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Yorodumi- PDB-1a5b: CRYO-CRYSTALLOGRAPHY OF A TRUE SUBSTRATE, INDOLE-3-GLYCEROL PHOSP... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1a5b | ||||||
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Title | CRYO-CRYSTALLOGRAPHY OF A TRUE SUBSTRATE, INDOLE-3-GLYCEROL PHOSPHATE, BOUND TO A MUTANT (ALPHA D60N) TRYPTOPHAN SYNTHASE ALPHA2BETA2 COMPLEX REVEALS THE CORRECT ORIENTATION OF ACTIVE SITE ALPHA GLU 49 | ||||||
Components | (TRYPTOPHAN SYNTHASE ...) x 2 | ||||||
Keywords | LYASE / CARBON-OXYGEN LYASE / MUTATION AT POSITION 60 (ASP --> ASN) IN THE A-SUBUNIT / TRUE SUBSTRATE INDOLE-3-GLYCEROL PHOSPHATE IN THE A-SUBUNIT | ||||||
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 / ISOMORPHOUS / Resolution: 2 Å | ||||||
Authors | Rhee, S. / Miles, E.W. / Davies, D.R. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 1998 Title: Cryo-crystallography of a true substrate, indole-3-glycerol phosphate, bound to a mutant (alphaD60N) tryptophan synthase alpha2beta2 complex reveals the correct orientation of active site alphaGlu49. Authors: Rhee, S. / Miles, E.W. / Davies, D.R. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1a5b.cif.gz | 136.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1a5b.ent.gz | 110.2 KB | Display | PDB format |
PDBx/mmJSON format | 1a5b.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1a5b_validation.pdf.gz | 770.9 KB | Display | wwPDB validaton report |
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Full document | 1a5b_full_validation.pdf.gz | 784.4 KB | Display | |
Data in XML | 1a5b_validation.xml.gz | 29 KB | Display | |
Data in CIF | 1a5b_validation.cif.gz | 41.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/a5/1a5b ftp://data.pdbj.org/pub/pdb/validation_reports/a5/1a5b | HTTPS FTP |
-Related structure data
-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: 28697.812 Da / Num. of mol.: 1 / Mutation: D60N Source method: isolated from a genetically manipulated source Details: LIGAND INDOLE-3-GLYCEROL PHOSPHATE BOUND TO THE A-SUBUNIT Source: (gene. exp.) Salmonella typhimurium (bacteria) / Cell line: CB149 / Gene: TRPA/TRPB / Plasmid: PSTB7 / Cell line (production host): CB149 / Gene (production host): TRPA/TRPB / Production host: Escherichia coli (E. coli) / References: UniProt: P00929, tryptophan synthase |
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#2: Protein | Mass: 42973.039 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: LIGAND INDOLE-3-GLYCEROL PHOSPHATE BOUND TO THE A-SUBUNIT Source: (gene. exp.) Salmonella typhimurium (bacteria) / Cell line: CB149 / Gene: TRPA/TRPB / Plasmid: PSTB7 / Cell line (production host): CB149 / Gene (production host): TRPA/TRPB / Production host: Escherichia coli (E. coli) / References: UniProt: P0A2K1, tryptophan synthase |
-Non-polymers , 4 types, 340 molecules
#3: Chemical | ChemComp-IGP / |
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#4: Chemical | ChemComp-K / |
#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: 2.4 Å3/Da / Density % sol: 48 % | ||||||||||||||||||||||||||||||||||||
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Crystal grow | pH: 7.8 Details: 50MM NABICINE (PH 7.8), 1MM NA-EDTA, 0.8-1.5MM SPERMINE, 12% PEG8000 | ||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Method: unknown | ||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 95 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RUH2R / Wavelength: 1.5418 |
Detector | Type: RIGAKU RAXIS IIC / Detector: IMAGE PLATE / Date: Jun 1, 1996 / Details: MIRROR |
Radiation | Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Highest resolution: 2 Å / Num. obs: 45501 / % possible obs: 92.8 % / Observed criterion σ(I): -3 / Redundancy: 4.3 % / Biso Wilson estimate: 15.7 Å2 / Rsym value: 0.057 / Net I/σ(I): 14.7 |
Reflection shell | Resolution: 2→2.05 Å / Redundancy: 3.2 % / Mean I/σ(I) obs: 2.4 / Rsym value: 0.463 / % possible all: 77.8 |
Reflection | *PLUS Rmerge(I) obs: 0.057 |
Reflection shell | *PLUS % possible obs: 79.4 % / Rmerge(I) obs: 0.424 |
-Processing
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Refinement | Method to determine structure: ISOMORPHOUS / Resolution: 2→8 Å / Data cutoff high absF: 100000 / Data cutoff low absF: 0.1 / Cross valid method: FREE R / σ(F): 2
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Displacement parameters | Biso mean: 26.4 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze | Luzzati coordinate error obs: 0.32 Å / Luzzati d res low obs: 5 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2→8 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2→2.09 Å / Total num. of bins used: 8
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Xplor file |
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Software | *PLUS Name: X-PLOR / Version: 3.1F / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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