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Yorodumi- PDB-1tnd: THE 2.2 ANGSTROMS CRYSTAL STRUCTURE OF TRANSDUCIN-ALPHA COMPLEXED... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1tnd | ||||||
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Title | THE 2.2 ANGSTROMS CRYSTAL STRUCTURE OF TRANSDUCIN-ALPHA COMPLEXED WITH GTP GAMMA S | ||||||
Components | TRANSDUCIN | ||||||
Keywords | BINDING PROTEIN(GTP) | ||||||
Function / homology | Function and homology information negative regulation of cyclic-nucleotide phosphodiesterase activity / G protein-coupled receptor complex / Inactivation, recovery and regulation of the phototransduction cascade / Activation of the phototransduction cascade / acyl binding / photoreceptor outer segment membrane / G alpha (i) signalling events / response to light stimulus / phototransduction / photoreceptor inner segment ...negative regulation of cyclic-nucleotide phosphodiesterase activity / G protein-coupled receptor complex / Inactivation, recovery and regulation of the phototransduction cascade / Activation of the phototransduction cascade / acyl binding / photoreceptor outer segment membrane / G alpha (i) signalling events / response to light stimulus / phototransduction / photoreceptor inner segment / visual perception / G protein-coupled receptor binding / G-protein beta/gamma-subunit complex binding / adenylate cyclase-modulating G protein-coupled receptor signaling pathway / photoreceptor disc membrane / GDP binding / heterotrimeric G-protein complex / GTPase activity / GTP binding / protein kinase binding / metal ion binding Similarity search - Function | ||||||
Biological species | Bos taurus (cattle) | ||||||
Method | X-RAY DIFFRACTION / Resolution: 2.2 Å | ||||||
Authors | Noel, J.P. / Hamm, H.E. / Sigler, P.B. | ||||||
Citation | Journal: Nature / Year: 1993 Title: The 2.2 A crystal structure of transducin-alpha complexed with GTP gamma S. Authors: Noel, J.P. / Hamm, H.E. / Sigler, P.B. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1tnd.cif.gz | 223.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1tnd.ent.gz | 177.2 KB | Display | PDB format |
PDBx/mmJSON format | 1tnd.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/tn/1tnd ftp://data.pdbj.org/pub/pdb/validation_reports/tn/1tnd | HTTPS FTP |
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-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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2 |
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3 |
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Unit cell |
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Atom site foot note | 1: CAC A 353, CAC B 353, AND CAC C 353 MODIFY CYS A 62, CYS B 62, AND CYS C 62, RESPECTIVELY. 2: CAC A 354, CAC B 354, AND CAC C 354 MODIFY CYS A 210, CYS B 210, AND CYS C 210, RESPECTIVELY. | ||||||||||||
Noncrystallographic symmetry (NCS) | NCS oper:
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Details | THERE ARE THREE COMPLEXES OF TRANSDUCIN ALPHA, GTP GAMMA S, AND MG+2 PER ASYMMETRIC UNIT. THE CHAIN IDENTIFIES ARE A, B, AND C. THE TRANSFORMATION PRESENTED ON *MTRIX 1* RECORDS BELOW WILL YIELD APPROXIMATE COORDINATES FOR CHAIN *A* WHEN APPLIED TO CHAIN *B*. THE TRANSFORMATION PRESENTED ON *MTRIX 2* RECORDS BELOW WILL YIELD APPROXIMATE COORDINATES FOR CHAIN *A* WHEN APPLIED TO CHAIN *C*. |
-Components
#1: Protein | Mass: 37141.465 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bos taurus (cattle) / References: UniProt: P04695 #2: Chemical | #3: Chemical | ChemComp-CAC / #4: Chemical | #5: Water | ChemComp-HOH / | Nonpolymer details | *CAC* IS A CACODYLIC ACID GROUP (DERIVED FROM CRYSTALLIZATION BUFFER - DIMETHYLARSINIC ACID) FOR ...*CAC* IS A CACODYLIC ACID GROUP (DERIVED FROM CRYSTALLIZ | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.65 Å3/Da / Density % sol: 53.51 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | *PLUS Temperature: -12.5 ℃ / pH: 6 / Method: vapor diffusion, hanging drop | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Reflection | *PLUS Highest resolution: 2.8 Å / Lowest resolution: 12.6 Å / Num. all: 58732 / Num. obs: 53289 / Rmerge(I) obs: 0.039 |
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-Processing
Software |
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Refinement | Resolution: 2.2→6 Å / σ(F): 2 /
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Refinement step | Cycle: LAST / Resolution: 2.2→6 Å
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Refine LS restraints |
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Software | *PLUS Name: X-PLOR / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Rfactor all: 0.19 / Rfactor obs: 0.178 / Rfactor Rfree: 0.304 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS Type: x_angle_d / Dev ideal: 1.8 |