, 2 mM Spermine, 2 mM NaN3, 8-12% PEG 8000. Crystal soaked in 15% PEG 8000, 20% Glycerol, 23 mM IGP, pH controlled at pH 9.0 before flash-cooling, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-3 / Wavelength: 0.93 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Sep 30, 2000 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.93 Å / Relative weight: 1 |
Reflection | Resolution: 1.7→55 Å / Num. all: 77139 / Num. obs: 77139 / % possible obs: 97.3 % / Observed criterion σ(I): -3 / Redundancy: 2.4 % / Biso Wilson estimate: 19.8 Å2 / Rmerge(I) obs: 0.055 / Net I/σ(I): 10.01 |
Reflection shell | Resolution: 1.7→1.8 Å / Rmerge(I) obs: 0.313 / Mean I/σ(I) obs: 2.46 / Num. unique all: 12104 / % possible all: 97.1 |
-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS / Resolution: 1.7→43.73 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.951 / SU B: 2.066 / SU ML: 0.068 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.097 / ESU R Free: 0.095 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. Program CNS has also been used in refinement
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 20.991 Å2
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Refinement step | Cycle: LAST / Resolution: 1.7→43.73 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.7→1.744 Å / Total num. of bins used: 20 /
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